Beginning Jan 1, 2003: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: chimera project (Mac OSX) Date: Fri, 03 Jan 2003 09:49:31 +0100 To: rasmol@lists.umass.edu Prospects for the future concerning the http://chimera.mozdev.org/ (etc.) browser(s) for use with the various incarnations of Rasmol? I came across this site again, while researching something else. A fantastic place for anyone interested in web programming! Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: chimera project (Mac OSX) Date: Fri, 03 Jan 2003 11:10:14 -0500 To: rasmol@lists.umass.edu at 9:49 AM EDT on (Friday) 3 January 2003 Lewis Edgel said: > Prospects for the future concerning the http://chimera.mozdev.org/ (etc.) > browser(s) for use with the various incarnations of Rasmol? I came across > this site again, while researching something else. A fantastic place for > anyone interested in web programming! > > Lewis Edgel > hi Lewis, I see no way to configure Chimera to use helper apps yet. once that functionality appears, one should be able to use RasMol/SPV/DSViewer/Cn3D as helper apps just like with other browsers. I do have hope for this in Chimera, though; it is still a pre-1.0 browser, and a darn fine one at that IMHO. Chimera appears to handle modern plug-ins without much trouble. (I have QT5 and Flash in my Internet Plugins folder, for example, and they work okay in Chimera.) unfortunately, Chime does not work in Chimera, despite the similarity in name ;-) :aside: AFAIK from reading various mozilla and netscape docs, last-generation plug-ins like Chime require some re-tooling in order to function in the next generation of mozilla-like browsers. the docs make it sound like a minor fix, but what do I know? :/aside: Java applet mol vis viewers show promise. for example, the Java-based QuickPdb applet available at the PDB works great. MICE, however, does not, possibly b/c it requires a more complicated combination of Java plugins? I can not find a VRML viewer native to OS X. hope that helps! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: VMRL in OSX Date: Fri, 03 Jan 2003 13:12:52 -0400 To: rasmol@lists.umass.edu Cc: timothy driscoll Tim Driscoll et al.: Cortona for OSX http://www.parallelgraphics.com/products/cortona/download/mac/ Works well with iCab and IE5.xx. I'll post a complrte compatibility matrix of my current survey. Yours Frank Johnston -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Cortona download Date: Fri, 03 Jan 2003 13:20:16 -0400 To: rasmol@lists.umass.edu http://www.parallelgraphics.com/products/downloads , http://www.parallelgraphics.com/products/cortonamacosx/ -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 12:27:12 -0500 To: Frank Johnston , LIST rasmol at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > Tim Driscoll et al.: > > Cortona for OSX > http://www.parallelgraphics.com/products/cortona/download/mac/ > > > Works well with iCab and IE5.xx. I'll post a complrte compatibility > matrix of my current survey. > intriguing. the Cortona installer is a Classic app, so I didn't bother to run it. I'd be interested to hear if you test it in Chimera. also, do you know if Cortona (in iCab-X or IE-X) works with the VRML resources at the PDB? regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 14:13:07 -0400 To: rasmol@lists.umass.edu Tim Driscoll: OSx version works well at the PDB site with iCab and IE5. Mozilla etc can be buggy, often crashing on quit or back execution. yours Frank Johnston >at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > >> Tim Driscoll et al.: >> >> Cortona for OSX >> http://www.parallelgraphics.com/products/cortona/download/mac/ >> >> >> Works well with iCab and IE5.xx. I'll post a complrte compatibility >> matrix of my current survey. >> > >intriguing. the Cortona installer is a Classic app, so I didn't bother to >run it. I'd be interested to hear if you test it in Chimera. also, do you >know if Cortona (in iCab-X or IE-X) works with the VRML resources at the >PDB? > >regards, > >:tim >-- >molvisions - molecular graphics & visualization > >usa:north carolina:wake forest > > > -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 13:38:50 -0500 To: rasmol@lists.umass.edu at 2:13 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > Tim Driscoll: > > OSx version works well at the PDB site with iCab and IE5. Mozilla etc > can be buggy, often crashing > on quit or back execution. > > yours > Frank Johnston > hi Frank, thanks for the info. I did not realize that to get the X version of Cortona, one needs to sign up as a beta tester. I'll add it to my list of potentially useful mol vis viewers. regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest > >at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > > > >> Tim Driscoll et al.: > >> > >> Cortona for OSX > >> http://www.parallelgraphics.com/products/cortona/download/mac/ > >> > >> > >> Works well with iCab and IE5.xx. I'll post a complrte compatibility > >> matrix of my current survey. > >> > > > >intriguing. the Cortona installer is a Classic app, so I didn't bother > >to run it. I'd be interested to hear if you test it in Chimera. also, > >do you know if Cortona (in iCab-X or IE-X) works with the VRML resources > >at the PDB? > > > >regards, > > > >:tim ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_s8ctxQn3lzNenq4s+MRexw)" References: ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 16:18:01 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_s8ctxQn3lzNenq4s+MRexw) Tim Driscoll: The OSX version of the Cortona plugin* visualizes the VRML files at the PDB in in the following browsers PDB/VRML Stable iCab 2.8.2 + + IE5.2.2 + + Mozilla 1.2 + + Chimera 0.6 + + Omniweb 4.1.1 - Opera 6.0 + + * http://www.parallelgraphics.com/products/cortonamacosx/ under OSX 10.1.5. Cheers Frank Johnston -- >at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > >> Tim Driscoll et al.: >> >> Cortona for OSX >> http://www.parallelgraphics.com/products/cortona/download/mac/ >> >> >> Works well with iCab and IE5.xx. I'll post a complrte compatibility >> matrix of my current survey. >> > >intriguing. the Cortona installer is a Classic app, so I didn't bother to >run it. I'd be interested to hear if you test it in Chimera. also, do you >know if Cortona (in iCab-X or IE-X) works with the VRML resources at the >PDB? > >regards, > >:tim >-- >molvisions - molecular graphics & visualization > >usa:north carolina:wake forest > > > -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: Re: VMRL in OSX Date: Fri, 03 Jan 2003 16:37:54 -0400 To: rasmol@lists.umass.edu Tim Driscoll: The OSX version of the Cortona plugin* visualizes the VRML files at the PDB in in the following browsers PDB/VRML Stable iCab 2.8.2 + + IE5.2.2 + + Mozilla 1.2 + + Chimera 0.6 + + Omniweb 4.1.1 - Opera 6.0 + + * http://www.parallelgraphics.com/products/cortonamacosx/ under OSX 10.1.5. Cheers Frank Johnston -- at 1:12 PM EDT on (Friday) 3 January 2003 Frank Johnston said: > Tim Driscoll et al.: > > Cortona for OSX > http://www.parallelgraphics.com/products/cortona/download/mac/ > > > Works well with iCab and IE5.xx. I'll post a complrte compatibility > matrix of my current survey. > intriguing. the Cortona installer is a Classic app, so I didn't bother to run it. I'd be interested to hear if you test it in Chimera. also, do you know if Cortona (in iCab-X or IE-X) works with the VRML resources at the PDB? regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: chimera project (Mac OSX) Date: Fri, 03 Jan 2003 15:32:30 -0600 To: rasmol@lists.umass.edu Hi Everyone- One thing to note about the not-so-good state of Chime on modern browsers in Mac OS X. I came across a web page whose subject was on Netscape 7 for OS X and plug-ins. It was stated that the plug-ins have to be developed with OS X in mind (carbonized?) in order to function. I do not know if this is indeed true, for without testing I believe older plugins function in N7 when installed, but this might explain why I can't get Chime to run in OS X-native browsers no matter what I do. I can get Chime to run in Netscape 4 and 7 as well as Explorer in OS 9. I think that the onus falls upon MDL, and not the browsers. Jamie On 1/3/03 10:10 AM, "timothy driscoll" wrote: > at 9:49 AM EDT on (Friday) 3 January 2003 Lewis Edgel said: > >> Prospects for the future concerning the http://chimera.mozdev.org/ (etc.) >> browser(s) for use with the various incarnations of Rasmol? I came across >> this site again, while researching something else. A fantastic place for >> anyone interested in web programming! >> >> Lewis Edgel >> > > hi Lewis, > > I see no way to configure Chimera to use helper apps yet. once that > functionality appears, one should be able to use RasMol/SPV/DSViewer/Cn3D as > helper apps just like with other browsers. I do have hope for this in > Chimera, though; it is still a pre-1.0 browser, and a darn fine one at that > IMHO. > > Chimera appears to handle modern plug-ins without much trouble. (I have QT5 > and Flash in my Internet Plugins folder, for example, and they work okay in > Chimera.) unfortunately, Chime does not work in Chimera, despite the > similarity in name ;-) > > :aside: > AFAIK from reading various mozilla and netscape docs, last-generation > plug-ins like Chime require some re-tooling in order to function in the next > generation of mozilla-like browsers. the docs make it sound like a minor > fix, but what do I know? > :/aside: > > Java applet mol vis viewers show promise. for example, the Java-based > QuickPdb applet available at the PDB works great. MICE, however, does not, > possibly b/c it requires a more complicated combination of Java plugins? > > I can not find a VRML viewer native to OS X. > > > hope that helps! > > :tim ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr. James Caras The Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 caras@mail.utexas.edu (512) 471-0416 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Trina Valencich Subject: Re: Visualization conference Date: Tue, 07 Jan 2003 09:35:58 -0700 To: rasmol@lists.umass.edu This sounds like me. I simulate collision dynamics for reactive systems. I want to learn about biochemistry & I always need a visual image, if only in my head, to understand chemistry. When I tried your web site, the page could not be found. We are between the Autumn & Spring semesters right now, so I'll try again later. Trina Valencich Chemistry Department University of Montana MIssoula, MT 59812 Office: 406-243-5227 FAX: 406-243-4227 At 05:24 PM 12/6/2002 -0500, you wrote: >Greetings from the Chair of the 2003 Gordon Conference on Visualization >in Science and Education. For those not familiar with the conference, >the focus is on creating visualizations that are accurate AND that help >students in learning concepts. (For more information, see the web site: >http://www.soton.ac.uk/~ecchemed/grc/). I am posting to this list >because I am trying to find someone who is involved with molecular-level >visualizations in biology or chemistry who is concerned with the >question of whether the visualizations help students learn or how they >help students learn? If this sounds like you, please email me >Mary.shultz@tufts.edu >(Note: no c in Shultz) >We can then talk further. Looking forward to hearing from you! > >Thanks >Mary Shultz > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: VMRL in OSX Date: Tue, 07 Jan 2003 20:38:11 +0100 To: rasmol@lists.umass.edu Anyone follow the links from www.parallelgraphics.com to the http://www.parallelgraphics.com/products/cortona/best list of sites,which links to the http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm site? I think this site has been mentioned once before in this mailing list. I don't recall the visualizations offered in the current variety of formats - the last time I visited it. It's worth adding to your "links" if not already visited. I think it would be a very good idea for as many people as possible to write to Parallel concerning the direction their software development takes while they finish up the VRML Client 4.1 Beta. This should be of special interest to anyone working with OSX for Mac. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Johnston Subject: RE: VMRL in OSX Date: Tue, 07 Jan 2003 16:53:37 -0400 To: rasmol@lists.umass.edu Lewis Edgel: The MOTM (Bristol) is the more eclectic of the two valuable MOTMs (http://www.rcsb.org/pdb/molecules/molecule_list.html). We should communicate our interests to Parallel Graphics as you suggest-I'm sure they will notice the number of downloads for the OSx Cortona plugin and that this will be persuasive if it is seen to be used. Cheers Frank Johnston >Anyone follow the links from www.parallelgraphics.com to the >http://www.parallelgraphics.com/products/cortona/best list of sites,which >links to the http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm site? I >think this site has been mentioned once before in this mailing list. I don't >recall the visualizations offered in the current variety of formats - the >last time I visited it. It's worth adding to your "links" if not already >visited. > >I think it would be a very good idea for as many people as possible to write >to Parallel concerning the direction their software development takes while >they finish up the VRML Client 4.1 Beta. This should be of special interest >to anyone working with OSX for Mac. > >Lewis Edgel > -- Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 2J1 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-MSMail-priority: Normal References: <5.2.0.9.0.20030107093210.03310c78@selway.umt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Foley Subject: Help modelling a sequence onto a known structure with a gap? Date: Thu, 09 Jan 2003 16:11:07 -0600 To: rasmol@lists.umass.edu Dear RasMol users, I would like to "map" or model the amino acid sequence of a HIV-1 gp120 envelope protein onto the known structure of another HIV-1 gp120 protein. SwissModel http://www.expasy.org/swissmod/SWISS-MODEL.html fails when I give it the amino acid sequence and the PDB file (19GM) because the 1G9M 3D structure was made from an env protein that had the variable loops removed. Thus the real sequence of HIV-1 gp120 has insertions relative to the 3D structure sequence. I don't expect, or even want, a "realistic" structure for these loops. I would be happy with any conformation in the loops. All I need is a 3D figure of gp120 that does not have these variable loops entirely missing. I have seen many figures indicating that the authors have done this sort of thing. For example: Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, Hendrickson WA. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure Fold Des. 2000 Dec 15;8(12):1329-39. PMID: 11188697 Shows a figure with the loops included. Is there any tool that helps people "invent" the 3D X-Y-Z coordinates for a segment of amino acids, given that the first amino acid needs to start with Cys126 here: ATOM 355 N CYS G 126 25.490 -4.700 61.405 1.00 72.28 N ATOM 356 CA CYS G 126 26.188 -4.085 60.270 1.00 78.01 C ATOM 357 C CYS G 126 26.107 -5.014 59.054 1.00 80.78 C ATOM 358 O CYS G 126 27.010 -5.823 58.824 1.00 81.12 O ATOM 359 CB CYS G 126 27.668 -3.853 60.582 1.00 79.71 C ATOM 360 SG CYS G 126 28.115 -3.229 62.233 1.00 82.97 S and end with CYS196 here: ATOM 387 N CYS G 196 26.818 1.002 60.259 1.00 86.32 N ATOM 388 CA CYS G 196 26.277 -0.036 61.129 1.00 84.01 C ATOM 389 C CYS G 196 24.940 0.380 61.728 1.00 82.05 C ATOM 390 O CYS G 196 24.884 1.273 62.574 1.00 82.37 O ATOM 391 CB CYS G 196 27.237 -0.327 62.280 1.00 84.47 C ATOM 392 SG CYS G 196 28.721 -1.315 61.912 1.00 85.15 S the "loop" which is missing in the structure has this amino acid sequence: CVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYA FFYKLDIIPIDNDTTSYKLTSC beginning with C = CYS 126 and ending with C = CYS 196 Thanks for any help you can give me. Brian Foley, PhD HIV Genetic Sequences and Immunology Databases btf@lanl.gov (505) 665-1970 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Help modelling a sequence onto a known structure with a gap? Date: Thu, 09 Jan 2003 18:33:28 -0500 To: rasmol@lists.umass.edu hi Brian, SwissPdbViewer has Loop building tools built in, and a tutorial online. I have not gone through the process but it looks to be exactly what you want. and knowing SPDBV, I imagine the loops would be fairly realistic. check out the loop-building tutorial at the SPDV home page is hth, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 4:11 PM EDT on (Thursday) 9 January 2003 Brian Foley said: > Dear RasMol users, > > I would like to "map" or model the amino acid sequence of a > HIV-1 gp120 envelope protein onto the known structure of another > HIV-1 gp120 protein. > SwissModel > http://www.expasy.org/swissmod/SWISS-MODEL.html > fails when I give it the amino acid sequence and the > PDB file (19GM) because the 1G9M 3D structure was made > from an env protein that had the variable loops removed. > Thus the real sequence of HIV-1 gp120 has insertions relative > to the 3D structure sequence. > > I don't expect, or even want, a "realistic" structure for these > loops. I would be happy with any conformation in the loops. > All I need is a 3D figure of gp120 that does not have these > variable loops entirely missing. > > I have seen many figures indicating that the authors have > done this sort of thing. For example: > > Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, Sodroski J, > Hendrickson WA. > Structures of HIV-1 gp120 envelope glycoproteins from > laboratory-adapted > and primary isolates. > Structure Fold Des. 2000 Dec 15;8(12):1329-39. > PMID: 11188697 > > Shows a figure with the loops included. > > Is there any tool that helps people "invent" the 3D X-Y-Z > coordinates for a segment of amino acids, given that the > first amino acid needs to start with Cys126 here: > ATOM 355 N CYS G 126 25.490 -4.700 61.405 1.00 72.28 > N > ATOM 356 CA CYS G 126 26.188 -4.085 60.270 1.00 78.01 > C > ATOM 357 C CYS G 126 26.107 -5.014 59.054 1.00 80.78 > C > ATOM 358 O CYS G 126 27.010 -5.823 58.824 1.00 81.12 > O > ATOM 359 CB CYS G 126 27.668 -3.853 60.582 1.00 79.71 > C > ATOM 360 SG CYS G 126 28.115 -3.229 62.233 1.00 82.97 > S > > and end with CYS196 here: > > ATOM 387 N CYS G 196 26.818 1.002 60.259 1.00 86.32 > N > ATOM 388 CA CYS G 196 26.277 -0.036 61.129 1.00 84.01 > C > ATOM 389 C CYS G 196 24.940 0.380 61.728 1.00 82.05 > C > ATOM 390 O CYS G 196 24.884 1.273 62.574 1.00 82.37 > O > ATOM 391 CB CYS G 196 27.237 -0.327 62.280 1.00 84.47 > C > ATOM 392 SG CYS G 196 28.721 -1.315 61.912 1.00 85.15 > S > > > the "loop" which is missing in the structure has this amino acid > sequence: > > CVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYA > FFYKLDIIPIDNDTTSYKLTSC > > beginning with C = CYS 126 and ending with C = CYS 196 > > > Thanks for any help you can give me. > > Brian Foley, PhD > HIV Genetic Sequences and Immunology Databases > btf@lanl.gov > (505) 665-1970 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Mail-followup-to: Rasmol List Content-disposition: inline User-Agent: Mutt/1.4i X-OriginalArrivalTime: 15 Jan 2003 03:44:06.0312 (UTC) FILETIME=[5A942280:01C2BC48] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Salter-Duke Subject: Launching Rasmol from browser under linux Date: Wed, 15 Jan 2003 13:13:07 +0930 To: Rasmol List I am trying to launch Rasmol from a browser under linux when a pdb file is received. I have set up the preferences to recognise chemical/x-pdb mime types with extension pdb. Now if a pdb file comes off the internet it works fine with both netscape and mozilla. Rasmol is launched with the molecule displayed. However, if I try to load a local pdb file in the browser it works with netscape (Rasmol is launched fine) but does not work with mozilla (the text of the pdb file appears in the browser. Does anyone have any idea what is happening here? Netscape 4.78/U.S., 25-Jun-01; (c) 1995-2000 Netscape Communications Corp. Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2.1) Gecko/20010901, build 2001090111 For mozilla I took the advice from:- http://www.dkfz-heidelberg.de/spec/sweet2/doc/plugin/fhelper.html and called rasmol from a wrapper script. Rasmol is:- Version 2.7.2.1 April 2001. Regards, Brian. -- Usenet is like a herd of performing elephants with diarrhea; massive, difficult to redirect, awe-inspiring, entertaining, and a source of mind-boggling amounts of excrement when you least expect it. -- Eugene Spafford. Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop 2.0.3 Date: Tue, 21 Jan 2003 22:21:14 -0800 To: pdb-l@rcsb.org, rasmol@lists.umass.edu Available for download at http://www.geneinfinity.org/rastop/download.htm. This is a tiny update; the code for povray script export is updated to povray, version 3.5. High quality pictures are now easily generated, even with multimolecules. Many thanks to John Wessel for his support. Feedback, bug reports, and suggestions always appreciated. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: rlight Subject: IE 6 and chime Date: Fri, 24 Jan 2003 10:47:48 -0500 To: rasmol@lists.umass.edu I may have asked this question earlier, but haven't gotten a response so I thought I'd try again. At some point my IE 6 (actually 6.0.2800.1106.xpsp1.020828-1920) quit loading opening pdb files with chime and instead I get the file download dialogue: File name: xxxxxx.pdb File type: ChimeShimLibrary Object, Etc With the choice to open the file or save to the computer. I have the latest Chime plugin installed (npchime.dll version is 2.6.1.1, ChimeShim.dll is version 1.0.0.0). IE works fine with pdb files that are imbedded in a web page. It just won't open a pdb file directly. (And I seem to recall that it worked okay in the not too distant past, so there may have been an IE upgrade that fouled things up). My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet Explorer\Plugins\Extension\.pdb shows: Name Type Data (Default) REG_SZ MDL Chime 2.6 SP4 Content Type REG_SZ chemical/x-pdb Location REG_SZ C:\Program Files\Internet Explorer\Plugins\npchime.dll Version REG_SZ 2,6,1,1 And the npchime.dll is in the correct directory as indicated here. Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, opening the pdb file directly in the browser. Any ideas anyone? Robley Light ************************************************************* Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: rlight@chem.fsu.edu Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390 Home Page: http://chemweb.chem.fsu.edu/editors/rlight --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: IE 6 and chime Date: Fri, 24 Jan 2003 10:45:05 -0600 (CST) To: rlight Cc: rasmol@lists.umass.edu Hi, Under Win 98 it works with IE6 and Chime SP3. I don't have current access to Win 200 or XP machine with the latest Chime. Have you uninstalled chime and then reinstalled it? Windows is very good at corrupting dll's or using incorrect version of them. Also, you may have to change a security setting in IE to open files. Regards Bruce On Fri, 24 Jan 2003, rlight wrote: > I may have asked this question earlier, but haven't gotten a response so I > thought I'd try again. > > At some point my IE 6 (actually 6.0.2800.1106.xpsp1.020828-1920) quit > loading opening pdb files with chime and instead I get the file download > dialogue: > > File name: xxxxxx.pdb > File type: ChimeShimLibrary Object, > Etc > With the choice to open the file or save to the computer. > > I have the latest Chime plugin installed (npchime.dll version is 2.6.1.1, > ChimeShim.dll is version 1.0.0.0). IE works fine with pdb files that are > imbedded in a web page. It just won't open a pdb file directly. (And I seem > to recall that it worked okay in the not too distant past, so there may have > been an IE upgrade that fouled things up). > > My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet > Explorer\Plugins\Extension\.pdb shows: > > Name Type Data > (Default) REG_SZ MDL Chime 2.6 SP4 > Content Type REG_SZ chemical/x-pdb > Location REG_SZ C:\Program Files\Internet Explorer\Plugins\npchime.dll > Version REG_SZ 2,6,1,1 > > And the npchime.dll is in the correct directory as indicated here. > > Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, opening > the pdb file directly in the browser. > > Any ideas anyone? > > Robley Light > ************************************************************* > Robley J. Light Professor of Chemistry and > Biochemistry > Department of Chemistry Phone: (850) 644-3844 > and Biochemistry Email: rlight@chem.fsu.edu > Florida State University Fax: (850) 644-8281 > Tallahassee, FL 32306-4390 Home Page: > http://chemweb.chem.fsu.edu/editors/rlight > > > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <000a01c2c3bf$f553b9b0$a00cba80@lightbyte> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: IE 6 and chime Date: Fri, 24 Jan 2003 18:17:45 +0100 To: rasmol@lists.umass.edu In windows explorer, are pdb files associated with Internet Explorer ? (Tools, Options, files type, and then check for the pdb file type) My two cents... Paul ----- Original Message ----- Sent: Friday, January 24, 2003 4:47 PM From: "rlight" Subject: IE 6 and chime To: > I may have asked this question earlier, but haven't gotten a response so I > thought I'd try again. > > At some point my IE 6 (actually 6.0.2800.1106.xpsp1.020828-1920) quit > loading opening pdb files with chime and instead I get the file download > dialogue: > > File name: xxxxxx.pdb > File type: ChimeShimLibrary Object, > Etc > With the choice to open the file or save to the computer. > > I have the latest Chime plugin installed (npchime.dll version is 2.6.1.1, > ChimeShim.dll is version 1.0.0.0). IE works fine with pdb files that are > imbedded in a web page. It just won't open a pdb file directly. (And I seem > to recall that it worked okay in the not too distant past, so there may have > been an IE upgrade that fouled things up). > > My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet > Explorer\Plugins\Extension\.pdb shows: > > Name Type Data > (Default) REG_SZ MDL Chime 2.6 SP4 > Content Type REG_SZ chemical/x-pdb > Location REG_SZ C:\Program Files\Internet Explorer\Plugins\npchime.dll > Version REG_SZ 2,6,1,1 > > And the npchime.dll is in the correct directory as indicated here. > > Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, opening > the pdb file directly in the browser. > > Any ideas anyone? > > Robley Light ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: rlight Subject: RE: IE 6 and chime Date: Fri, 24 Jan 2003 12:49:53 -0500 To: rasmol@lists.umass.edu Yes, I forgot to mention that. .pdb files are associated with IE. ************************************************************* Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: rlight@chem.fsu.edu Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390 Home Page: http://chemweb.chem.fsu.edu/editors/rlight > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu] On Behalf Of Paul Pillot > Sent: Friday, January 24, 2003 12:18 PM > To: rasmol@lists.umass.edu > Subject: Re: IE 6 and chime > > > In windows explorer, are pdb files associated with Internet > Explorer ? (Tools, Options, files type, and then check for > the pdb file type) > > My two cents... > Paul > > ----- Original Message ----- > From: "rlight" > To: > Sent: Friday, January 24, 2003 4:47 PM > Subject: IE 6 and chime > > > > I may have asked this question earlier, but haven't gotten > a response > > so I thought I'd try again. > > > > At some point my IE 6 (actually > 6.0.2800.1106.xpsp1.020828-1920) quit > > loading opening pdb files with chime and instead I get the file > > download > > dialogue: > > > > File name: xxxxxx.pdb > > File type: ChimeShimLibrary Object, > > Etc > > With the choice to open the file or save to the computer. > > > > I have the latest Chime plugin installed (npchime.dll version is > > 2.6.1.1, ChimeShim.dll is version 1.0.0.0). IE works fine with pdb > > files that are imbedded in a web page. It just won't open > a pdb file > > directly. (And I > seem > > to recall that it worked okay in the not too distant past, so there > > may > have > > been an IE upgrade that fouled things up). > > > > My registry under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Internet > > Explorer\Plugins\Extension\.pdb shows: > > > > Name Type Data > > (Default) REG_SZ MDL Chime 2.6 SP4 > > Content Type REG_SZ chemical/x-pdb > > Location REG_SZ C:\Program Files\Internet > Explorer\Plugins\npchime.dll > > Version REG_SZ 2,6,1,1 > > > > And the npchime.dll is in the correct directory as indicated here. > > > > Incidentally, both Netscape 4.7 and Netscape 7.01 work just fine, > > opening the pdb file directly in the browser. > > > > Any ideas anyone? > > > > Robley Light > > > -------------------------------------------------------------- > --rasmol-+ > > To change your address, unsubscribe, view previous > messages/history, receive messages as weekly digests, or for > any other information about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > -------------------------------------------------------------- > --rasmol-- > > --- > Incoming mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 > > --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.443 / Virus Database: 248 - Release Date: 1/10/2003 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime's "show pdbheader" crashes Internet Explorer Date: Sun, 26 Jan 2003 15:29:06 -0500 To: rasmol@lists.umass.edu Dear Chimeleons: At my request, Jean Holt of MDL kindly added a new command to Chime 2.6, "show pdbheader". This command returns the entire PDB file header (all lines before the first ATOM line) as a single message via MessageCallback, thereby making the header accessible to javascript. (The header string is returned with formfeeds delimiting lines.) We have been developing a display of information in the PDB file header (resolution, date of release, experimental method, sites described and identified by the authors, etc.) within Protein Explorer, and testing it in Netscape with the expectation of being able to get this to work also in Internet Explorer. I didn't test the 'show pdbheader' command in Internet Explorer until now, when Paul Pillot alerted me that it doesn't work. This appears to preclude use of 'show pdbheader' in Internet Explorer unless and until MDL fixes this problem. (We will probably use another method to get the PDB header into IE's javascript, but it will be more laborious and cumbersome.) I have confirmed that sending the 'show pdbheader' command to Chime causes Internet Explorer to crash with 100% reproducibility. If anyone comes up with a way to work around this, please let me know! The crash happens even in the simplest implementation I can envision, which is demonstrated at http://www.umass.edu/microbio/chime/beta/headtest/ (can be run on-line, and from which site there is also a link to download this test). This implementation avoids attempting to display the (long) header string in a form textarea, which itself is problematic even in Netscape -- any message longer than 1,000 bytes is put directly into a javascript string variable. If there is no PDB header in the PDB file (as for 1atom.pdb, loaded in the invocation of Chime in my test site), Chime returns the message 'No pdb header available' in both Netscape and IE, without any problems. If there is a PDB header, it is returned without problems in Netscape. The largest header I know of (1jj2.pdb, 290 Kbytes) is returned in a few seconds, and can be parsed in javascript in less than 30 seconds on an 800 MHz computer. My tests with IE went as follows: Windows 98, IE 6.0 SP1, Chime 2.6 SP4: IE crashes and often crashes Windows as well. Windows 2000, IE 6.0 SP1, Chime 2.6 SP4: IE crashes (Windows survives). Windows XP, IE 6.0 (no SP), Chime 2.6 SP3: IE crashes (Windows survives). All tests were done from local files. Windows 98 was also tested on-line from the above URL with the same results. In Windows 98, IE also crashed with debugscript=off, and when 'show pdbheader' was sent from a static Chime button instead of via IMBIF. The static button spared Windows 98 in my tests, unlike IMBIF. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: Can RasMol be used in a commercial application? Thread-Index: AcLE9/RO+9kxBx9BSMCj25HozT/CRQBEG5eQ content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 08:42:49 -0500 To: rasmol@lists.umass.edu We are developing an application for users in chemical R&D. Our focus is on automating lab equipment and organizing data from lab instrumentation. In many places we display a chemical structure, and up until now, we've been using our client's ChemDraw plug-in. We need to be independent of ChemDraw (not all clients have ChemDraw). Essentially all we need is a program, or piece of code, that turns a mol file into an image (bmp, wmf or whatever). Nothing very fancy, a simple 2-D view is sufficient. I think that Rasmol would be good fit, or at least a good starting point. Is anyone familiar enough with the license to comment on whether or not we could adapt rasmol for our application? We can supply the full Rasmol with the app, and will give credit to rasmol. Comments? Can anyone suggest another piece of code that can convert a mol file to an image? We're willing to pay a one time developer fee, but a run-time royalty is not very workable. Our platform is MS and our primary tool is C#. Thanks. Mitch Barker Avantium Technologies Inc. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 09:28:05 -0500 (EST) To: rasmol@lists.umass.edu The RasMol 2.7 series is open source, with the following license: ================================================================ Subject to your acceptance of the conditions stated [in the notices that come with RasMol], and your respect, if you are not going to make any modifications or create derived works, you are given permission to freely copy and distribute this package, provided you do the following: * 1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and * 2. Give credit where credit is due citing the version and original authors properly; and * 3. Do not give anyone the impression that the original authors are providing a warranty of any kind. In addition, you may also modify this package and create derived works provided you do the following: * 4. Explain in your documentation how what you did differs from this version of RasMol; and * 5. Make your modified source code available. ====================================================================== Since you are not proposing to modify RasMol, you free to redistribute RasMol under terms 1, 2 and 3, above, either including the full documentation, or pointing to the web site: http://www.RasMol.org In addition to the appropriate versions of the binary (we recommend 2.7.2.1), you will want to include at a minimum rasmol.hlp, raswin.hlp, NOTICE and the English html version of the manual and the Spanish html version of the manual. Please contact me if you have any difficulty setting up your distribution. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 27 Jan 2003, Mitch Barker wrote: > We are developing an application for users in chemical R&D. Our focus is > on automating lab equipment and organizing data from lab > instrumentation. In many places we display a chemical structure, and up > until now, we've been using our client's ChemDraw plug-in. We need to be > independent of ChemDraw (not all clients have ChemDraw). > > Essentially all we need is a program, or piece of code, that turns a mol > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > 2-D view is sufficient. I think that Rasmol would be good fit, or at > least a good starting point. Is anyone familiar enough with the license > to comment on whether or not we could adapt rasmol for our application? > We can supply the full Rasmol with the app, and will give credit to > rasmol. > > Comments? Can anyone suggest another piece of code that can convert a > mol file to an image? We're willing to pay a one time developer fee, but > a run-time royalty is not very workable. > > Our platform is MS and our primary tool is C#. > > Thanks. > > Mitch Barker > Avantium Technologies Inc. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Command line size limit Date: Mon, 27 Jan 2003 15:28:08 +0000 (GMT) To: rasmol@lists.umass.edu This is the first post of a bounced message. > Sorry if this question has been answered, > because I couldn't see a post in the last > three years, and then I gave up reading > about all kinds of limitation, limited > testing and all the other limits that > people have been talking about.... there > were quite a lot! > > Any way, when scripting, I somtimes get the > message error message... > > line 314: Script command line too long! > (it is a long script!) > > I would like to know exactly how long this line > can be, so I can issue another define command... > > I was doing every thing with growing define commands, > for example > > define domain1 100a > define domain1 domain1, 101a > define domain1 domain1, 102a > define domain1 domain1, 103a, > ... > > I was doing it like this because of the command line limit > wouldn't allow a single big define... > > Now I am using some code from the perl Set::Range > module, so I can just issue a few > > define domain1 100-200a, 300-400a > > type commands, I switched over to this style because > the fomer was really slow to load a big script. > > However, some of the latter are still too long for a > single line.! > > I guess I have the answer - just curious now. Cheers, Dan. > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 09:41:37 -0600 (CST) To: rasmol@lists.umass.edu Hi, This is not a simple question and is not trivial! So this is only my opinion that you take at your own risk - I am not a lawyer! RasMol is an open source project. You can obtain the open version at http://openrasmol.org/ as well as the license information. There are a few 'strings' attached that may not suit your company. VERY IMPORTANT: OpenRasMol is open source - you MUST release or provide access to the source code by anyone who wants it! The short answer is yes provided you follow the license terms. So I strongly recommend finding a lawyer because of the issues involved - especially if you modify it. Some pointers to information: In the FAQ are: 1) http://openrasmol.org/FAQ.html#distribution Can RasMol be distributed freely, on CD-ROMs, and used freely even for commercial purposes? 2) Does this mean I can't make a commercial graphics program based on RasMol? http://openrasmol.org/FAQ.html#infectious Also, there are also issues if you get the code written for you especially if the code of other programs that do what you want have been seen by those writing the code. Regards Bruce On Mon, 27 Jan 2003, Mitch Barker wrote: > We are developing an application for users in chemical R&D. Our focus is > on automating lab equipment and organizing data from lab > instrumentation. In many places we display a chemical structure, and up > until now, we've been using our client's ChemDraw plug-in. We need to be > independent of ChemDraw (not all clients have ChemDraw). > > Essentially all we need is a program, or piece of code, that turns a mol > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > 2-D view is sufficient. I think that Rasmol would be good fit, or at > least a good starting point. Is anyone familiar enough with the license > to comment on whether or not we could adapt rasmol for our application? > We can supply the full Rasmol with the app, and will give credit to > rasmol. > > Comments? Can anyone suggest another piece of code that can convert a > mol file to an image? We're willing to pay a one time developer fee, but > a run-time royalty is not very workable. > > Our platform is MS and our primary tool is C#. > > Thanks. > > Mitch Barker > Avantium Technologies Inc. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Command line size limit Date: Mon, 27 Jan 2003 10:54:43 -0500 To: rasmol@lists.umass.edu At 1/27/03, you wrote: > > Any way, when scripting, I somtimes get the > > message error message... > >line 314: Script command line too long! The way I avoid long lines when defining large sets is by breaking up the select commands into multiple lines: select a, b, c, d, e, f ... select selected or g, h, i, j, k, ... select selected or l, m, n, o, p, q, ... define newtoken selected -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Command line size limit Date: Mon, 27 Jan 2003 15:55:28 +0000 (GMT) To: rasmol@lists.umass.edu How many lines do I need to break it up into? When should I choose to break a line? Thanks, Dan. On Mon, 27 Jan 2003, Eric Martz wrote: > At 1/27/03, you wrote: > > > Any way, when scripting, I somtimes get the > > > message error message... > > >line 314: Script command line too long! > > > The way I avoid long lines when defining large sets is by breaking up the > select commands into multiple lines: > > select a, b, c, d, e, f ... > select selected or g, h, i, j, k, ... > select selected or l, m, n, o, p, q, ... > define newtoken selected > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Command line size limit Date: Mon, 27 Jan 2003 15:55:58 +0000 (GMT) To: rasmol@lists.umass.edu Will this technique speed up reading a script file? Ta, Dan. On Mon, 27 Jan 2003, Eric Martz wrote: > At 1/27/03, you wrote: > > > Any way, when scripting, I somtimes get the > > > message error message... > > >line 314: Script command line too long! > > > The way I avoid long lines when defining large sets is by breaking up the > select commands into multiple lines: > > select a, b, c, d, e, f ... > select selected or g, h, i, j, k, ... > select selected or l, m, n, o, p, q, ... > define newtoken selected > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 27 Jan 2003 22:11:16 -0800 To: rasmol@lists.umass.edu RasMol open source license is GPL-like. This means that if you link your software with rasmol you must open your software code under the same license (infectivity). If this is too restrictive for your company, rasmol 2.6.4 code is probably ok for your purpose and is in the public domain. Best regards, Philippe Valadon ----- Original Message ----- Sent: Monday, January 27, 2003 5:42 AM From: "Mitch Barker" Subject: Can RasMol be used in a commercial application? To: > We are developing an application for users in chemical R&D. Our focus is > on automating lab equipment and organizing data from lab > instrumentation. In many places we display a chemical structure, and up > until now, we've been using our client's ChemDraw plug-in. We need to be > independent of ChemDraw (not all clients have ChemDraw). > > Essentially all we need is a program, or piece of code, that turns a mol > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > 2-D view is sufficient. I think that Rasmol would be good fit, or at > least a good starting point. Is anyone familiar enough with the license > to comment on whether or not we could adapt rasmol for our application? > We can supply the full Rasmol with the app, and will give credit to > rasmol. > > Comments? Can anyone suggest another piece of code that can convert a > mol file to an image? We're willing to pay a one time developer fee, but > a run-time royalty is not very workable. > > Our platform is MS and our primary tool is C#. > > Thanks. > > Mitch Barker > Avantium Technologies Inc. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Why is rasmol so slow... Date: Tue, 28 Jan 2003 09:16:15 +0000 (GMT) To: rasmol@lists.umass.edu Why is rasmol so slow to read script files? perl for example can parse a million lines of a sequence database in less than 2 min. ? Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 08:30:55 -0600 (CST) To: rasmol@lists.umass.edu Hi, No, the OpenRasMol license is not GPL-like! The only similarity is that it is based on the part of the GPL's spirit. There are many misconceptions regarding the GPL especially in terms of what the goal is and what it actual provides. There are rather obvious differences between the licenses include: The GPL forces/demands that you to make the code available. In contrast, the OpenRasMol license request (uses please a lot) that you make it available. The OpenRasMol license requires you to tell the user where it differs from the original. The latest GPL only requires you to provide the modified code (earlier version has different requirements - always check the license used!). The OpenRasMol license tells you that you have to give credit by citation. There is no such requirement in the GPL. The OpenRasMol license tells you that you have to provide complete documentation or where to get it. There is no such requirement in the GPL. This is not meant to say what they are doing is bad but that I think the license is weak. Better Open Source licenses can be found at http://www.opensource.org. Regards Bruce On Mon, 27 Jan 2003, Philippe wrote: > RasMol open source license is GPL-like. This means that if you link your > software with rasmol you must open your software code under the same license > (infectivity). If this is too restrictive for your company, rasmol 2.6.4 > code is probably ok for your purpose and is in the public domain. > > Best regards, > Philippe Valadon > > > > ----- Original Message ----- > From: "Mitch Barker" > To: > Sent: Monday, January 27, 2003 5:42 AM > Subject: Can RasMol be used in a commercial application? > > > > We are developing an application for users in chemical R&D. Our focus is > > on automating lab equipment and organizing data from lab > > instrumentation. In many places we display a chemical structure, and up > > until now, we've been using our client's ChemDraw plug-in. We need to be > > independent of ChemDraw (not all clients have ChemDraw). > > > > Essentially all we need is a program, or piece of code, that turns a mol > > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > > 2-D view is sufficient. I think that Rasmol would be good fit, or at > > least a good starting point. Is anyone familiar enough with the license > > to comment on whether or not we could adapt rasmol for our application? > > We can supply the full Rasmol with the app, and will give credit to > > rasmol. > > > > Comments? Can anyone suggest another piece of code that can convert a > > mol file to an image? We're willing to pay a one time developer fee, but > > a run-time royalty is not very workable. > > > > Our platform is MS and our primary tool is C#. > > > > Thanks. > > > > Mitch Barker > > Avantium Technologies Inc. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 11:01:18 -0500 (EST) To: rasmol@lists.umass.edu Actually, the current RasMol license is GPL-like, and, the first release we make after moving the GIF code out into a separate module will in fact be explicitly GPL. The plan to move RasMol under the GPL has been discussed with Richard Stallman and Roger Sayle, and the old problem with the IUCr CIF patent vs. GPL has been resolved. The points raised are interesting, but do not represent a substantive conflict with the GPL. Both the GPL and the RasMol license make use of an interesting aspect of the law, that it is important for all internet software users to understand: Unless you have an explicit license to do so, you have no right to copy any document you encounter. There are some limited exceptions to this rule, but, especially for major programs, you need permission to make copies. If you read the RasMol notices carefully, you will find that, despite the polite language, the only way you may properly make a copy is by respecting the open source requirements. We consider the documentation an important part of RasMol as a program. Much of it even has its own source file (rasmol.doc). If you do not consider the non-source code portions of an open source release to be covered by the licenses in the package, then you have no right to copy or modify that material at all. Most developers I know treat the documentation of open source programs as part of the source. The programs diff and patch make compliance with our requirement to provide changes functionally equivalent to the GPL requirement to provide modified code, and in practice I have cheerfully accepted modified code instead of changes. I have had requests to distribute variants of RasMol without the long and growing list of credits. I am a stickler on giving credit where credit is due, so I prefer to retain such credit lists. Even when we move under the GPL, that will be a requirement in making copies of RasMol, as will the requirements on the documentation. Please note that the strength of all these licenses lies in the Copyright law. To avoid any misunderstanding arising from the assertion that the current license is "weak", be assured that we have enforced the RasMol license in the past and will enforce it in the future. The RasMol 2.7 series is open source and will remain so. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Jan 2003 southey@ux1.cso.uiuc.edu wrote: > Hi, > > No, the OpenRasMol license is not GPL-like! The only similarity is that > it is based on the part of the GPL's spirit. There are many > misconceptions regarding the GPL especially in terms of what the goal is > and what it actual provides. > > There are rather obvious differences between the licenses include: > > The GPL forces/demands that you to make the code available. In > contrast, the OpenRasMol license request (uses please a lot) that you make > it available. > > The OpenRasMol license requires you to tell the user where it differs from > the original. The latest GPL only requires you to provide the modified > code (earlier version has different requirements - always check the > license used!). > > The OpenRasMol license tells you that you have to give credit by citation. > There is no such requirement in the GPL. > > The OpenRasMol license tells you that you have to provide complete > documentation or where to get it. There is no such requirement in the GPL. > > This is not meant to say what they are doing is bad but that I think the > license is weak. Better Open Source licenses can be found at > http://www.opensource.org. > > Regards > Bruce > > On Mon, 27 Jan 2003, Philippe wrote: > > > RasMol open source license is GPL-like. This means that if you link your > > software with rasmol you must open your software code under the same license > > (infectivity). If this is too restrictive for your company, rasmol 2.6.4 > > code is probably ok for your purpose and is in the public domain. > > > > Best regards, > > Philippe Valadon > > > > > > > > ----- Original Message ----- > > From: "Mitch Barker" > > To: > > Sent: Monday, January 27, 2003 5:42 AM > > Subject: Can RasMol be used in a commercial application? > > > > > > > We are developing an application for users in chemical R&D. Our focus is > > > on automating lab equipment and organizing data from lab > > > instrumentation. In many places we display a chemical structure, and up > > > until now, we've been using our client's ChemDraw plug-in. We need to be > > > independent of ChemDraw (not all clients have ChemDraw). > > > > > > Essentially all we need is a program, or piece of code, that turns a mol > > > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > > > 2-D view is sufficient. I think that Rasmol would be good fit, or at > > > least a good starting point. Is anyone familiar enough with the license > > > to comment on whether or not we could adapt rasmol for our application? > > > We can supply the full Rasmol with the app, and will give credit to > > > rasmol. > > > > > > Comments? Can anyone suggest another piece of code that can convert a > > > mol file to an image? We're willing to pay a one time developer fee, but > > > a run-time royalty is not very workable. > > > > > > Our platform is MS and our primary tool is C#. > > > > > > Thanks. > > > > > > Mitch Barker > > > Avantium Technologies Inc. > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Why is rasmol so slow... (fwd) Date: Tue, 28 Jan 2003 11:16:30 -0500 (EST) To: rasmol@lists.umass.edu Cc: Dan Bolser Please provide a samples of slow script and I'll investigate the problem. If the data files being read are not standard PDb entries, please remember to include them. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== > ---------- Forwarded message ---------- > Date: Tue, 28 Jan 2003 09:16:15 +0000 (GMT) > From: Dan Bolser > Reply-To: rasmol@lists.umass.edu > To: rasmol@lists.umass.edu > Subject: Why is rasmol so slow... > > > Why is rasmol so slow > to read script files? > > perl for example can parse > a million lines of a > sequence database in less > than 2 min. > > ? > Dan. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 11:04:43 -0600 (CST) To: rasmol@lists.umass.edu Hi, Yes they ARE a conflict with the GPL! Please reread the GPL and you will see this. Let me very clear and say I don't have a problem with the OpenRasMol license in the 'spirit' of the GPL. But the 'spirit' aspect of the GPL carries no legal weight. What I have the problem with is the OpenRasMol license being called GPL-like when it is clearly NOT in the license view. Can the OpenRasMol conform to the GPL? Not in the present state and that is why is can not be considered GPL-like from a license view. Otherwise Stallman would love the BSD and similar licenses - which is far from the case. Bruce On Tue, 28 Jan 2003, Herbert J. Bernstein wrote: > Actually, the current RasMol license is GPL-like, and, the first release > we make after moving the GIF code out into a separate module will in fact > be explicitly GPL. The plan to move RasMol under the GPL has been > discussed with Richard Stallman and Roger Sayle, and the old problem with > the IUCr CIF patent vs. GPL has been resolved. > > The points raised are interesting, but do not represent a substantive > conflict with the GPL. Both the GPL and the RasMol license make use > of an interesting aspect of the law, that it is important for all > internet software users to understand: > > Unless you have an explicit license to do so, you have no right > to copy any document you encounter. > > There are some limited exceptions to this rule, but, especially for major > programs, you need permission to make copies. If you read the RasMol > notices carefully, you will find that, despite the polite language, > the only way you may properly make a copy is by respecting the open > source requirements. > > We consider the documentation an important part of RasMol as a program. > Much of it even has its own source file (rasmol.doc). If you do not > consider the non-source code portions of an open source release to be > covered by the licenses in the package, then you have no right to copy or > modify that material at all. Most developers I know treat the > documentation of open source programs as part of the source. > > The programs diff and patch make compliance with our requirement to > provide changes functionally equivalent to the GPL requirement to provide > modified code, and in practice I have cheerfully accepted modified code > instead of changes. > > I have had requests to distribute variants of RasMol without the long > and growing list of credits. I am a stickler on giving credit where > credit is due, so I prefer to retain such credit lists. Even when we > move under the GPL, that will be a requirement in making copies of > RasMol, as will the requirements on the documentation. > > Please note that the strength of all these licenses lies in the Copyright > law. To avoid any misunderstanding arising from the assertion that the > current license is "weak", be assured that we have enforced the RasMol > license in the past and will enforce it in the future. The RasMol 2.7 > series is open source and will remain so. > > Regards, > Herbert J. Bernstein > > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Tue, 28 Jan 2003 southey@ux1.cso.uiuc.edu wrote: > > > Hi, > > > > No, the OpenRasMol license is not GPL-like! The only similarity is that > > it is based on the part of the GPL's spirit. There are many > > misconceptions regarding the GPL especially in terms of what the goal is > > and what it actual provides. > > > > There are rather obvious differences between the licenses include: > > > > The GPL forces/demands that you to make the code available. In > > contrast, the OpenRasMol license request (uses please a lot) that you make > > it available. > > > > The OpenRasMol license requires you to tell the user where it differs from > > the original. The latest GPL only requires you to provide the modified > > code (earlier version has different requirements - always check the > > license used!). > > > > The OpenRasMol license tells you that you have to give credit by citation. > > There is no such requirement in the GPL. > > > > The OpenRasMol license tells you that you have to provide complete > > documentation or where to get it. There is no such requirement in the GPL. > > > > This is not meant to say what they are doing is bad but that I think the > > license is weak. Better Open Source licenses can be found at > > http://www.opensource.org. > > > > Regards > > Bruce > > > > On Mon, 27 Jan 2003, Philippe wrote: > > > > > RasMol open source license is GPL-like. This means that if you link your > > > software with rasmol you must open your software code under the same license > > > (infectivity). If this is too restrictive for your company, rasmol 2.6.4 > > > code is probably ok for your purpose and is in the public domain. > > > > > > Best regards, > > > Philippe Valadon > > > > > > > > > > > > ----- Original Message ----- > > > From: "Mitch Barker" > > > To: > > > Sent: Monday, January 27, 2003 5:42 AM > > > Subject: Can RasMol be used in a commercial application? > > > > > > > > > > We are developing an application for users in chemical R&D. Our focus is > > > > on automating lab equipment and organizing data from lab > > > > instrumentation. In many places we display a chemical structure, and up > > > > until now, we've been using our client's ChemDraw plug-in. We need to be > > > > independent of ChemDraw (not all clients have ChemDraw). > > > > > > > > Essentially all we need is a program, or piece of code, that turns a mol > > > > file into an image (bmp, wmf or whatever). Nothing very fancy, a simple > > > > 2-D view is sufficient. I think that Rasmol would be good fit, or at > > > > least a good starting point. Is anyone familiar enough with the license > > > > to comment on whether or not we could adapt rasmol for our application? > > > > We can supply the full Rasmol with the app, and will give credit to > > > > rasmol. > > > > > > > > Comments? Can anyone suggest another piece of code that can convert a > > > > mol file to an image? We're willing to pay a one time developer fee, but > > > > a run-time royalty is not very workable. > > > > > > > > Our platform is MS and our primary tool is C#. > > > > > > > > Thanks. > > > > > > > > Mitch Barker > > > > Avantium Technologies Inc. > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 13:12:56 -0500 (EST) To: rasmol@lists.umass.edu Dear Bruce, There is a difference between a conflict and simply having some additional license terms which do not conflict with keeping the program open source. Requiring someone to keep the documentation available or to cite authors does not "conflict" with the GPL. The place where the RasMol license and the GPL have a substantive difference is an area in which the RasMol license is silent: patents. That issue has now been resolved, and, as I said, we will be adopting the GPL as the license for the first release of RasMol after we segregate the GIF code. Please do not confuse the RasMol license with the BSD license. The RasMol license (like the GPL license) is "infectious", requires you to make source code available and applies to programs you derive from RasMol. The current BSD and MIT licenses are much less infectious, only requiring you to carry forward some notices. There are arguments pro and con on the two approaches. For RasMol, we have chosen to follow Stallman's approach. It seems to be appropriate for the tools used in science. I would suggest that, as a courtesy to the others on this list, if you have further discussion on the details of this particular license, we take it off-line from the list for a while, and, then, is something interesting arises from the discussion, we post one (or two) summary messages back to the list when we are done. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Jan 2003 southey@ux1.cso.uiuc.edu wrote: > Hi, > > Yes they ARE a conflict with the GPL! Please reread the GPL and you will > see this. Let me very clear and say I don't have a problem with the > OpenRasMol license in the 'spirit' of the GPL. But the 'spirit' aspect of > the GPL carries no legal weight. What I have the problem with is the > OpenRasMol license being called GPL-like when it is clearly NOT in the > license view. Can the OpenRasMol conform to the GPL? Not in the present > state and that is why is can not be considered GPL-like from a license > view. Otherwise Stallman would love the BSD and similar licenses - which > is far from the case. > > Bruce > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: valadon@ix.netcom.com Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 11:07:00 -0800 (PST) To: rasmol@lists.umass.edu Please, keep this discussion in clear on the list. It might be to technical for many, but it is important for the record to have these points explained and discussed in details. I realize that it is an elusive goal to try to classify open source licenses on their behavior so dramatic can be the effect of just changing one word. I used the term GLP-like regarding the infectivity. I think we agree that rasmol license is infective. For those who wonder what infectivity means, let's take a practical example. If you incorporate rasmol code into your own software, then your entire software becomes a derivative work and must be released under the rasmol license, not just the modifications you made to rasmol code. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: Installing MolMol on MacOS X Date: Wed, 29 Jan 2003 14:23:32 +1300 To: rasmol@lists.umass.edu Hi all, my apologies if this is not the right place to ask, but after long years on the Mac I feel somewhat lost on OS X. I would like to install MolMol and some other molecular biology apps on OS X. I installed Apples X11 beta, and afterwards installed MolMol - but when I start it I get an error: "MenuBar file could not be opened, check installation (setting of MOLMOLHOME)" ... I'm at a loss (aka I'm not even sure what to ask here). How do I get MolMol to run? Any advice would be highly appreciated. Best Regards Markus -- Dr. Markus Winter Tel: 0064 (0)9 373 7599 (wait for message then type extension) 83960 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: RE: Installing MolMol on MacOS X Date: Tue, 28 Jan 2003 21:01:29 -0500 To: rasmol@lists.umass.edu I do not run OS X myself, but found some info via google (for MOLMOL and scientific apps): http://dryden.biol.yorku.ca/darwin.html http://www.apple.com/scitech/unixports/ search google for your error to, using some sort of variation of "check installation MOLMOLHOME" -- I saw a few things that might help you out but first, make sure you have the following file: ./molmol/setup/MenuBar if not, that could be the source of your problem hope that helps- Doug > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of Markus Winter > Sent: Tuesday, January 28, 2003 8:24 PM > To: rasmol@lists.umass.edu > Subject: Installing MolMol on MacOS X > > Hi all, > > my apologies if this is not the right place to ask, but after long years > on > the Mac I feel somewhat lost on OS X. I would like to install MolMol and > some other molecular biology apps on OS X. I installed Apples X11 beta, > and > afterwards installed MolMol - but when I start it I get an error: "MenuBar > file could not be opened, check installation (setting of MOLMOLHOME)" ... > I'm at a loss (aka I'm not even sure what to ask here). How do I get > MolMol > to run? > > Any advice would be highly appreciated. > > Best Regards > > Markus > > -- > > Dr. Markus Winter > Tel: 0064 (0)9 373 7599 (wait for message then type extension) 83960 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: secondary structure prediction Date: Tue, 28 Jan 2003 21:43:01 -0500 To: rasmol@lists.umass.edu Hi All- Quick question: does anyone know of a secondary structure prediction program that will output a formatted file (postscript, etc.) with "graphic" helices/sheets (similar to ESPript postscript output). Note: I need it for a prediction; not to read and output from a pdb file Thanks! Doug ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Can RasMol be used in a commercial application? Date: Tue, 28 Jan 2003 21:49:15 -0800 To: rasmol@lists.umass.edu ----- Original Message ----- From: "Herbert J. Bernstein" /.../ > I have had requests to distribute variants of RasMol without the long > and growing list of credits. I am a stickler on giving credit where > credit is due, so I prefer to retain such credit lists. /.../> Regards, > Herbert J. Bernstein > The license states: "Give credit where credit is due citing the version and original authors properly", but does not say that each author and each variant name, variant version and variant date must listed in each source file of the distribution and that each source file should be updated each time a new version is released. RasMol would be curiously alone in the open source world with such a requirement (That would definitively transform Mozilla in Godzilla!). On the other hand, I noticed that we tend to over-credit main contributors, where I see around me several open sources with a single list of credited people that is more extended and precise, and rewarding for those who committed themselves in very small, but fundamental contributions. If we ever switch to GPL, we should consider rewriting the credit line. I quote also: > Please do not confuse the RasMol license with the BSD license. The RasMol > license (like the GPL license) is "infectious", requires you to make > source code available and applies to programs you derive from RasMol. > The current BSD and MIT licenses are much less infectious, only requiring > you to carry forward some notices. There are arguments pro and con on the > two approaches. For RasMol, we have chosen to follow Stallman's > approach. It seems to be appropriate for the tools used in science. I guess most people in this list ask at this point if we shall ever make something Chime-like out of the nouveau rasmol. Can a browser plug-in be under the GPL? I'd like to be sure before we commit rasmol under the GPL. Can anyone shed some light here? Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Can RasMol be used in a commercial application? Date: Wed, 29 Jan 2003 07:35:33 -0500 (EST) To: rasmol@lists.umass.edu The only tricky part of creating a plug-in version of RasMol is that, to avoid legal tangles, it needs to be done by somebody who has never downloaded or used Chime, so that there cannot be any possibility that they have reversed engineered their code. This is call "clean-room" development. Any volunteers? ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Jan 2003, Philippe wrote: > ----- Original Message ----- > From: "Herbert J. Bernstein" > > /.../ > > I have had requests to distribute variants of RasMol without the long > > and growing list of credits. I am a stickler on giving credit where > > credit is due, so I prefer to retain such credit lists. > /.../> Regards, > > Herbert J. Bernstein > > > > The license states: "Give credit where credit is due citing the version and > original authors properly", but does not say that each author and each > variant name, variant version and variant date must listed in each source > file of the distribution and that each source file should be updated each > time a new version is released. RasMol would be curiously alone in the open > source world with such a requirement (That would definitively transform > Mozilla in Godzilla!). On the other hand, I noticed that we tend to > over-credit main contributors, where I see around me several open sources > with a single list of credited people that is more extended and precise, and > rewarding for those who committed themselves in very small, but fundamental > contributions. If we ever switch to GPL, we should consider rewriting the > credit line. > > I quote also: > > > Please do not confuse the RasMol license with the BSD license. The RasMol > > license (like the GPL license) is "infectious", requires you to make > > source code available and applies to programs you derive from RasMol. > > The current BSD and MIT licenses are much less infectious, only requiring > > you to carry forward some notices. There are arguments pro and con on the > > two approaches. For RasMol, we have chosen to follow Stallman's > > approach. It seems to be appropriate for the tools used in science. > > I guess most people in this list ask at this point if we shall ever make > something Chime-like out of the nouveau rasmol. Can a browser plug-in be > under the GPL? I'd like to be sure before we commit rasmol under the GPL. > Can anyone shed some light here? > > Philippe Valadon > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: rasmol 2.7? Date: Wed, 29 Jan 2003 13:51:14 +0000 (GMT) To: rasmol@lists.umass.edu Is there a call for functionality? Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Joseph Mazurkiewicz Subject: Re: secondary structure prediction Date: Wed, 29 Jan 2003 12:00:12 -0500 To: rasmol@lists.umass.edu You could try the GCG Wisconsin Package. It has a protein analysis module called PeptideStructure that makes secondary structure predictions. PlotStructure then displays the predictions graphically. http://www.accelrys.com/products/gcg_wisconsin_package/ I have no financial interest in GCG, just use the program. Joseph E. Mazurkiewicz, Ph.D. Center for Neuropharmacology and Neuroscience Mail Code 136 Albany Medical College Albany, NY 12208 Phone: 518-262-5381 FAX: 518-262-5799 e-mail: mazurkj@mail.amc.edu >>> djkojeti@unity.ncsu.edu 01/28/03 09:43PM >>> Hi All- Quick question: does anyone know of a secondary structure prediction program that will output a formatted file (postscript, etc.) with "graphic" helices/sheets (similar to ESPript postscript output). Note: I need it for a prediction; not to read and output from a pdb file Thanks! Doug ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Molecular Machinery poster Date: Wed, 29 Jan 2003 14:37:19 -0600 (CST) To: rasmol@lists.umass.edu Hi, >From the PDB molecule of the month site: http://www.rcsb.org/pdb/molecules/molecule_list.html For copies of the poster, "Molecular Machinery: A Tour of the Protein Data Bank", please send your postal address to info@rcsb.org . A 2-sided, 8 1/2" x 11" quick reference guide--showing the images and their structure names and PDB ID's. There is also a link to a pdf version - about 5,113KB! Regards Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 boundary="Boundary_(ID_YQYnV/p97KCx3d1YOZnBgw)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: molecular 3D literacy Date: Wed, 29 Jan 2003 17:29:51 -0600 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_YQYnV/p97KCx3d1YOZnBgw) Colleagues: Those teaching and performing research in the molecular sciences, especially chemistry and biochemistry, are aware of the need for both students and practitioners to possess a kind of "literacy" which is based on multiple dimensions, both spatial and temporal. It is difficult to define precisely what skills one must possess before one can be considered literate in this manner, but it is important to do so from a pedagogical point of view. I have posted a draft list of such skills at http://orca.st.usm.edu/~rbateman/kinemage/mol-literacy.htm and would appreciate feedback from this list to refine it. Sincerely, Bob Bateman Robert C. Bateman, Jr. Professor and Chair Department of Chemistry and Biochemistry University of Southern Mississippi Hattiesburg, MS 39406-5043 Robert.Bateman@usm.edu www.chem.usm.edu 601-266-4701 (department office) 601-266-6075 (fax) ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Why is rasmol so slow... Date: Wed, 29 Jan 2003 20:30:00 -0500 To: rasmol@lists.umass.edu [[ I am posting this message from Roger Sayle to the list to circumvent technical difficulties with the original transmission. -Eric Martz]] ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Why is rasmol so slow... Date: Tue, 28 Jan 2003 10:58:55 -0700 (MST) To: Dan Bolser Cc: rasmol@lists.umass.edu [I'm Cc'ing this response to the RasMol list as some of the hints and tricks to speeding up scripts may not be generally known.] To answer one of your original questions, the maximum command line length in RasMol is 256 characters (though this may have been increased in later versions). I'll explain a little of how RasMol works under the surface. The RasMol "define" command is implemented underneath the surface as a single symbolic name for a linked list of pointer to atoms. It actually does slightly better than a linked list, by chunking the list into blocks of upto ten atom pointers at a time. First tip, "define id1 id2", i.e. creating a synonym for a set of atoms is actually quite expensive. i.e. this requires two separate lists to be stored. RasMol could switch to reference counting like Perl, but it was assumed that duplicate lists would be rare. Hence, I'd recommend removing the "SUNID_*" and "SID_*" identifier synonyms. Grouping defines together in batches is a huge performance win. define D4 526A define D4 D4, 558A is much slower than define D4 526A, 558A In the first example, RasMol traverses the molecule querying each atom to determine if "526A" is true, and if so adds it to the linked list for the set D4. Then on the second line, it runs through every atom in the molecule again testing whether "D4, 558A" is true. To make things worse, "D4" is implemented by searching through the D4 linked list to see if the atom being tested is a member of the set. The alternative "define D4 526A,558A,758A" traverses the molecule only once, testing the expression "526A,558A,758A" at each atom, and doesn't ever have to test set membership. Most of your D# sets can be defined on a single line, and the remaining few can be split across lines should you reach 200 characters or so. When defining large sets it also make sense to use RasMol's selection mechanism. Selecting atoms and bonds in RasMol is, unlike user-defined sets, stored by representing a true or false flag in each atom. Hence "define D5 selected, 526B" is much faster than "define D5 D4, 526B" as testing for membership in "selected" is almost instantaneous. Hence, the sequence: select 525, 526, 527, 528, 529, 530 select selected, 531, 532, 533, 534 define D6 selected, 535, 536, 537, 538 is the optimal way to build up large RasMol sets. This also has the advantage that "define foo foo,bar", as described above, generates a copy rather than appends to a list. i.e. tmp = allocate (foo, bar) deallocate (foo) foo = tmp i.e. there's a lot of memory intensive allocation and deallocation going on, that doesn't occur using "select". I'm sure with the "optmization hints" provided above you should be able to create a version of your script that takes a fraction of the time, i.e. a second or two rather than over a minute. I hope this helps. Roger -- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Toobers in Science Education Date: Sat, 01 Feb 2003 12:30:03 -0500 To: rasmol@lists.umass.edu Dear Educators and Students: I first learned about "toobers" from Tim Herman and Michael Patrick in their SEPA Workshops for high-school teachers. Toobers are soft, flexible, inexpensive foam plastic rods about a meter long, and as big around as a good-sized carrot. They are easily bent and hold their shape, due to an aluminum wire running down the center. Originally designed as a component of toys named Toobers and Zots, they are manufactured by Hands-On Toys. Last year I bought a bunch of toobers and as I taught my immunology class, I kept finding new ways to use them to illustrate structural concepts in lecture, especially protein structural concepts. Concepts that were iffy to convey with static slides and hand-waving came across much more clearly with toobers. Examples include discontinuous protein epitopes made of multiple loops, heat denaturation of discontinuous epitopes, buried linear epitopes for MHC and T cells, the six CDR's in antibody, and how they line up in multiple sequence alignments as hypervariable regions. I have just made a website with some photos and three short movie clips illustrating how I use toobers in lectures - http://www.umass.edu/molvis/toobers/ I know that the Herman & Patrick group in Wisconsin is very actively using toobers and will soon have some information about their work on the web. Meanwhile, if you know of related resources please let me know so I can link them to my toobers website (see links at the bottom of the page). Sincerely, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: Can RasMol be used in a commercial application? Thread-Index: AcLLkvWRfDHehRWSTkS3cUP1nPetWA== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: RE: Can RasMol be used in a commercial application? Date: Mon, 03 Feb 2003 09:45:56 -0500 To: rasmol@lists.umass.edu I guess I'm most confused about the "infectivity" of the license. If for example we modify part of rasmol to run under windows .Net (a new MS "platform"), we'd gladly give these mods back to the rasmol, and would comply with any requirements to give credit and supply documentation. But does this mean that ALL the source code of our product now must itself be open source? I've been a commercial software developer of scientific software for 15 years, and the current surge of open source is quite interesting. The concept is compelling, but the rules seem a bit opaque. I don't know how modular rasmol is, but I would think that we'd only pick off a piece or two of it's functionality. (we could still provide the entire package intact though if that were a license requirement). Any comments on using just a single module of rasmol. Thanks. Mitch ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RE: Can RasMol be used in a commercial application? Date: Mon, 03 Feb 2003 10:24:53 -0500 (EST) To: rasmol@lists.umass.edu Dear Mitch, The RasMol license is just as infectious as the GPL. So, if you modify RasMol to make a new program, that new program is covered by the RasMol license. If you make a new, independent, program which only calls RasMol through its specified external interfaces, e.g. by creating scripts and allowing RasMol to run them, the license status of that new program _might_ not be controlled by the RasMol license. As they say, "God and the Devil are in the details." The only way to be certain if a use of RasMol is sufficiently independent of RasMol to avoid the infectious nature of the license is to have all the details of the proposed use. If you effectively integrate any signficant portion of RasMol (whether binary, source code or documentation) into a new package, creating what is called in law a "derived work", then the entirety of that new package is covered by the RasMol license. For example, if you strip out some portion of RasMol, make it into a library or DDL, and use that to make your new program function, then your new program is infected. I know this sounds complicated, and it definitely needs a lawyer to untangle, but that only becomes an issue if you are trying to create closed source proprietary products out of the community's open source resources. As long as you keep making open source programs out of open source programs, things are quite simple. In other words, if you want to make a closed source proprietary molecular graphics program, you are probably better off starting from a different base than RasMol. To repeat the answer in the FAQ: Does this mean I can't make a commercial graphics program based on RasMol? If what you mean by "commercial" is that you want to distribute binary versions and keep the source code as a secret, no, you may not do that, but if what you mean by "commercial" is that you wish to sell programs and services based on RasMol, that you certainly may do. Just remember that your new and wonderful program has to include or reference all the original source code and documentation, including the file NOTICE, which will allow other people to copy your program. In other words the rules for distributing copies of RasMol that you have taken advantage of will also apply to people who wish to make copes of your program. A lot of people find it easy to work within this framework, but if you need to do commerical development which does not fit the open source model, you may not make use of any substantial portion of the RasMol 2.7 series to develop your own product. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 3 Feb 2003, Mitch Barker wrote: > I guess I'm most confused about the "infectivity" of the license. If for > example we modify part of rasmol to run under windows .Net (a new MS > "platform"), we'd gladly give these mods back to the rasmol, and would > comply with any requirements to give credit and supply documentation. > But does this mean that ALL the source code of our product now must > itself be open source? > > I've been a commercial software developer of scientific software for 15 > years, and the current surge of open source is quite interesting. The > concept is compelling, but the rules seem a bit opaque. > > I don't know how modular rasmol is, but I would think that we'd only > pick off a piece or two of it's functionality. (we could still provide > the entire package intact though if that were a license requirement). > Any comments on using just a single module of rasmol. > > Thanks. > > Mitch > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES References: <0H9O00KL30L2XA@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Re: molecular 3D literacy Date: Mon, 03 Feb 2003 12:10:56 -0800 To: Robert Bateman , rasmol@lists.umass.edu Hello Bob: Thank you for raising this important issue. I believe the spatial "literacy" now required in biochemistry has traditionally been reserved for artist, specifically sculptors, architects, and other 3D professionals. If we are truly interested in expanding spatial literacy, we must extend science literacy to segments of the population usually put-off by the standard approach to science education. For example, future scientist should not be put through a "linear thought" filter (such as text-based tests) and then be expected to excel in spatial, visual-motor skills. This integration of disparate skillsets is the basis for a program I've developed called STArt! teaching Science Through Art. Using hands-on models and molecular visualization, I've introduced third graders to the concept of atoms and molecules, as now required by the new California science curriculum standards. An additional bonus: young students get very excited and interested in science. Best regards, Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 239 Sunridge Street Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair American Chemical Society, Los Angeles Section --------------------------------------------------------------- > > Subject: molecular 3D literacy > Date: Wed, 29 Jan 2003 17:29:51 -0600 > From: Robert Bateman > To: rasmol@lists.umass.edu > > Colleagues: > > Those teaching and performing research in the molecular sciences, > especially chemistry and biochemistry, are aware of the need for both > students and practitioners to possess a kind of "literacy" which is > based on multiple dimensions, both spatial and temporal. It is > difficult to define precisely what skills one must possess before one > can be considered literate in this manner, but it is important to do > so from a pedagogical point of view. I have posted a draft list of > such skills at > > > > http://orca.st.usm.edu/~rbateman/kinemage/mol-literacy.htm > > > > and would appreciate feedback from this list to refine it. > > > > Sincerely, > > Bob Bateman > > > > > > Robert C. Bateman, Jr. > > Professor and Chair > > Department of Chemistry and Biochemistry > > University of Southern Mississippi > > Hattiesburg, MS 39406-5043 > > Robert.Bateman@usm.edu > > www.chem.usm.edu > > 601-266-4701 (department office) > > 601-266-6075 (fax) > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: List History Update Date: Mon, 03 Feb 2003 15:31:04 -0500 To: rasmol@lists.umass.edu I have updated the history archives for this email list (separating the 2002 file from the current file for 2003). Also, I moved the history archives to a new server (click on the link labeled "View/Search Past Discussion on the List" at the URL below, which has not changed). The subscribership has plateaued for the past year at about 600 addresses. In 2002, we averaged 1.2 messages/day or 9 messages/week. - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 Molecular Visualization Freeware EMail Discussion List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable from the above link. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: pdb format from Cn3D/VAST? Date: Mon, 03 Feb 2003 17:51:15 -0500 To: rasmol@lists.umass.edu [This reply is redirected from Steve Bryant of NCBI regarding Tim Driscoll's question below (paraphrased) "Can a VAST alignment be obtained in PDB format?" Other options for obtaining alignments in PDB format are explained at http://www.umass.edu/microbio/chime/morpher/morphmtd.htm#am Due to problems I had with my email in January, posting this reply to the list was delayed one month. My apologies.] Hi Eric, Thanks for your question! The quick answer is "no", unfortunately. Our VAST alignment server doesn't any longer try to present structure alignment results in PDB format. Older versions did something like this, up to a few months ago. But we dropped the feature because it wasn't used much - most of our users have Cn3D - and because it was difficult to explain what was going on. What the old version did, if I recall correctly, was to send a PDB file for the first of the selected structure neighbors, rotated and translated so as to superimpose on the query domain. Users had to concatenate these files themselves, using MODEL/ENDMDL or different chain codes, as required for the viewer they wanted to use. The current VAST server version does have a feature that may be of interest. The "ASN1" display option will send a compact file that gives alignment information only, in print-format (text) ASN1. It's easy to parse the rotation-translation matrix from this file. So without too much effort one can write a program or server that reads this matrix and PDB files for the structure neighbors, does the rotation and translation, and then writes out concatenated PDB files with whatever secondary processing one prefers, like inserting MODEL/ENDMDL. As you know, I can't offer to take on user support for viewers other than Cn3D. But if you or other developers want to make something like this, to show VAST alignments with other viewers, I'll be happy to advise as best I can. Steve -----Original Message----- Sent: Monday, December 30, 2002 2:10 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Fwd: pdb format from Cn3D/VAST? To: bryant@ncbi.nlm.nih.gov Cc: driscoll@molvisions.com Hi, Steve. The inquiry below was sent to the RasMol list (600 subscribers) by Tim Driscoll, who wrote the Chime websites for Lehninger's Principles of Biochem, Stryer's Biochem, and Garland's Biol of the Cell by Alberts et al. I'm interested in the answer, too. I know you now offer ASN.1 reformatted as PDB on your structure site for single asymmetric units, but I'm not sure about VAST alignments. If you do, it would be ideal for RasMol/Chime/PE to include MODEL #/ENDMDL records between models in the alignments. If you don't mind, I'll forward the answer to the RasMol list. -Eric >Date: Sun, 29 Dec 2002 18:23:10 -0500 >From: timothy driscoll >Subject: pdb format from Cn3D/VAST? >Sender: owner-rasmol@lists.umass.edu >To: LIST rasmol >Reply-to: rasmol@lists.umass.edu >X-Mailer: Mailsmith 1.5.3 (Blindsider) > >hi, > >I used VAST at the NCBI Web site >(http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml) to align two 3d >structures. I downloaded the alignment and viewed it using Cn3D, and it >looks great. now I'd like to be able to save it as a simple pdb file (text >format with atom records) for use in rasmol/chime/spv/wlvp. does anyone >know how to do this, or if it is even possible? > >thanks! > >:tim >-- >molvisions - molecular graphics & visualization > >usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <007f01c2c75a$28b04560$1ed4fea9@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: "Peter C. McCluskey" Subject: Re: Can RasMol be used in a commercial application? Date: Mon, 10 Feb 2003 11:47:05 -0800 (PST) To: rasmol@lists.umass.edu yaya@bernstein-plus-sons.com (Herbert J. Bernstein) writes: >The only tricky part of creating a plug-in version of RasMol is that, >to avoid legal tangles, it needs to be done by somebody who has never >downloaded or used Chime, so that there cannot be any possibility that >they have reversed engineered their code. This is call "clean-room" >development. Any volunteers? I'm potentially interested, but as I've never used Chime (I've only seen a brief demo) I don't have much of an idea how hard it would take to make a plug-in with power comparable to Chime. >> I guess most people in this list ask at this point if we shall ever make >> something Chime-like out of the nouveau rasmol. Can a browser plug-in be >> under the GPL? I'd like to be sure before we commit rasmol under the GPL. >> Can anyone shed some light here? A quick google for GPL'd plug-in's suggests that there are quite a few. http://www.gnu.org/licenses/gpl-faq.html#GPLAndPlugins indicates that whether such plug-in's can be used with proprietary browsers depends on how those browsers call the plug-in, which might be hard to determine. It adds: "However, you can resolve that legal problem by adding an exception to your program's license which gives permission to link it with the non-free main program." I think that switching to a well understood license such as GPL would be a clear improvement over an obscure license that looks substantially less precise than what a lawyer would write. It might be a good idea to add an exception for linking with proprietary browsers. Or it might be even better to use the LGPL license. -- ------------------------------------------------------------------------------ Peter McCluskey | http://www.rahul.net/pcm | ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <5.2.0.9.2.20030201120525.00a7c9a0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Quick Script Date: Tue, 18 Feb 2003 09:29:43 -0500 To: rasmol@lists.umass.edu, "milesjj@jmu.edu" This is a multi-part message in MIME format. --Boundary_(ID_FyPudftbJ+X+kafRVAb7kw) Hello to All, One of my students, Peter Miles, has written a Visual Basic program that automatically generates Rasmol scripts for a number of different kinds of animation. We tested this with the students in one of my classes with good success. Peter would be interested in any feedback you have on whether this program might be more generally useful. He would like to add more features and would like to hear from you about features that might be useful. This program can be downloaded from his web page at: http://www.isat.jmu.edu/users/klevicca/milespjPortfolio/Main.html (Click on his "Programs" icon to go directly to the download location.) (It is called "Quick Script") You can send feedback to Peter from the mailto link on his page or directly at milesjj@jmu.edu Thanks in advance for your help. Cindy Klevickis --Boundary_(ID_FyPudftbJ+X+kafRVAb7kw) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_FyPudftbJ+X+kafRVAb7kw)-- References: <5.2.0.9.2.20030201120525.00a7c9a0@marlin.bio.umass.edu> <3E524357.FECA98B6@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: Re: Quick Script Date: Wed, 19 Feb 2003 08:31:38 -0400 To: rasmol@lists.umass.edu, "milesjj@jmu.edu" Dear Cindy, Will this program run on Macs as well as PCs? I tried to download it and it was an exe file (not mac). How do I get it for Mac? Judy At 9:29 AM -0500 2/18/03, Cindy Klevickis wrote: >Hello to All, > >One of my students, Peter Miles, has written a Visual Basic program that >automatically generates Rasmol scripts for a number of different kinds of >animation. We tested this with the students in one of my classes with good >success. > >Peter would be interested in any feedback you have on whether this program >might be more generally useful. He would like to add more features and would >like to hear from you about features that might be useful. > >This program can be downloaded from his web page at: > >http://www.isat.jmu.edu/users/klevicca/milespjPortfolio/Main.html >(Click on his "Programs" icon to go directly to the download location.) > >(It is called "Quick Script") > >You can send feedback to Peter from the mailto link on his page or directly at >milesjj@jmu.edu > >Thanks in advance for your help. > >Cindy Klevickis > >Content-type: text/x-vcard; name=klevicca.vcf; charset=us-ascii >Content-description: Card for Cindy Klevickis >Content-disposition: attachment; filename=klevicca.vcf >Content-transfer-encoding: 7BIT > >Attachment converted: Macintosh HD:klevicca.vcf 19 (TEXT/MSWD) (0004889E) -- Judith G. Voet, J. H. Hammons Professor Swarthmore College jvoet1@swarthmore.edu Department of Chemistry 610-328-8520 500 College Avenue FAX 610-328-7355 Swarthmore, PA 19081-1390 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Announcement: DSMM: a Database of Simulated Molecular Motions Date: Wed, 19 Feb 2003 11:05:00 -0500 To: rasmol@lists.umass.edu Dear All, If you are interested in finding movies resulting from biomolecular simulation studies, please take a look at this new website: http://projects.villa-bosch.de/mcm/database/dsmm where you will find: "DSMM: a Database of Simulated Molecular Motions". You can read about it in Finocchiaro, G. , Wang, T., Hoffmann, R., Gonzalez, A., Wade, R.C. Nucleic Acids Research, 2003, 31, 456. at: http://nar.oupjournals.org/cgi/content/abstract/31/1/456. Please do submit your own molecular movies and email your feedback to dsmm@eml.villa-bosch.de. Rebecca Wade wade@EMBL-Heidelberg.DE European Media Laboratory, Heidelberg European Molecular Biology Laboratory, Heidelberg dsmm@eml.villa-bosch.de ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Quick Script Date: Wed, 19 Feb 2003 08:46:35 -0800 To: rasmol@lists.umass.edu Visual Basic doesn't compile for the Mac. If REALbasic (http://www.realsoftware.com) were used instead, then this would be possible. Maybe the author would consider porting their code to the Mac using this language. The development environment is currently Mac only, but sometime this quarter they will release a Windows version that will also cross-compile for Windows, Mac Classic, and Mac OS X. There is even a VB to RB code conversion utility that comes with the current version. Dave Hurley Biology Department University of Washington On Wednesday, February 19, 2003, at 04:31 AM, Judy Voet wrote: > Dear Cindy, > Will this program run on Macs as well as PCs? I tried to download it > and it was an exe file (not mac). How do I get it for Mac? > Judy > > At 9:29 AM -0500 2/18/03, Cindy Klevickis wrote: >> Hello to All, >> >> One of my students, Peter Miles, has written a Visual Basic program >> that >> automatically generates Rasmol scripts for a number of different >> kinds of >> animation. We tested this with the students in one of my classes >> with good >> success. >> >> Peter would be interested in any feedback you have on whether this >> program >> might be more generally useful. He would like to add more features >> and would >> like to hear from you about features that might be useful. >> >> This program can be downloaded from his web page at: >> >> http://www.isat.jmu.edu/users/klevicca/milespjPortfolio/Main.html >> (Click on his "Programs" icon to go directly to the download >> location.) >> >> (It is called "Quick Script") >> >> You can send feedback to Peter from the mailto link on his page or >> directly at >> milesjj@jmu.edu >> >> Thanks in advance for your help. >> >> Cindy Klevickis >> >> Content-type: text/x-vcard; name=klevicca.vcf; charset=us-ascii >> Content-description: Card for Cindy Klevickis >> Content-disposition: attachment; filename=klevicca.vcf >> Content-transfer-encoding: 7BIT >> >> Attachment converted: Macintosh HD:klevicca.vcf 19 (TEXT/MSWD) >> (0004889E) > > > -- > Judith G. Voet, J. H. Hammons Professor Swarthmore College > jvoet1@swarthmore.edu Department of > Chemistry > 610-328-8520 500 College Avenue > FAX 610-328-7355 Swarthmore, > PA 19081-1390 > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Re: Quick Script Date: Wed, 19 Feb 2003 17:59:21 +0100 (CET) To: rasmol@lists.umass.edu On Wed, 19 Feb 2003, Dave Hurley wrote: > Visual Basic doesn't compile for the Mac. If REALbasic > (http://www.realsoftware.com) were used instead, then this would be > possible. Maybe the author would consider porting their code to the Mac > using this language. The development environment is currently Mac only, I haven't seen the code, but I very much doubt it's hard to port to Perl, Python or Ruby. These are crossplatform languages, open source. > but sometime this quarter they will release a Windows version that will > also cross-compile for Windows, Mac Classic, and Mac OS X. There is > even a VB to RB code conversion utility that comes with the current > version. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <5.2.0.9.2.20030219110357.024bc6d0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Reseting Rasmol inbetween scripts Date: Wed, 19 Feb 2003 19:44:29 -0500 To: rasmol@lists.umass.edu Cc: hellermj@jmu.edu This is a multi-part message in MIME format. --Boundary_(ID_YtEsTOty89Kk20it9epW3w) Hello to All from Cindy Klevickis, My students are writing Rasmol scripts in teams that collaborate with each other. They have found that sometimes they can have a script that runs perfectly on its own. But, when it is executed following a different script it has many error messages that say "unable to allocate shade." They have tried including "zap" and "reset" at the end of the first script with no success. Closing Rasmol entirely and opening it up again before running the second script fixes this problem. In trying to troubleshoot their difficulties, they sent me this question. "Within the RasMol command line, is there a command or set of command that could be used to "reset" all of the setting in RasMol established by previous scripts? By "reset" I mean to set up RasMol just as it would be if the program were closed and re-opened." Thank you in advance for any advice you might have. --Boundary_(ID_YtEsTOty89Kk20it9epW3w) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_YtEsTOty89Kk20it9epW3w)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Reseting Rasmol inbetween scripts Date: Wed, 19 Feb 2003 20:52:47 -0500 To: rasmol@lists.umass.edu at 7:44 PM EDT on (Wednesday) 19 February 2003 Cindy Klevickis said: > Hello to All from Cindy Klevickis, > > My students are writing Rasmol scripts in teams that collaborate with > each other. They have found that sometimes they can have a script that > runs perfectly on its own. But, when it is executed following a > different script it has many error messages that say "unable to allocate > shade." They have tried including "zap" and "reset" at the end of the > first script with no success. Closing Rasmol entirely and opening it up > again before running the second script fixes this problem. In trying to > troubleshoot their difficulties, they sent me this question. > > "Within the RasMol command line, is there a command or set of command > that could be used to "reset" all of the setting in RasMol established by > previous scripts? By "reset" I mean to set up RasMol just as it would be > if the program were closed and re-opened." > > Thank you in advance for any advice you might have. > I believe you can fix the allocate shade error with color white which clears the palette. otherwise, I know of no single command except a load command that clears everything. maybe someone else does? :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Reseting Rasmol inbetween scripts Date: Wed, 19 Feb 2003 21:57:35 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_l9T2z88QtlPkKeu6FD+SBA) Thanks VERY much. This sounds good. It worked when I tested it on my computer here at home and I forwarded this to my students so that they can test them on the picky school computers. Cindy Klevickis timothy driscoll wrote: > at 7:44 PM EDT on (Wednesday) 19 February 2003 Cindy Klevickis said: > > > Hello to All from Cindy Klevickis, > > > > My students are writing Rasmol scripts in teams that collaborate with > > each other. They have found that sometimes they can have a script that > > runs perfectly on its own. But, when it is executed following a > > different script it has many error messages that say "unable to allocate > > shade." They have tried including "zap" and "reset" at the end of the > > first script with no success. Closing Rasmol entirely and opening it up > > again before running the second script fixes this problem. In trying to > > troubleshoot their difficulties, they sent me this question. > > > > "Within the RasMol command line, is there a command or set of command > > that could be used to "reset" all of the setting in RasMol established by > > previous scripts? By "reset" I mean to set up RasMol just as it would be > > if the program were closed and re-opened." > > > > Thank you in advance for any advice you might have. > > > > I believe you can fix the allocate shade error with > > color white > > which clears the palette. otherwise, I know of no single command except a > load command that clears everything. maybe someone else does? > > :tim > -- > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > --Boundary_(ID_l9T2z88QtlPkKeu6FD+SBA) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_l9T2z88QtlPkKeu6FD+SBA)-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Bruce Branchini Subject: Re:selective display Date: Thu, 20 Feb 2003 11:19:43 +0100 To: rasmol@lists.umass.edu Hello All, Does anyone know a way in Rasmol to display only a selected area of a protein structure. I have tried coloring all residues I don't want to display black using a black background and this works OK, except that with certain views the black lines make it difficult to see certain features like H bonding. I have also tried a white background with whited colored residues with no improvement. Thanks in advance for your help. Bruce Branchini ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_wz5S2rYzIdspPhGmcSGheg)" ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 12:15:20 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_wz5S2rYzIdspPhGmcSGheg) Dear colleagues, I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta=20= version) and, not being exactly a guru of UNIX systems/subsistems I got=20= lost. Is there a manual with easier instructions (something that goes=20 beyond " ...set the CFLAGS for your platform...."? Thanks for any help. Sincerely Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it= --Boundary_(ID_wz5S2rYzIdspPhGmcSGheg) Dear colleagues, I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta version) and, not being exactly a guru of UNIX systems/subsistems I got lost. Is there a manual with easier instructions (something that goes beyond " ...set the CFLAGS for your platform...."? Thanks for any help. Sincerely Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it= --Boundary_(ID_wz5S2rYzIdspPhGmcSGheg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re:selective display Date: Thu, 20 Feb 2003 06:22:32 -0500 To: rasmol@lists.umass.edu hi Bruce, try "restrict". for example, restrict none will make everything disappear. hth, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 11:19 AM EDT on (Thursday) 20 February 2003 Bruce Branchini said: > Hello All, > > Does anyone know a way in Rasmol to display only a selected area of a > protein structure. I have tried coloring all residues I don't want to > display black using a black background and this works OK, except that with > certain views the black lines make it difficult to see certain features > like H bonding. I have also tried a white background with whited colored > residues with no improvement. > > Thanks in advance for your help. > > Bruce Branchini > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 06:24:52 -0500 To: rasmol@lists.umass.edu at 12:15 PM EDT on (Thursday) 20 February 2003 adriano ceccarelli said: > Dear colleagues, > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I got > lost. Is there a manual with easier instructions (something that goes > beyond " ...set the CFLAGS for your platform...."? > I have not found anything helpful for myself, being quite the novice unix weenie. but please, if you find something more helpful, I would love to hear about it! thanks, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mathy Froeyen Subject: multiple molecules in rasmol 2.7.2.1 Date: Thu, 20 Feb 2003 13:50:10 +0100 To: "rasmol@lists.umass.edu" Dear all, In rasmol 2.7.2.1 there is a possibility to load several molecules at the same time. However when I load more than one molecule, each molecule is centered individually to its own center point. This is a problem if you do structure comparisons where you have overlayed the structures (by an external program) and want to look at RMS differences. I looked in the c-code and tried to patch the centering routines but had only partial success ( My code destroys the zooming functions). Any ideas? regards, Mathy Froeyen ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20030219110357.024bc6d0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Reseting Rasmol inbetween scripts Date: Thu, 20 Feb 2003 07:44:06 -0500 To: rasmol@lists.umass.edu At 2/19/03, Cindy Klevickis wrote: >"unable to allocate shade." Chime and RasMol 2.6 (2.7?) both suffer from this limitation. This can be corrected with: select all color [any single plain color, e.g. white] [now apply a new color scheme] When the "unable to allocate shade" error occurs in Protein Explorer, the above information is offered automatically, including: "The best way to avoid the "Unable to allocate shade" problem is to start with simple color schemes (plain colors or Element/CPK), and end with complex ones that use up lots of colors (notably "N->C Rainbow" aka "Group", or Temperature)." (The problem arises when you apply a complex color scheme that "uses up" RasMol's internal palette, and then try to add additional colors by selecting a subset of the atoms and applying a different color scheme.) In Chime, if you have generated a surface and applied multiple colors to it, you may need to delete the surface in order to avoid "unable to allocate shade". -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3E54441E.806948E6@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re:selective display Date: Thu, 20 Feb 2003 07:52:39 -0500 To: rasmol@lists.umass.edu On 2/20/03, Bruce Branchini asked how to hide subsets of the atoms in a PDB file. Tim's recommendation to use the 'restrict' command is correct. In Protein Explorer, you can select what you want to see (from the SELECT menu), then open the DISPLAY menu and select "Only" (display only what is selected). This hides non-selected atoms. Alternatively, select what you don't want to see, then open the DISPLAY menu and select *Hide*. You are then presented with a list of options: Hide everything Hide hydrogen bonds in selected atoms. Hide disulfide (SS) bonds in selected atoms. Hide dots for all atoms. Hide selected atoms and bonds. Hide non-selected atoms and bonds (same as DISPLAY Only [selected]). Delete surface. Such menu operations generate the appropriate RasMol/Chime commands and send them to Chime. The commands are displayed in the message box. Watching the commands generated by Protein Explorer is a good way to learn which commands to use for a particular purpose in RasMol. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Antivirus: scanned by sophie at shiva.jussieu.fr ++++------+------+------+------+------+------+------+------+------+------+ From: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 13:38:49 +0100 (FRA Hiver) To: rasmol@lists.umass.edu Dear Adriano, > Dear colleagues, > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I got > lost. Is there a manual with easier instructions (something that goes > beyond " ...set the CFLAGS for your platform...."? Why do not you install it through Fink ? Fink is a package holder that allows you to download-patch-compile THOUSANDS of softwares (essentially from Unix/Linux world), including rasmol, xmgrace, gnuplot, x11, TeX, even KDE, Gimp, etc... AUTOMATICALLY, with little knowledge. Sounds magic ? http://fink.sourceforge.net/ Personnally, I installed Rasmol in few minutes... without effort. Furthermore, Fink webpage gives hints to port softs to OSX... and the values for CFLAGS you are looking for... If you really insist to do it by hand... -- Christian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ)" User-Agent: Microsoft-Entourage/10.1.1.2418 X-OriginalArrivalTime: 20 Feb 2003 14:48:39.0288 (UTC) FILETIME=[27986F80:01C2D8EF] ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 08:48:53 -0600 To: rasmol@lists.umass.edu > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ) 20 February, 2003 Adriano, On 2/20/03 5:15 AM, "adriano ceccarelli" wrote: > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I got > lost. Is there a manual with easier instructions (something that goes > beyond " ...set the CFLAGS for your platform...."? !~~~~~~~~~~~~~~~~~~ I have been using RasMol 2.7.2 under X11 and found the following set-up works pretty well: 1. First, I created a folder within my =B3Documents=B2 folder called =B3pdb_files= =B2 where I place all my pdb files. The path to this folder is =B3~/Documents/pdb_files=B2 2. Second, I placed the rasmol folder that I downloaded in the =B3Applications=B2 folder. The path to the executable is =B3/Applications/rasmol/bin/rasmol-32=B2 3. Third, I launched X11 and selected =B3Customize=B2 from the =B3Applications=B2 menu and pressed the =B3New=B2 button. Under the =B3Name=B2 column I typed in =B3RasMol=B2, and under the =B3Command=B2 column I typed in =B3cd ~/Documents/pdb_files; xterm -e /Applications/rasmol/bin/rasmol-32=B2. This will create an item named =B3RasMol=B2 in the X11 =B3Applications=B2 menu. 4. When I want to run Rasmol, I launch X11 and select =B3RasMol=B2 from the =B3Applications=B2 menu. This changes the working directory to the folder containing my pdb files and then launches rasmol within an xterm session. The purpose behind changing the working directory to the folder containing the pdb files is that I only need to type in the name of the pdb file without its path when loading files. I hope this is helpful. Warren !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Warren Gallagher Associate Professor Chemistry Department University of Wisconsin-Eau Claire Eau Claire, WI 54702 TEL: (715) 836-5388 FAX: (715) 836-4979 --Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ) Re: rasmol 2.7.2 install in Mac OSX 20 February, 2003

Adriano,

On 2/20/03 5:15 AM, "adriano ceccarelli" <adriano.ceccarelli@unito.it> wrote:
> I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta
> version) and, not being exactly a guru of UNIX systems/subsistems I got
> lost. Is there a manual with easier instructions (something that goes
> beyond " ...set the CFLAGS for your platform...."?
!~~~~~~~~~~~~~~~~~~

    I have been using RasMol 2.7.2 under X11 and found the following set-up works pretty well:

  1. First, I created a folder within my “Documents” folder called “pdb_files” where I place all my pdb files.  The path to this folder is “~/Documents/pdb_files”
  2. Second, I placed the rasmol folder that I downloaded in the “Applications” folder.  The path to the executable is “/Applications/rasmol/bin/rasmol-32”
  3. Third, I launched X11 and selected “Customize” from the “Applications” menu and pressed the “New” button.  Under the “Name” column I typed in “RasMol”, and under the “Command” column I typed in “cd ~/Documents/pdb_files; xterm -e /Applications/rasmol/bin/rasmol-32”.  This will  create an item named “RasMol” in the X11 “Applications” menu.
  4. When I want to run Rasmol,  I launch X11 and select “RasMol” from the “Applications” menu.  This changes the working directory to the folder containing my pdb files and then launches rasmol within an xterm session.  The purpose behind changing the working directory to the folder containing the pdb files is that I only need to type in the name of the pdb file without its path when loading files.

I hope this is helpful.

Warren

!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Warren Gallagher
Associate Professor
Chemistry Department
University of Wisconsin-Eau Claire
Eau Claire, WI 54702
TEL: (715) 836-5388
FAX: (715) 836-4979

 --Boundary_(ID_3EuRCK5ve0TrEgrD1tsfDQ)-- Originator-info: login-token=Mulberry:01YaOmUNgQ1sBzES7WqCTWrfQDIX3s1x/OGNS1lyM=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: will mcclure Subject: Re: multiple molecules in rasmol 2.7.2.1 Date: Thu, 20 Feb 2003 11:46:16 -0500 To: rasmol@lists.umass.edu What works in RasMol 2.6 (and Chime) is to make separate MODELs of each superposed coordinate set in one file. This requires the addition of dividers in the superposed file. For two sets of coordinates, use: MODEL 1 coordinates for first structure ENDMDL MODEL 2 coordinates for second structure ENDMDL END Then use, 'load nmrpdb filename.pdb' The various models are displayed, etc. with 'select ::1' or 'restrict ::2', etc. -Will McClure --On Thursday, February 20, 2003 1:50 PM +0100 Mathy Froeyen wrote: > Dear all, > > In rasmol 2.7.2.1 there is a possibility to load several molecules > at the same time. > > However when I load more than one molecule, > each molecule is centered individually to its own center point. > This is a problem if you do structure comparisons where you > have overlayed the structures (by an external program) and > want to look at RMS differences. > > I looked in the c-code and tried to patch the centering routines > but had only partial success > ( My code destroys the zooming functions). > > Any ideas? > > regards, > Mathy Froeyen > > > ----------------------------------------------------------------ras > mol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------ras > mol-- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp03.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVagQoWmCZHCBwIXgiDJ8mUp6czyZB7WdTkLaqQd3CUiznejebGGrap3 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h1KHjvf19671 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Thu, 20 Feb 2003 12:45:53 -0500 To: rasmol@lists.umass.edu As others have suggested, installing Fink will take some time, but Fink makes installing a large number of Unix applications very easy. One minor annoyance I have with the RasMol installed via Fink (I assume the same thing happens if RasMol is installed by other means) is that RasMol is very picky about the form of a file's name. If the path to the file that is to be displayed contains a space, RasMol will not be able to find the file (I tried escaping with \ and I tried putting quotes around any folder name that contains spaces). I haven't done much with it yet, but PyMol, which can be installed using Fink, doesn't have a problem with non-Unix-y file names. It might be a good alternative/supplement to RasMol. Chris On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli wrote: > Dear colleagues, > I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta > version) and, not being exactly a guru of UNIX systems/subsistems I > got lost. Is there a manual with easier instructions (something that > goes beyond " ...set the CFLAGS for your platform...."? > > Thanks for any help. > > Sincerely > > Adriano Ceccarelli > > > > Prof. Adriano Ceccarelli > Facoltà di Medicina e Chirurgia > Dip. Scienze Cliniche e Biologiche > Osp. S. Luigi Gonzaga - Orbassano > Torino - ITALY > phone +39116708109 > fax +39119038639 > email adriano.ceccarelli@unito.it ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3E54441E.806948E6@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Re:selective display Date: Fri, 21 Feb 2003 09:40:50 +1030 To: rasmol@lists.umass.edu G'Day All At 11:19 20/02/2003 +0100, you wrote: >Hello All, > >Does anyone know a way in Rasmol to display only a selected area of a >protein structure. I have tried coloring all residues I don't want to >display black using a black background and this works OK, except that with >certain views the black lines make it difficult to see certain features >like H bonding. I have also tried a white background with whited colored >residues with no improvement. There are two basic ways to do this, Tim Driscol has mentioned one, using restrict, and the other is using select. Both are approximately the same, but have a few quirks. [load protein file, say on with multiple chains and a ligand bound to it] The default display is in wireframe, so we will stick with this at the moment. restrict *A [restricts to chain A, looks good] restrict 100-200A [restricts to amino acids 100-200 in A] restrict lys123A [restricts to just the lysine 123 in chain A, nice zoom in] This is all fine and dandy, now lets try and go back restrict 100-200A [this gives the message 232 atoms selected, but the display hasn't changed, RESTRICT turns off the WIREFRAME (or CARTOON or SPACEFILL) so you have to turn on the WIREFRAME again] wireframe on [restores your previous view] Similar sequence using select select all wireframe off select *A wireframe on wireframe off select 100-200A wireframe on wireframe off select lys123A wireframe on wireframe off select 100-200A wireframe on Restrict is more efficient than select, so long as you remember to turn wireframe ON when backing out of a zoom-in sequence, or if you want to swap from wireframe to some other view. Also, if you have got your selected portion of the protein set up, then want to show a ligand binding to it, you have to use select to turn on the hetero group, as restrict will make your protein disaster. eg. [load protein file, say on with multiple chains and a ligand bound to it] restrict 100-200A [restricts to amino acids 100-200 in A] select hetero wireframe on Cheers! Ian (see http://home.mira.net/~reynella/chime/adr_tuta.htm for a limited version of the above) =============================================================== Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au Senior Lecturer, Dept. Clinical and Experimental Pharmacology University of Adelaide, SA, 5005, Australia Phone +61 8 83033905 Fax +61 8 8224 0685 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_8TOHxmozh+9+GDmBRdO35g)" ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 09:26:15 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_8TOHxmozh+9+GDmBRdO35g) Dear Chris and all the ones who sent helpful suggestions, which I have followed the most carefully I could, I am afraid I still =20= am in troubles. I have downloaded and installed Fink with no pain at all. I already had =20= installed X11 package from Apple (beta test version). I followed fink =20= instructions to download and install rasmol as source package and I was =20= prompted with the need to install 5 more packages, including =20 xfree86-rootless. But while installing, it stopped with an error =20 message: "configure: error: no acceptable cc in $PATH" I have looked in =20= all the troubleshooting docs I could find but coudn't solve the =20 problem. As far as my knowledge of UNIX goes, that means it cannot find =20= a compiler. Correct? However, I couldn't locate gcc or cc anywhere in =20= my directories. Is that normal, am I missing some sw, or have I messed =20= it up by reinstalling xfree86 on a preexisting x11 installation? I will be grateful for more help. Thanks Adriano Gioved=EC, 20 Feb 2003, alle 18:45 Europe/Rome, Christopher Masi ha =20 scritto: > As others have suggested, installing Fink will take some time, but =20= > Fink makes installing a large number of Unix applications very easy. =20= > One minor annoyance I have with the RasMol installed via Fink (I =20 > assume the same thing happens if RasMol is installed by other means) =20= > is that RasMol is very picky about the form of a file's name. > If the path to the file that is to be displayed contains a space, =20= > RasMol will not be able to find the file (I tried escaping with \ and =20= > I tried putting quotes around any folder name that contains spaces). > I haven't done much with it yet, but PyMol, which can be installed =20= > using Fink, doesn't have a problem with non-Unix-y file names. It =20 > might be a good alternative/supplement to RasMol. > > Chris > > > On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli = wrote: > >> Dear colleagues, >> I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 =20 >> (beta version) and, not being exactly a guru of UNIX =20 >> systems/subsistems I got lost. Is there a manual with easier =20 >> instructions (something that goes beyond " ...set the CFLAGS for your = =20 >> platform...."? >> >> Thanks for any help. >> >> Sincerely >> >> Adriano Ceccarelli >> >> >> >> Prof. Adriano Ceccarelli >> Facolt=E0 di Medicina e Chirurgia >> Dip. Scienze Cliniche e Biologiche >> Osp. S. Luigi Gonzaga - Orbassano >> Torino - ITALY >> phone +39116708109 >> fax +39119038639 >> email adriano.ceccarelli@unito.it > ----------------------------------------------------------------=20 > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------=20 > rasmol-- > > Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_8TOHxmozh+9+GDmBRdO35g) Dear Chris and all the ones who sent helpful suggestions, which I have followed the most carefully I could, I am afraid I still am in troubles. I have downloaded and installed Fink with no pain at all. I already had installed X11 package from Apple (beta test version). I followed fink instructions to download and install rasmol as source package and I was prompted with the need to install 5 more packages, including xfree86-rootless. But while installing, it stopped with an error message: "configure: error: no acceptable cc in $PATH" I have looked in all the troubleshooting docs I could find but coudn't solve the problem. As far as my knowledge of UNIX goes, that means it cannot find a compiler. Correct? However, I couldn't locate gcc or cc anywhere in my directories. Is that normal, am I missing some sw, or have I messed it up by reinstalling xfree86 on a preexisting x11 installation? I will be grateful for more help. Thanks Adriano Gioved=EC, 20 Feb 2003, alle 18:45 Europe/Rome, Christopher Masi ha scritto: As others have suggested, installing Fink will take some time, but Fink makes installing a large number of Unix applications very easy. One minor annoyance I have with the RasMol installed via Fink (I assume the same thing happens if RasMol is installed by other means) is that RasMol is very picky about the form of a file's name. If the path to the file that is to be displayed contains a space, RasMol will not be able to find the file (I tried escaping with \ and I tried putting quotes around any folder name that contains spaces). I haven't done much with it yet, but PyMol, which can be installed using Fink, doesn't have a problem with non-Unix-y file names. It might be a good alternative/supplement to RasMol. Chris On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli wrote: Dear colleagues, I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 (beta version) and, not being exactly a guru of UNIX systems/subsistems I got lost. Is there a manual with easier instructions (something that goes beyond " ...set the CFLAGS for your platform...."? Thanks for any help. Sincerely Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it = ----------------------------------------------------------------= rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_8TOHxmozh+9+GDmBRdO35g)-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mathy Froeyen Subject: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 10:33:39 +0100 To: "rasmol@lists.umass.edu" Dear Mathy I use to compare several PDB files with rasmol but after making the superposition of the structures with another program (SwissPDB Viewer is very good for this http://us.expasy.org/spdbv/ and is available for all platforms). The trick for distinguish the different superposed PDB from within RasMol is to label the coordinates for each PDB file with a different chain name (this can be easily done from within SwissPDB Viewer also). This allow you to use all the rich rasmol syntax to select which part of the structures do you want to work. If you have any doubts or more questions about this, please don't heasitate to e-mail me. Best regards Gerard PS: my you be so kind to redirect this message to the rasmol list? I have problems with the alias of my e-mail address and this mail is refused by the listserver -- =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== > >In rasmol 2.7.2.1 there is a possibility to load several molecules >at the same time. > >However when I load more than one molecule, >each molecule is centered individually to its own center point. >This is a problem if you do structure comparisons where you >have overlayed the structures (by an external program) and >want to look at RMS differences. > >I looked in the c-code and tried to patch the centering routines >but had only partial success >( My code destroys the zooming functions). > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Antivirus: scanned by sophie at shiva.jussieu.fr ++++------+------+------+------+------+------+------+------+------+------+ From: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 09:56:46 +0100 (FRA Hiver) To: rasmol@lists.umass.edu Dear Adriano, > I have downloaded and installed Fink with no pain at all. I already had > installed X11 package from Apple (beta test version). Easy, isn'it ? > I followed fink > instructions to download and install rasmol as source package and I was > prompted with the need to install 5 more packages, including > xfree86-rootless. But while installing, it stopped with an error > message: "configure: error: no acceptable cc in $PATH" I have looked in > all the troubleshooting docs I could find but coudn't solve the > problem. As far as my knowledge of UNIX goes, that means it cannot find > a compiler. Correct? However, I couldn't locate gcc or cc anywhere in > my directories. Is that normal, am I missing some sw, or have I messed > it up by reinstalling xfree86 on a preexisting x11 installation? Yes it is normal. I am almost sure you did not installed Apple's SDK, did you ? (Soft Developpement Toolkit ? which include all these stuff and more, for free ?) But we should now go on with Fink's mailing list. See you there ! -- Christian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h1LAH3f23068 ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 05:15:33 -0500 To: rasmol@lists.umass.edu hi, I concur with Gerard - Swiss Pdb Viewer is wonderful for aligning multiple structures in seconds. if you use it, though, be aware that SPV is more picky than rasmol about non-standard pdb files and may have trouble with nucleic acids, carbohydrates, etc. on a more philosophical note (if I may), I prefer using multiple MODEL records for aligned structures in the same file, instead of chain designations. the issue is minor, and I have not found any practical pros or cons as far as implementing rasmol commands ("select :a" vs "select model=1"). but I instinctively regard different chains as belonging to the same structure, and different models as being somewhat more independent of each other. a blurry distinction, to be sure, and quite possibly bogus - but my two cents. if you work in graphics, I think of multiple models existing on different layers, with multiple chains being on the same layer. anyway... the drawback of course, is that creating multiple model files still requires editing the raw pdb file, at least as far as I know. but wil mcclure's instructions are easy to follow: at 11:46 AM EDT on (Thursday) 20 February 2003 will mcclure said: > > > > What works in RasMol 2.6 (and Chime) is to make separate MODELs of > > each superposed coordinate set in one file. This requires the > > addition of dividers in the superposed file. For two sets of > > coordinates, use: > > > > MODEL 1 > > coordinates for first structure > > ENDMDL > > MODEL 2 > > coordinates for second structure > > ENDMDL > > END if you have any trouble, you can email the files to me directly. I'll be happy to convert them to a multiple model file for you (it's that easy). in fact, I'm working on an online tool to do this sort of thing - you submit multiple sets of coordinates and it returns the coordinates in a multiple-model file. it's just not ready yet :-) best regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest --------original message-------- at 10:33 AM EDT on (Friday) 21 February 2003 Mathy Froeyen said: > Dear Mathy > > I use to compare several PDB files with rasmol but after making the > superposition of the structures with another program (SwissPDB Viewer > is very good for this http://us.expasy.org/spdbv/ and is available > for all platforms). The trick for distinguish the different > superposed PDB from within RasMol is to label the coordinates for > each PDB file with a different chain name (this can be easily done > from within SwissPDB Viewer also). This allow you to use all the rich > rasmol syntax to select which part of the structures do you want to > work. > > If you have any doubts or more questions about this, please don't > heasitate to e-mail me. > > Best regards > > Gerard > > PS: my you be so kind to redirect this message to the rasmol list? I > have problems with the alias of my e-mail address and this mail is > refused by the listserver > -- > =========================================================================== > DR. GERARD PUJADAS > BIOTECNOLOGIA COMPUTACIONAL > DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es > UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 > PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 > 43005 TARRAGONA (CATALONIA) > STATE: SPAIN (EUROPEAN UNION) > =========================================================================== > > > > > > >In rasmol 2.7.2.1 there is a possibility to load several molecules > >at the same time. > > > >However when I load more than one molecule, > >each molecule is centered individually to its own center point. > >This is a problem if you do structure comparisons where you > >have overlayed the structures (by an external program) and > >want to look at RMS differences. > > > >I looked in the c-code and tried to patch the centering routines > >but had only partial success > >( My code destroys the zooming functions). > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_Hox8YllcxqigB0EqLXacsw)" ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 13:08:57 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_Hox8YllcxqigB0EqLXacsw) Dear Christian, I am not sure which one of the available lists you mean. I have=20 obviously subscribed to the beginners.... However, I did get the x11SDKForMAcOS.pkg, but when I install it it=20 says "disk space required =3D 0 Kb" so I suspect something is wrong = there. I will look for a reply on the fink list. Thanks Adriano Venerd=EC, 21 Feb 2003, alle 09:56 Europe/Rome, Christian Simon ha=20 scritto: > christian.simon@ppce.jussieu.fr (Christian Simon) Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_Hox8YllcxqigB0EqLXacsw) Dear Christian, I am not sure which one of the available lists you mean. I have obviously subscribed to the beginners.... However, I did get the x11SDKForMAcOS.pkg, but when I install it it says "disk space required =3D 0 Kb" so I suspect something is wrong there. I will look for a reply on the fink list. Thanks Adriano Venerd=EC, 21 Feb 2003, alle 09:56 Europe/Rome, Christian Simon ha scritto: christian.simon@ppce.jussieu.fr (Christian Simon) Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it --Boundary_(ID_Hox8YllcxqigB0EqLXacsw)-- References: <3E55F273.95604E1F@rega.kuleuven.ac.be> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 09:41:00 -0500 To: rasmol@lists.umass.edu At 2/21/03, Tim Driscoll wrote: >the drawback of course, is that creating multiple model files still requires >editing the raw pdb file, at least as far as I know. If you are satisfied with aligning two protein chains (not multiple-chain complexes) and you don't mind losing hetero atoms, you can do the alignment automatically at http://cl.sdsc.edu/ce.html (use the TWO CHAINS link). The result can be downloaded directly from that site in multiple-model (MODEL #/ENDMDL) PDB format ready for use in RasMol, PE, etc. The alignment at this site is akin to the iterative magic fit in DeepView. That is, it is intelligent about ignoring parts of the chains that don't align well, and aligning the remainder more closely. This kind of information is available in Protein Explorer's Help/Index/Glossary, e.g. http://molvis.sdsc.edu/protexpl/igloss.htm#alignments DeepView is more powerful and flexible, but takes longer. I think I have asked the DeepView authors to put MODEL #/ENDMDL records in the saved PDB files for multiple layers. Perhaps if more of us ask, they will do it. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 boundary="Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg)" Thread-Topic: Substructure search Thread-Index: AcLZyd7HOJ4gg8VtTPCPWFAViQh96A== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: Substructure search Date: Fri, 21 Feb 2003 11:54:17 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg) This may be slightly off topic, but maybe someone can point me in the correct direction: Does anyone know of a technique to search a bunch of mol files looking for a "sub-structure"? One thought has been to convert the mol file to a SMILES string, then search the SMILES strings looking for a sub structure. Does this sound feasible? Does anyone know conceptually how some of the larger chem database companies do this? Thanks. Mitch --Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg) Message
This = may be slightly=20 off topic, but maybe someone can point me in the correct=20 direction:
 
Does = anyone know of=20 a technique to search a bunch of mol files looking for a=20 "sub-structure"?
 
One = thought has been=20 to convert the mol file to a SMILES string, then search the=20 SMILES strings
looking for a sub=20 structure. Does this sound feasible?
 
Does = anyone know=20 conceptually how
some = of the larger=20 chem database companies do this?
 
Thanks.
 
Mitch
=00 --Boundary_(ID_LzyYbXOxAzQOvQaMwyzCfg)-- X-Info: This message was accepted for relay by smtp03.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVbXKhjMKbaOzRhtvSPnv3+B+V6L8PybO5rMUFfyVrgZoLuFq9X7Cn4V X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h1LHctf13548 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Fri, 21 Feb 2003 12:38:59 -0500 To: rasmol@lists.umass.edu Dear Adriano, First, I must add that I am NOT a Unix expert, I am a beginner. My guess is that Fink and X11 were installed OK, and that you are missing the X11 SDK, Apple's Development Tools, and Fink doesn't know that you have Apple's X11 application installed. The "no acceptable cc in $PATH" makes me think that you didn't install Apple's Developers tools? The comment by Fink that you need to install Xfree86-rootless makes me think that you didn't tell Fink that you have Apple's X11 application installed. The following page is a great source of information for getting thing up and going with XWindows and Fink http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html The quick run through to get things working is Install Apple's Developer Tools. Most people are recommending (it might be required) that the December 2002 Developer's tools be installed. Since I bought OS 10.2 before December I had to download the Dev Tools at http://developer.apple.com/tools/ The download is free. However, you have to sign up, and it is a 300+ MB download. Install Apple's X11 application (get the newest one. Feb 10 I think. The Feb 5 one doesn't start up with Apple's window manager) Install Apple's X11 Software Development Kit (SDK) When I launch the installer it says the installation requires 0 MB of disk space. Install Fink Tell Fink that you have installed Apple's X11 software (the page I mentioned up top tells you how to do this). Tell Fink to install a Fortran compiler (the page I mentioned at the top also tells you what to do here) and any of the other software that you want. I cannot stress how helpful this page http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html has been for me. Sincerely, Chris On Friday, February 21, 2003, at 03:26 AM, adriano ceccarelli wrote: > Dear Chris and all the ones who sent helpful suggestions, > which I have followed the most carefully I could, I am afraid I still > am in troubles. > > I have downloaded and installed Fink with no pain at all. I already > had installed X11 package from Apple (beta test version). I followed > fink instructions to download and install rasmol as source package and > I was prompted with the need to install 5 more packages, including > xfree86-rootless. But while installing, it stopped with an error > message: "configure: error: no acceptable cc in $PATH" I have looked > in all the troubleshooting docs I could find but coudn't solve the > problem. As far as my knowledge of UNIX goes, that means it cannot > find a compiler. Correct? However, I couldn't locate gcc or cc > anywhere in my directories. Is that normal, am I missing some sw, or > have I messed it up by reinstalling xfree86 on a preexisting x11 > installation? > > I will be grateful for more help. > > Thanks > > Adriano > > > > > > Giovedì, 20 Feb 2003, alle 18:45 Europe/Rome, Christopher Masi ha > scritto: > >> As others have suggested, installing Fink will take some time, but >> Fink makes installing a large number of Unix applications very easy. >> One minor annoyance I have with the RasMol installed via Fink (I >> assume the same thing happens if RasMol is installed by other means) >> is that RasMol is very picky about the form of a file's name. >> If the path to the file that is to be displayed contains a space, >> RasMol will not be able to find the file (I tried escaping with \ and >> I tried putting quotes around any folder name that contains spaces). >> I haven't done much with it yet, but PyMol, which can be installed >> using Fink, doesn't have a problem with non-Unix-y file names. It >> might be a good alternative/supplement to RasMol. >> >> Chris >> >> >> On Thursday, February 20, 2003, at 06:15 AM, adriano ceccarelli >> wrote: >> >>> Dear colleagues, >>> I tried to install the Rasmol 2.7.2 version for Mac OSX with X11 >>> (beta version) and, not being exactly a guru of UNIX >>> systems/subsistems I got lost. Is there a manual with easier >>> instructions (something that goes beyond " ...set the CFLAGS for >>> your platform...."? >>> >>> Thanks for any help. >>> >>> Sincerely >>> >>> Adriano Ceccarelli >>> >>> >>> >>> Prof. Adriano Ceccarelli >>> Facoltà di Medicina e Chirurgia >>> Dip. Scienze Cliniche e Biologiche >>> Osp. S. Luigi Gonzaga - Orbassano >>> Torino - ITALY >>> phone +39116708109 >>> fax +39119038639 >>> email adriano.ceccarelli@unito.it >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> >> >> > Prof. Adriano Ceccarelli > Facoltà di Medicina e Chirurgia > Dip. Scienze Cliniche e Biologiche > Osp. S. Luigi Gonzaga - Orbassano > Torino - ITALY > phone +39116708109 > fax +39119038639 > email adriano.ceccarelli@unito.it ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: [Fwd: Re: multiple molecules in rasmol 2.7.2.1] Date: Fri, 21 Feb 2003 12:54:27 -0500 To: rasmol@lists.umass.edu at 9:41 AM EDT on (Friday) 21 February 2003 Eric Martz said: > At 2/21/03, Tim Driscoll wrote: > >the drawback of course, is that creating multiple model files still > >requires editing the raw pdb file, at least as far as I know. > > If you are satisfied with aligning two protein chains (not multiple-chain > complexes) and you don't mind losing hetero atoms, you can do the > alignment automatically at http://cl.sdsc.edu/ce.html (use the TWO CHAINS > link). > > The result can be downloaded directly from that site in multiple-model > (MODEL #/ENDMDL) PDB format ready for use in RasMol, PE, etc. > of course! CE is a great site, and I just used it recently. doh. thanks for the reminder, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Substructure search Date: Fri, 21 Feb 2003 12:56:45 -0500 To: rasmol@lists.umass.edu hi Mitch, can you clarify what you mean by sub-structure? do you mean domains and motifs, or a certain sequence, or...? sorry - the fog has not quite cleared yet today for me. thanks, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 11:54 AM EDT on (Friday) 21 February 2003 Mitch Barker said: > This may be slightly off topic, but maybe someone can point me in the > correct direction: > > Does anyone know of a technique to search a bunch of mol files looking > for a "sub-structure"? > > One thought has been to convert the mol file to a SMILES string, then > search the SMILES strings > looking for a sub structure. Does this sound feasible? > > Does anyone know conceptually how > some of the larger chem database companies do this? > > Thanks. > > Mitch ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: Substructure search Thread-Index: AcLZ06VK8pTLwKfNTnGNmr7pRIcj2wAA3kOw content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: RE: Substructure search Date: Fri, 21 Feb 2003 13:32:59 -0500 To: rasmol@lists.umass.edu >> can you clarify what you mean by sub-structure? >> do you mean domains and motifs, or a >>certain sequence, or...? For example, I may want to search for molecules that contain a benzene ring. The people who use our software work with molecules of lets say up to 50 atoms (excluding H's). Mitch at 11:54 AM EDT on (Friday) 21 February 2003 Mitch Barker said: > This may be slightly off topic, but maybe someone can point me in the > correct direction: > > Does anyone know of a technique to search a bunch of mol files looking > for a "sub-structure"? > > One thought has been to convert the mol file to a SMILES string, then > search the SMILES strings looking for a sub structure. Does this sound > feasible? > > Does anyone know conceptually how > some of the larger chem database companies do this? > > Thanks. > > Mitch ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: stereo projection technology Date: Sat, 22 Feb 2003 16:32:00 -0500 To: rasmol@lists.umass.edu I'm forwarding this from David Cassinelli (dcassinelli@jrti.com) as it may interest some subscribers. -Eric Martz Hello Professor Matrz: Is 3D Stereo visualization a technology that would help in your research projects? I'm hopeful that it is something you are interested in. I sell an affordable, portable, platform independent, passive 3D Immersive Large Screen Visualization system known as Viz EveryWhere (VEW). Here is a link for more information http://www.jrti.com/vew/viz3.html This system consists of a Workstation (one I could provide or an existing one), a Converter box, two projectors and a non-depolarizing screen. This is suitable for a classroom or an auditorium and as I said - portable. It is passive technology - so there is no need for expensive active goggles. It is a projection system - front or rear! Prices start at $30K for an XGA (1024x786) and $40K for an SXGA (1280x1024)solution. If your application supports frame sequential stereo then this solution is plug and play. Here is a link of applications that currently support this feature: http://www.stereographics.com/support/srsoftware/index.html If you would like to understand how this technology can accelerate the time to discovery I encourage you to contact me for more details. I look forward to hearing from you! David Cassinelli James River Technical 120 Quarry Dr Milford, MA 01757 508-381-6311 Office 508-667-3311 Cell 508-381-6981 Fax www.jrti.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Virus-Scanned: by amavisd-milter (http://amavis.org/) ++++------+------+------+------+------+------+------+------+------+------+ From: Harold Schranz Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 23 Feb 2003 14:01:09 +1100 To: rasmol@lists.umass.edu Cc: Harold Schranz On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > Dear Chris and all the ones who sent helpful suggestions, > which I have followed the most carefully I could, I am afraid I still > am in troubles. Dear Adriano Hopefully I correctly understand your predicament! A simple approach MIGHT be the following (assuming you have OS X 10.2 or later): 1) In case the route involving getting the bits and pieces together as in Christopher Masi's post is too hard (at first) you could just download one of the precompiled executables from: http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ Mac_OS_X_10.2.2_PPC/ (e.g. the 32 bit one if your display covers that range) and the corresponding help file from: http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ rasmol.hlp.gz which I put both (after gunzipping) in /usr/local/bin (a little less elegant than the full Fink install procedure but it works). (see http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for details) Of course, you will still need (for example) X11 for Mac OS X Public Beta, which is an implementation of the X Window System that makes it possible to run X11-based applications in Mac OS http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) 2) Eventually, if you do get the energy, (as stated by others) the following link is invaluable http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html to get all of the appropriate pieces together and use Fink for the compile/install procedures (rasmol executable will end up in /sw/bin/ and not overwrite /usr/local/bin/). Just a matter of being persistent and careful and a little patient. I've actually got Rasmol installed by both routes (but gave/linked them to unique names); don't ask why I bothered ... just bored I guess. 8-) I hope this helps! Good Luck Harry. ------------------------------------------------------------------------ ---- Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 8919 School of Chemistry, University College (UNSW) Fax: +61 2 6268 8002 Australian Defence Force Academy Fax: +61 2 6268 8017 Canberra ACT 2600, Australia Email: Harold.Schranz@adfa.edu.au Visiting Fellow, Biophysics Group, Department of Theoretical Physics and ANU Supercomputer Facility and Research School of Chemistry Australian National University, Canberra ACT 0200, Australia Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 6533 ------------------------------------------------------------------------ ---- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sat, 22 Feb 2003 23:09:52 -0500 (EST) To: rasmol@lists.umass.edu Cc: Harold Schranz Unfortunately, option 2 is a step backwards from option 1. Option 1 gives you RasMol 2.7.2.1, while Option 2 takes you back to RasMol 2.7.1.1. Judging by the current downloads, most people prefer 2.7.2.1 -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Sun, 23 Feb 2003, Harold Schranz wrote: > On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > > Dear Chris and all the ones who sent helpful suggestions, > > which I have followed the most carefully I could, I am afraid I still > > am in troubles. > > Dear Adriano > > Hopefully I correctly understand your predicament! > > A simple approach MIGHT be the following (assuming you have OS X 10.2 > or later): > > 1) In case the route involving getting the bits and pieces together as > in > Christopher Masi's post is too hard (at first) you could just download > one of the precompiled executables from: > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > (e.g. the 32 bit one if your display covers that range) > and the corresponding help file from: > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > rasmol.hlp.gz > which I put both (after gunzipping) in /usr/local/bin > (a little less elegant than the full Fink install procedure but it > works). > (see > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for > details) > > Of course, you will still need (for example) X11 for Mac OS X Public > Beta, which > is an implementation of the X Window System that makes it possible to > run X11-based applications in Mac OS > http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) > > 2) Eventually, if you do get the energy, (as stated by others) the > following link is invaluable > http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > to get all of the appropriate pieces together and use Fink for the > compile/install procedures > (rasmol executable will end up in /sw/bin/ and not overwrite > /usr/local/bin/). > Just a matter of being persistent and careful and a little patient. > > I've actually got Rasmol installed by both routes (but gave/linked them > to unique names); > don't ask why I bothered ... just bored I guess. 8-) > > I hope this helps! > > Good Luck > Harry. > > ------------------------------------------------------------------------ > ---- > Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 > 8919 > School of Chemistry, University College (UNSW) Fax: +61 2 6268 > 8002 > Australian Defence Force Academy Fax: +61 2 6268 > 8017 > Canberra ACT 2600, Australia Email: > Harold.Schranz@adfa.edu.au > > Visiting Fellow, Biophysics Group, Department of Theoretical Physics > and ANU Supercomputer Facility and Research School of Chemistry > Australian National University, Canberra ACT 0200, Australia > Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 > 6533 > ------------------------------------------------------------------------ > ---- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en References: <8918FD882FEE0344B2E8C6311140E06A0372A7@carbon.us.avantium.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Substructure search Date: Sun, 23 Feb 2003 10:09:17 +0200 To: rasmol@lists.umass.edu Dear Mitch,

For proteins, much work was done to look for the 'common' substructure, as found in the 'structural neighbors' field in each protein entry in the RCSB PDB. For an efficient sequence-independent data-minig a pre-processing is needed, as done in the geometric hashing method. For more details (and some new downloadable algorithms for multiple structural alignment) see: http://bioinfo3d.cs.tau.ac.il/.

Best regards,

Ilan

~~~~~~~~~~~~~~~~~
Ilan Samish
Plant Sciences Dept.
Weizmann Institute of Science
Rehovot, Israel
Lab: 972-8-9344300
Cell: 972-53-321150
Fax: 972-8-9344181
ilan.samish@weizmann.ac.il

Mitch Barker wrote:
  
can you clarify what you mean by sub-structure?  
do you mean domains and motifs, or a >>certain sequence, or...?
      

For example, I may want to search for molecules that contain a benzene
ring. The people
who use our software work with molecules of lets say up to 50 atoms
(excluding H's).

Mitch

at 11:54 AM EDT on (Friday) 21 February 2003 Mitch Barker said:

  
This may be slightly off topic, but maybe someone can point me in the 
correct direction:
 
Does anyone know of a technique to search a bunch of mol files looking
    

  
for a "sub-structure"?
 
One thought has been to convert the mol file to a SMILES string, then 
search the SMILES strings looking for a sub structure. Does this sound
    

  
feasible?
 
Does anyone know conceptually how
some of the larger chem database companies do this?
 
Thanks.
 
Mitch

----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.4i References: <8918FD882FEE0344B2E8C6311140E06A0372A7@carbon.us.avantium.com> <3E5881AD.7040002@weizmann.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Johannes Ranke Subject: Re: Substructure search Date: Sun, 23 Feb 2003 14:04:12 +0100 To: rasmol@lists.umass.edu Hi > Does anyone know of a technique to search a bunch of mol files looking > for a "sub-structure"? Sounds like a perfect task for the CACTVS tools: http://www2.ccc.uni-erlangen.de/software/cactvs/ They consist of a couple of tcl/tk extensions and work nicely under linux and SGI Irix. Unfortunately, very sparsely documented. I figured out how to do substructure searches only by corresponding with the author. But the tools are very powerful and free for academic purposes, unfortunately not open source at all. Hannes P.S.: In the future, the Java CDK might be a replacement. It already can do substructure searches http://cdk.sf.net > One thought has been to convert the mol file to a SMILES string, then > search the SMILES strings looking for a sub structure. Does this sound > feasible? > > Does anyone know conceptually how > some of the larger chem database companies do this? > > Thanks. > > Mitch > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Xu Yong Subject: select Date: Wed, 26 Feb 2003 09:56:17 +0800 To: "rasmol@lists.umass.edu" Dear rasmoler how to select specific residues which is within 5.0A from residue32/h2o10 I can select atom within this radius but not residues. thank you in advance xy ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: standards for mol vis Date: Thu, 27 Feb 2003 05:55:11 -0500 To: LIST rasmol hello all, I am compiling a list of standard representations used for molecular visualization. for example: depiction of protein secondary structures (helices are cylinders, strands are arrows); atoms as solid spheres and bonds as connecting rods; element coloring - cpk scheme; etc. if you have any others that you would like to share, I would be grateful! you can email me off-list if you prefer - . regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: standards for mol vis Date: Thu, 27 Feb 2003 12:50:54 +0000 (GMT) To: rasmol@lists.umass.edu timothy driscoll said: > hello all, > > I am compiling a list of standard representations used for molecular > visualization. for example: > > depiction of protein secondary structures (helices are cylinders, strands are > arrows); > atoms as solid spheres and bonds as connecting rods; > element coloring - cpk scheme; > etc. two basics, (in case replies have been low) is coloring - hydrophobicity / tipical pk of atoms depiction - surface representation some others are, structure factors - how well the molecule was resolved in x-ray for example. > > if you have any others that you would like to share, I would be grateful! you can > email me off-list if you prefer - . > > regards, > > :tim > -- > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: standards for mol vis Date: Thu, 27 Feb 2003 15:38:18 -0500 To: rasmol@lists.umass.edu hi Dan, thanks for the response, and to other list members who have sent me ideas off-list. I'll be working on this for the next few days, so if you think of any others please feel free to send them along. when I compile a fair list, I'll post the url for criticism and feedback. regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 12:50 PM EDT on (Thursday) 27 February 2003 Dan Bolser said: > timothy driscoll said: > > hello all, > > > > I am compiling a list of standard representations used for molecular > > visualization. for example: > > > > depiction of protein secondary structures (helices are cylinders, > > strands are arrows); atoms as solid spheres and bonds as connecting > > rods; element coloring - cpk scheme; etc. > > two basics, (in case replies have been low) is > > coloring - hydrophobicity / tipical pk of atoms > depiction - surface representation > > some others are, > structure factors - how well the molecule was resolved > in x-ray for example. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: standards for mol vis Date: Sat, 01 Mar 2003 11:57:09 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_rTL6TyFVtWfiF1yReLw8+g) At 2/27/03, you wrote: >I am compiling a list of standard representations used for molecular >visualization. Last summer I spent quite a bit of time writing some entries on this for a dictionary of bioinformatics that has yet to be published. I've attached them -- they may be useful. -Eric ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: oops Date: Sat, 01 Mar 2003 14:18:08 -0500 To: rasmol@lists.umass.edu My sincere apologies for burdening everyone on the list with a large attachment that I intended only for Tim Driscoll. -Eric Martz (red faced) ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: my favorite protein structure literature Date: Sat, 01 Mar 2003 15:20:40 -0500 To: rasmol@lists.umass.edu I have posted some of my favorite protein structure literature (books and journal articles) at http://molvis.sdsc.edu/protexpl/favlit.htm I particularly recommend two books just published: -- Structural Bioinformatics, edited by Bourne and Weissig -- Introduction to Bioinformatics, edited by Krawetz and Womble More about each book is at the above link. (This document is not yet included in the downloadable version of Protein Explorer. It will be included whenever the next numbered release occurs, probably sometime this summer.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: George Tzotzos Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 04:35:07 -0800 To: rasmol@lists.umass.edu Cc: rasmol@lists.umass.edu, Harold Schranz Hi there, I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 and rasmol.help both downloaded from arcib.dowling.edu and moved to the /usr/local/bin directory. Encountered the following problems: 1. On trying to open files with .pdb extension rasmol is overriden by iMol (native OSX program). 2. On trying to open rasmol scripted files (.ras extension), system OS9 is fired up and the file is open by RasMol 2.6 for system 9. Both of the above even if I reboot and try to open files from the X11 window. Would be grateful for any suggestions. George Dr George Tzotzos UNIDO, Vienna, Austria Tel: +43-1-26026 4336 Fax: +43-1-26026 6810 email: g.tzotzos@unido.org On Saturday, February 22, 2003, at 07:01PM, Harold Schranz wrote: >On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >> Dear Chris and all the ones who sent helpful suggestions, >> which I have followed the most carefully I could, I am afraid I still >> am in troubles. > >Dear Adriano > >Hopefully I correctly understand your predicament! > >A simple approach MIGHT be the following (assuming you have OS X 10.2 >or later): > >1) In case the route involving getting the bits and pieces together as >in >Christopher Masi's post is too hard (at first) you could just download >one of the precompiled executables from: >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >Mac_OS_X_10.2.2_PPC/ >(e.g. the 32 bit one if your display covers that range) >and the corresponding help file from: >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >rasmol.hlp.gz >which I put both (after gunzipping) in /usr/local/bin >(a little less elegant than the full Fink install procedure but it >works). >(see >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for >details) > >Of course, you will still need (for example) X11 for Mac OS X Public >Beta, which >is an implementation of the X Window System that makes it possible to >run X11-based applications in Mac OS >http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) > >2) Eventually, if you do get the energy, (as stated by others) the >following link is invaluable >http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >to get all of the appropriate pieces together and use Fink for the >compile/install procedures >(rasmol executable will end up in /sw/bin/ and not overwrite >/usr/local/bin/). >Just a matter of being persistent and careful and a little patient. > >I've actually got Rasmol installed by both routes (but gave/linked them >to unique names); >don't ask why I bothered ... just bored I guess. 8-) > >I hope this helps! > >Good Luck >Harry. > >------------------------------------------------------------------------ >---- >Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 >8919 >School of Chemistry, University College (UNSW) Fax: +61 2 6268 >8002 >Australian Defence Force Academy Fax: +61 2 6268 >8017 >Canberra ACT 2600, Australia Email: >Harold.Schranz@adfa.edu.au > >Visiting Fellow, Biophysics Group, Department of Theoretical Physics >and ANU Supercomputer Facility and Research School of Chemistry >Australian National University, Canberra ACT 0200, Australia >Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 >6533 >------------------------------------------------------------------------ >---- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 09:04:35 -0500 To: rasmol@lists.umass.edu hi George, did you try the OSX method? just in case, here it is: single-click on any pdb file (in the Finder) and choose Get Info (control- or right-click, cmd-I, or File:Get Info at your discretion). switch to the "Open With" pane. from the option list there, choose rasmol 2.7.2.1 (if it is not present, there is an Other... option at the very bottom of the list that allows you browse to the app). click the Change All button to make this the default for all files of this type on your computer. repeat for ras files, scr files - any files you want to double-click and launch rasmol 2.7.2.1. hth, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > Hi there, > > I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 and > rasmol.help both downloaded from arcib.dowling.edu and moved to the > /usr/local/bin directory. > > Encountered the following problems: > > 1. On trying to open files with .pdb extension rasmol is overriden by iMol > (native OSX program). > 2. On trying to open rasmol scripted files (.ras extension), system OS9 is > fired up and the file is open by RasMol 2.6 for system 9. > > Both of the above even if I reboot and try to open files from the X11 > window. > > Would be grateful for any suggestions. > > George > > Dr George Tzotzos > UNIDO, Vienna, Austria > > Tel: +43-1-26026 4336 > Fax: +43-1-26026 6810 > email: g.tzotzos@unido.org > > > > On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > wrote: > > >On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > >> Dear Chris and all the ones who sent helpful suggestions, > >> which I have followed the most carefully I could, I am afraid I still > >> am in troubles. > > > >Dear Adriano > > > >Hopefully I correctly understand your predicament! > > > >A simple approach MIGHT be the following (assuming you have OS X 10.2 > >or later): > > > >1) In case the route involving getting the bits and pieces together as > >in > >Christopher Masi's post is too hard (at first) you could just download > >one of the precompiled executables from: > >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >Mac_OS_X_10.2.2_PPC/ > >(e.g. the 32 bit one if your display covers that range) > >and the corresponding help file from: > >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >rasmol.hlp.gz > >which I put both (after gunzipping) in /usr/local/bin > >(a little less elegant than the full Fink install procedure but it > >works). > >(see > >http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ for > >details) > > > >Of course, you will still need (for example) X11 for Mac OS X Public > >Beta, which > >is an implementation of the X Window System that makes it possible to > >run X11-based applications in Mac OS > >http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) > > > >2) Eventually, if you do get the energy, (as stated by others) the > >following link is invaluable > >http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >to get all of the appropriate pieces together and use Fink for the > >compile/install procedures > >(rasmol executable will end up in /sw/bin/ and not overwrite > >/usr/local/bin/). > >Just a matter of being persistent and careful and a little patient. > > > >I've actually got Rasmol installed by both routes (but gave/linked them > >to unique names); > >don't ask why I bothered ... just bored I guess. 8-) > > > >I hope this helps! > > > >Good Luck > >Harry. > > > >------------------------------------------------------------------------ > >---- > >Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 6268 > >8919 > >School of Chemistry, University College (UNSW) Fax: +61 2 6268 > >8002 > >Australian Defence Force Academy Fax: +61 2 6268 > >8017 > >Canberra ACT 2600, Australia Email: > >Harold.Schranz@adfa.edu.au > > > >Visiting Fellow, Biophysics Group, Department of Theoretical Physics > >and ANU Supercomputer Facility and Research School of Chemistry > >Australian National University, Canberra ACT 0200, Australia > >Email: Harold.Schranz@anu.edu.au Phone: +61 2 6125 > >6533 > >------------------------------------------------------------------------ > >---- > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp01.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVY2oqJAw/vty7q2XPP0MuSP7xPjEr4qT6UUSnriXM70ifZU+wy0jM2s ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 09:18:53 -0500 To: rasmol@lists.umass.edu I am starting with the assumption that you are double clicking the files to open them. Rasmol 2.7.2 is running on OS X's Darwin core, and the only way to interact with the program is by a terminal emulator (xTerm or Apple's Terminal). The only way to display the output is through an X 11 window. Essentially, OS X has a mild case of MPD. iMol is a full fledged OS X program. Rasmol 2.6 is a "Classic" application. Rasmol 2.7.2 is a Darwin application. The Finder only "knows" about Classic and OS X applications. It does not know about Darwin applications. When you double click the pdb file, the Finder looks for a program that has the correct creator type and tells that program to open the file. Since the Finder doesn't know that rasmol 2.7.2 exists the Finder instructs iMol to open the pdb file (iMol is newer than Rasmol 2.6). When you double click the .ras file, the Finder looks for an application to use. The Finder still doesn't know about Rasmol 2.7.2, and iMol cannot open (or at least the Finder doesn't think it can open) .ras files, so the Finder goes to the only application that it knows about that can open the .ras file, Rasmol 2.6. Because rasmol 2.7.2 was installed as a Darwin/Unix application it is not double clickable. Try finding rasmol 2.7.2 and double clicking it. It will not start. If everything is set up correctly, to use Rasmol 2.7.2 to open a pdb file you have to 1. have X11 running. Double click Apple's X11.app 2. in an xTerm window or (if configured the right way) or a Terminal.app window navigate to the directory that contains all the pbds that you want to view and type rasmol 3. in the window that was used to launch rasmol type load 1ADO.pdb where 1ADO.pdb is the name of the file that you want to open. Chris On Sunday, March 2, 2003, at 07:35 AM, George Tzotzos wrote: > Hi there, > > I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 > and rasmol.help both downloaded from arcib.dowling.edu and moved to > the /usr/local/bin directory. > > Encountered the following problems: > > 1. On trying to open files with .pdb extension rasmol is overriden by > iMol (native OSX program). > 2. On trying to open rasmol scripted files (.ras extension), system > OS9 is fired up and the file is open by RasMol 2.6 for system 9. > > Both of the above even if I reboot and try to open files from the X11 > window. > > Would be grateful for any suggestions. > > George > > Dr George Tzotzos > UNIDO, Vienna, Austria > > Tel: +43-1-26026 4336 > Fax: +43-1-26026 6810 > email: g.tzotzos@unido.org > > > > On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > wrote: > >> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >>> Dear Chris and all the ones who sent helpful suggestions, >>> which I have followed the most carefully I could, I am afraid I still >>> am in troubles. >> >> Dear Adriano >> >> Hopefully I correctly understand your predicament! >> >> A simple approach MIGHT be the following (assuming you have OS X 10.2 >> or later): >> >> 1) In case the route involving getting the bits and pieces together as >> in >> Christopher Masi's post is too hard (at first) you could just download >> one of the precompiled executables from: >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >> Mac_OS_X_10.2.2_PPC/ >> (e.g. the 32 bit one if your display covers that range) >> and the corresponding help file from: >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >> rasmol.hlp.gz >> which I put both (after gunzipping) in /usr/local/bin >> (a little less elegant than the full Fink install procedure but it >> works). >> (see >> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >> for >> details) >> >> Of course, you will still need (for example) X11 for Mac OS X Public >> Beta, which >> is an implementation of the X Window System that makes it possible to >> run X11-based applications in Mac OS >> http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) >> >> 2) Eventually, if you do get the energy, (as stated by others) the >> following link is invaluable >> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >> to get all of the appropriate pieces together and use Fink for the >> compile/install procedures >> (rasmol executable will end up in /sw/bin/ and not overwrite >> /usr/local/bin/). >> Just a matter of being persistent and careful and a little patient. >> >> I've actually got Rasmol installed by both routes (but gave/linked >> them >> to unique names); >> don't ask why I bothered ... just bored I guess. 8-) >> >> I hope this helps! >> >> Good Luck >> Harry. >> >> ---------------------------------------------------------------------- >> -- >> ---- >> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 >> 6268 >> 8919 >> School of Chemistry, University College (UNSW) Fax: +61 2 >> 6268 >> 8002 >> Australian Defence Force Academy Fax: +61 2 >> 6268 >> 8017 >> Canberra ACT 2600, Australia Email: >> Harold.Schranz@adfa.edu.au >> >> Visiting Fellow, Biophysics Group, Department of Theoretical Physics >> and ANU Supercomputer Facility and Research School of Chemistry >> Australian National University, Canberra ACT 0200, Australia >> Email: Harold.Schranz@anu.edu.au Phone: +61 2 >> 6125 >> 6533 >> ---------------------------------------------------------------------- >> -- >> ---- >> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp01.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVbfqgFE7zVV7XtvFDE3O57/VM8ag58CFlwStA9VLDkAE/phuSgnxLr0 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 11:39:13 -0500 To: rasmol@lists.umass.edu That doesn't work here. I installed 2.7.1 via Fink and 2.7.2 via the following link http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ Mac_OS_X_10.2.2_PPC/ and neither is recognized by OS X 10.2.4 as a suitable "Open with" application even when "All Applications" is selected in the Open with dialogue box. If you have found a way to make this work, I would love more details on how I might get my system to do it too. Thanks, Chris On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > hi George, > > did you try the OSX method? just in case, here it is: > > single-click on any pdb file (in the Finder) and choose Get Info > (control- > or right-click, cmd-I, or File:Get Info at your discretion). > > switch to the "Open With" pane. from the option list there, choose > rasmol > 2.7.2.1 (if it is not present, there is an Other... option at the very > bottom of the list that allows you browse to the app). > > click the Change All button to make this the default for all files of > this > type on your computer. > > repeat for ras files, scr files - any files you want to double-click > and > launch rasmol 2.7.2.1. > > > hth, > > :tim > -- > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > >> Hi there, >> >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 >> and >> rasmol.help both downloaded from arcib.dowling.edu and moved to the >> /usr/local/bin directory. >> >> Encountered the following problems: >> >> 1. On trying to open files with .pdb extension rasmol is overriden by >> iMol >> (native OSX program). >> 2. On trying to open rasmol scripted files (.ras extension), system >> OS9 is >> fired up and the file is open by RasMol 2.6 for system 9. >> >> Both of the above even if I reboot and try to open files from the X11 >> window. >> >> Would be grateful for any suggestions. >> >> George >> >> Dr George Tzotzos >> UNIDO, Vienna, Austria >> >> Tel: +43-1-26026 4336 >> Fax: +43-1-26026 6810 >> email: g.tzotzos@unido.org >> >> >> >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz >> wrote: >> >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >>>> Dear Chris and all the ones who sent helpful suggestions, >>>> which I have followed the most carefully I could, I am afraid I >>>> still >>>> am in troubles. >>> >>> Dear Adriano >>> >>> Hopefully I correctly understand your predicament! >>> >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 >>> or later): >>> >>> 1) In case the route involving getting the bits and pieces together >>> as >>> in >>> Christopher Masi's post is too hard (at first) you could just >>> download >>> one of the precompiled executables from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> Mac_OS_X_10.2.2_PPC/ >>> (e.g. the 32 bit one if your display covers that range) >>> and the corresponding help file from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> rasmol.hlp.gz >>> which I put both (after gunzipping) in /usr/local/bin >>> (a little less elegant than the full Fink install procedure but it >>> works). >>> (see >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> for >>> details) >>> >>> Of course, you will still need (for example) X11 for Mac OS X Public >>> Beta, which >>> is an implementation of the X Window System that makes it possible to >>> run X11-based applications in Mac OS >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html >>> (41.8MB) >>> >>> 2) Eventually, if you do get the energy, (as stated by others) the >>> following link is invaluable >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >>> to get all of the appropriate pieces together and use Fink for the >>> compile/install procedures >>> (rasmol executable will end up in /sw/bin/ and not overwrite >>> /usr/local/bin/). >>> Just a matter of being persistent and careful and a little patient. >>> >>> I've actually got Rasmol installed by both routes (but gave/linked >>> them >>> to unique names); >>> don't ask why I bothered ... just bored I guess. 8-) >>> >>> I hope this helps! >>> >>> Good Luck >>> Harry. >>> >>> --------------------------------------------------------------------- >>> --- >>> ---- >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 >>> 6268 >>> 8919 >>> School of Chemistry, University College (UNSW) Fax: +61 2 >>> 6268 >>> 8002 >>> Australian Defence Force Academy Fax: +61 2 >>> 6268 >>> 8017 >>> Canberra ACT 2600, Australia Email: >>> Harold.Schranz@adfa.edu.au >>> >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics >>> and ANU Supercomputer Facility and Research School of Chemistry >>> Australian National University, Canberra ACT 0200, Australia >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 >>> 6125 >>> 6533 >>> --------------------------------------------------------------------- >>> --- >>> ---- >>> >>> >>> >>> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 12:30:33 -0500 (EST) To: rasmol@lists.umass.edu If it is important to you to have the system allow you to double click files to have them opended by RasMol, then I would suggest you install the Mac Classic version of RasMol 2.7.2.1, instead of the X-windows based version you have installed. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Sun, 2 Mar 2003, Christopher Masi wrote: > That doesn't work here. > > I installed 2.7.1 via Fink and 2.7.2 via the following link > > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > > and neither is recognized by OS X 10.2.4 as a suitable "Open with" > application even when "All Applications" is selected in the Open with > dialogue box. If you have found a way to make this work, I would love > more details on how I might get my system to do it too. > > Thanks, > Chris > > On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > > > hi George, > > > > did you try the OSX method? just in case, here it is: > > > > single-click on any pdb file (in the Finder) and choose Get Info > > (control- > > or right-click, cmd-I, or File:Get Info at your discretion). > > > > switch to the "Open With" pane. from the option list there, choose > > rasmol > > 2.7.2.1 (if it is not present, there is an Other... option at the very > > bottom of the list that allows you browse to the app). > > > > click the Change All button to make this the default for all files of > > this > > type on your computer. > > > > repeat for ras files, scr files - any files you want to double-click > > and > > launch rasmol 2.7.2.1. > > > > > > hth, > > > > :tim > > -- > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > > > >> Hi there, > >> > >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 > >> and > >> rasmol.help both downloaded from arcib.dowling.edu and moved to the > >> /usr/local/bin directory. > >> > >> Encountered the following problems: > >> > >> 1. On trying to open files with .pdb extension rasmol is overriden by > >> iMol > >> (native OSX program). > >> 2. On trying to open rasmol scripted files (.ras extension), system > >> OS9 is > >> fired up and the file is open by RasMol 2.6 for system 9. > >> > >> Both of the above even if I reboot and try to open files from the X11 > >> window. > >> > >> Would be grateful for any suggestions. > >> > >> George > >> > >> Dr George Tzotzos > >> UNIDO, Vienna, Austria > >> > >> Tel: +43-1-26026 4336 > >> Fax: +43-1-26026 6810 > >> email: g.tzotzos@unido.org > >> > >> > >> > >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > >> wrote: > >> > >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > >>>> Dear Chris and all the ones who sent helpful suggestions, > >>>> which I have followed the most carefully I could, I am afraid I > >>>> still > >>>> am in troubles. > >>> > >>> Dear Adriano > >>> > >>> Hopefully I correctly understand your predicament! > >>> > >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 > >>> or later): > >>> > >>> 1) In case the route involving getting the bits and pieces together > >>> as > >>> in > >>> Christopher Masi's post is too hard (at first) you could just > >>> download > >>> one of the precompiled executables from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> Mac_OS_X_10.2.2_PPC/ > >>> (e.g. the 32 bit one if your display covers that range) > >>> and the corresponding help file from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> rasmol.hlp.gz > >>> which I put both (after gunzipping) in /usr/local/bin > >>> (a little less elegant than the full Fink install procedure but it > >>> works). > >>> (see > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> for > >>> details) > >>> > >>> Of course, you will still need (for example) X11 for Mac OS X Public > >>> Beta, which > >>> is an implementation of the X Window System that makes it possible to > >>> run X11-based applications in Mac OS > >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html > >>> (41.8MB) > >>> > >>> 2) Eventually, if you do get the energy, (as stated by others) the > >>> following link is invaluable > >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >>> to get all of the appropriate pieces together and use Fink for the > >>> compile/install procedures > >>> (rasmol executable will end up in /sw/bin/ and not overwrite > >>> /usr/local/bin/). > >>> Just a matter of being persistent and careful and a little patient. > >>> > >>> I've actually got Rasmol installed by both routes (but gave/linked > >>> them > >>> to unique names); > >>> don't ask why I bothered ... just bored I guess. 8-) > >>> > >>> I hope this helps! > >>> > >>> Good Luck > >>> Harry. > >>> > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 > >>> 6268 > >>> 8919 > >>> School of Chemistry, University College (UNSW) Fax: +61 2 > >>> 6268 > >>> 8002 > >>> Australian Defence Force Academy Fax: +61 2 > >>> 6268 > >>> 8017 > >>> Canberra ACT 2600, Australia Email: > >>> Harold.Schranz@adfa.edu.au > >>> > >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics > >>> and ANU Supercomputer Facility and Research School of Chemistry > >>> Australian National University, Canberra ACT 0200, Australia > >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 > >>> 6125 > >>> 6533 > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> > >>> > >>> > >>> > >> > >> > >> > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Sun, 02 Mar 2003 13:07:21 -0500 To: rasmol@lists.umass.edu at 11:39 AM EDT on (Sunday) 2 March 2003 Christopher Masi said: > That doesn't work here. > bummer. sorry. > I installed 2.7.1 via Fink and 2.7.2 via the following link > > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > > and neither is recognized by OS X 10.2.4 as a suitable "Open with" > application even when "All Applications" is selected in the Open with > dialogue box. If you have found a way to make this work, I would love > more details on how I might get my system to do it too. > um, no. I had neither time nor energy to try very hard, though ;-) I always have Classic running for one reason or another, so it is just as easy for me to use an older version of rasmol. hope you get it worked out, though! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest > Thanks, > Chris > > On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > > > hi George, > > > > did you try the OSX method? just in case, here it is: > > > > single-click on any pdb file (in the Finder) and choose Get Info > > (control- > > or right-click, cmd-I, or File:Get Info at your discretion). > > > > switch to the "Open With" pane. from the option list there, choose > > rasmol > > 2.7.2.1 (if it is not present, there is an Other... option at the very > > bottom of the list that allows you browse to the app). > > > > click the Change All button to make this the default for all files of > > this > > type on your computer. > > > > repeat for ras files, scr files - any files you want to double-click > > and > > launch rasmol 2.7.2.1. > > > > > > hth, > > > > :tim > > -- > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > > > >> Hi there, > >> > >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 > >> and > >> rasmol.help both downloaded from arcib.dowling.edu and moved to the > >> /usr/local/bin directory. > >> > >> Encountered the following problems: > >> > >> 1. On trying to open files with .pdb extension rasmol is overriden by > >> iMol > >> (native OSX program). > >> 2. On trying to open rasmol scripted files (.ras extension), system > >> OS9 is > >> fired up and the file is open by RasMol 2.6 for system 9. > >> > >> Both of the above even if I reboot and try to open files from the X11 > >> window. > >> > >> Would be grateful for any suggestions. > >> > >> George > >> > >> Dr George Tzotzos > >> UNIDO, Vienna, Austria > >> > >> Tel: +43-1-26026 4336 > >> Fax: +43-1-26026 6810 > >> email: g.tzotzos@unido.org > >> > >> > >> > >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > >> wrote: > >> > >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: > >>>> Dear Chris and all the ones who sent helpful suggestions, > >>>> which I have followed the most carefully I could, I am afraid I > >>>> still > >>>> am in troubles. > >>> > >>> Dear Adriano > >>> > >>> Hopefully I correctly understand your predicament! > >>> > >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 > >>> or later): > >>> > >>> 1) In case the route involving getting the bits and pieces together > >>> as > >>> in > >>> Christopher Masi's post is too hard (at first) you could just > >>> download > >>> one of the precompiled executables from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> Mac_OS_X_10.2.2_PPC/ > >>> (e.g. the 32 bit one if your display covers that range) > >>> and the corresponding help file from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> rasmol.hlp.gz > >>> which I put both (after gunzipping) in /usr/local/bin > >>> (a little less elegant than the full Fink install procedure but it > >>> works). > >>> (see > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> for > >>> details) > >>> > >>> Of course, you will still need (for example) X11 for Mac OS X Public > >>> Beta, which > >>> is an implementation of the X Window System that makes it possible to > >>> run X11-based applications in Mac OS > >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html > >>> (41.8MB) > >>> > >>> 2) Eventually, if you do get the energy, (as stated by others) the > >>> following link is invaluable > >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >>> to get all of the appropriate pieces together and use Fink for the > >>> compile/install procedures > >>> (rasmol executable will end up in /sw/bin/ and not overwrite > >>> /usr/local/bin/). > >>> Just a matter of being persistent and careful and a little patient. > >>> > >>> I've actually got Rasmol installed by both routes (but gave/linked > >>> them > >>> to unique names); > >>> don't ask why I bothered ... just bored I guess. 8-) > >>> > >>> I hope this helps! > >>> > >>> Good Luck > >>> Harry. > >>> > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 > >>> 6268 > >>> 8919 > >>> School of Chemistry, University College (UNSW) Fax: +61 2 > >>> 6268 > >>> 8002 > >>> Australian Defence Force Academy Fax: +61 2 > >>> 6268 > >>> 8017 > >>> Canberra ACT 2600, Australia Email: > >>> Harold.Schranz@adfa.edu.au > >>> > >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics > >>> and ANU Supercomputer Facility and Research School of Chemistry > >>> Australian National University, Canberra ACT 0200, Australia > >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 > >>> 6125 > >>> 6533 > >>> --------------------------------------------------------------------- > >>> --- > >>> ---- > >>> > >>> > >>> > >>> > >> > >> > >> > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20030301114541.024a9b90@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: standards for mol vis Date: Mon, 03 Mar 2003 00:51:40 +0000 (GMT) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu Eric Martz said: > At 2/27/03, you wrote: >>I am compiling a list of standard representations used for molecular >> visualization. > > Last summer I spent quite a bit of time writing some entries on this for a > dictionary of bioinformatics that has yet to be published. I've attached them -- > they may be useful. > > -Eric you couldnt post up an rtf version of this file could you? ;) ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-MSMail-priority: Normal X-Scanner: exiscan *18pjdz-0001aq-00*Lve11Eos4AE* (University of Pretoria, South Africa) References: <5.2.0.9.2.20030301141629.024bf7d0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Kiggundu Subject: Re: oops Date: Mon, 03 Mar 2003 08:43:27 +0200 To: rasmol@lists.umass.edu Any how it interesting to some of us new to Bioinformatics!!! ----- Original Message ----- Sent: Saturday, March 01, 2003 9:18 PM From: "Eric Martz" Subject: oops To: > My sincere apologies for burdening everyone on the list with a large > attachment that I intended only for Tim Driscoll. -Eric Martz (red faced) > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: rasmol 2.7.2 install in Mac OSX Thread-Index: AcLg6cyZSqxtvmlaT0mlmvQ0fpM3vAApJ4pg content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: RE: rasmol 2.7.2 install in Mac OSX Date: Mon, 03 Mar 2003 09:11:27 -0500 To: rasmol@lists.umass.edu Maybe you could use apple script? I installed another X windows application called "openOffice", and the package came with some double clickable scripts to start openOffice. I've never done any apple scripting; this is just kind of a guess... Mitch -----Original Message----- Sent: Sunday, March 02, 2003 1:07 PM From: timothy driscoll [mailto:listsub@molvisions.com] Subject: Re: rasmol 2.7.2 install in Mac OSX To: rasmol@lists.umass.edu at 11:39 AM EDT on (Sunday) 2 March 2003 Christopher Masi said: > That doesn't work here. > bummer. sorry. > I installed 2.7.1 via Fink and 2.7.2 via the following link > > http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > Mac_OS_X_10.2.2_PPC/ > > and neither is recognized by OS X 10.2.4 as a suitable "Open with" > application even when "All Applications" is selected in the Open with > dialogue box. If you have found a way to make this work, I would love > more details on how I might get my system to do it too. > um, no. I had neither time nor energy to try very hard, though ;-) I always have Classic running for one reason or another, so it is just as easy for me to use an older version of rasmol. hope you get it worked out, though! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest > Thanks, > Chris > > On Sunday, March 2, 2003, at 09:04 AM, timothy driscoll wrote: > > > hi George, > > > > did you try the OSX method? just in case, here it is: > > > > single-click on any pdb file (in the Finder) and choose Get Info > > (control- > > or right-click, cmd-I, or File:Get Info at your discretion). > > > > switch to the "Open With" pane. from the option list there, choose > > rasmol > > 2.7.2.1 (if it is not present, there is an Other... option at the very > > bottom of the list that allows you browse to the app). > > > > click the Change All button to make this the default for all files > > of > > this > > type on your computer. > > > > repeat for ras files, scr files - any files you want to double-click > > and > > launch rasmol 2.7.2.1. > > > > > > hth, > > > > :tim > > -- > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > > > > > > at 4:35 AM EDT on (Sunday) 2 March 2003 George Tzotzos said: > > > >> Hi there, > >> > >> I followed Harold's option 1. X11 properly installed, rasmol > >> 2.7.2.1 > >> and > >> rasmol.help both downloaded from arcib.dowling.edu and moved to the > >> /usr/local/bin directory. > >> > >> Encountered the following problems: > >> > >> 1. On trying to open files with .pdb extension rasmol is overriden > >> by > >> iMol > >> (native OSX program). > >> 2. On trying to open rasmol scripted files (.ras extension), system > >> OS9 is > >> fired up and the file is open by RasMol 2.6 for system 9. > >> > >> Both of the above even if I reboot and try to open files from the > >> X11 window. > >> > >> Would be grateful for any suggestions. > >> > >> George > >> > >> Dr George Tzotzos > >> UNIDO, Vienna, Austria > >> > >> Tel: +43-1-26026 4336 > >> Fax: +43-1-26026 6810 > >> email: g.tzotzos@unido.org > >> > >> > >> > >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz > >> wrote: > >> > >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli > >>> wrote: > >>>> Dear Chris and all the ones who sent helpful suggestions, which I > >>>> have followed the most carefully I could, I am afraid I > >>>> still > >>>> am in troubles. > >>> > >>> Dear Adriano > >>> > >>> Hopefully I correctly understand your predicament! > >>> > >>> A simple approach MIGHT be the following (assuming you have OS X > >>> 10.2 or later): > >>> > >>> 1) In case the route involving getting the bits and pieces > >>> together > >>> as > >>> in > >>> Christopher Masi's post is too hard (at first) you could just > >>> download > >>> one of the precompiled executables from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> Mac_OS_X_10.2.2_PPC/ > >>> (e.g. the 32 bit one if your display covers that range) > >>> and the corresponding help file from: > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> rasmol.hlp.gz > >>> which I put both (after gunzipping) in /usr/local/bin > >>> (a little less elegant than the full Fink install procedure but it > >>> works). > >>> (see > >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ > >>> for > >>> details) > >>> > >>> Of course, you will still need (for example) X11 for Mac OS X > >>> Public Beta, which is an implementation of the X Window System > >>> that makes it possible to run X11-based applications in Mac OS > >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html > >>> (41.8MB) > >>> > >>> 2) Eventually, if you do get the energy, (as stated by others) the > >>> following link is invaluable > >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html > >>> to get all of the appropriate pieces together and use Fink for the > >>> compile/install procedures (rasmol executable will end up in > >>> /sw/bin/ and not overwrite /usr/local/bin/). > >>> Just a matter of being persistent and careful and a little patient. > >>> > >>> I've actually got Rasmol installed by both routes (but gave/linked > >>> them > >>> to unique names); > >>> don't ask why I bothered ... just bored I guess. 8-) > >>> > >>> I hope this helps! > >>> > >>> Good Luck > >>> Harry. > >>> > >>> ------------------------------------------------------------------ > >>> --- > >>> --- > >>> ---- > >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 > >>> 6268 > >>> 8919 > >>> School of Chemistry, University College (UNSW) Fax: +61 2 > >>> 6268 > >>> 8002 > >>> Australian Defence Force Academy Fax: +61 2 > >>> 6268 > >>> 8017 > >>> Canberra ACT 2600, Australia Email: > >>> Harold.Schranz@adfa.edu.au > >>> > >>> Visiting Fellow, Biophysics Group, Department of Theoretical > >>> Physics and ANU Supercomputer Facility and Research School of > >>> Chemistry Australian National University, Canberra ACT 0200, Australia > >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 > >>> 6125 > >>> 6533 > >>> ------------------------------------------------------------------ > >>> --- > >>> --- > >>> ---- > >>> > >>> > >>> > >>> > >> > >> > >> > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: George Tzotzos Subject: Re: rasmol 2.7.2 install in Mac OSX Date: Tue, 04 Mar 2003 00:35:55 -0800 To: rasmol@lists.umass.edu Chris' solution works. Many thanks. George Dr George Tzotzos UNIDO Vienna, Austria Tel: +43-1-26026 4336 Fax: +43-1-26026 810 -------------- On Sunday, March 02, 2003, at 06:18AM, Christopher Masi wrote: >I am starting with the assumption that you are double clicking the >files to open them. > > Rasmol 2.7.2 is running on OS X's Darwin core, and the only way to >interact with the program is by a terminal emulator (xTerm or Apple's >Terminal). The only way to display the output is through an X 11 window. > Essentially, OS X has a mild case of MPD. iMol is a full fledged OS X >program. Rasmol 2.6 is a "Classic" application. Rasmol 2.7.2 is a >Darwin application. The Finder only "knows" about Classic and OS X >applications. It does not know about Darwin applications. > When you double click the pdb file, the Finder looks for a program >that has the correct creator type and tells that program to open the >file. Since the Finder doesn't know that rasmol 2.7.2 exists the Finder >instructs iMol to open the pdb file (iMol is newer than Rasmol 2.6). >When you double click the .ras file, the Finder looks for an >application to use. The Finder still doesn't know about Rasmol 2.7.2, >and iMol cannot open (or at least the Finder doesn't think it can open) >.ras files, so the Finder goes to the only application that it knows >about that can open the .ras file, Rasmol 2.6. > Because rasmol 2.7.2 was installed as a Darwin/Unix application it is >not double clickable. Try finding rasmol 2.7.2 and double clicking it. >It will not start. If everything is set up correctly, to use Rasmol >2.7.2 to open a pdb file you have to > >1. have X11 running. Double click Apple's X11.app >2. in an xTerm window or (if configured the right way) or a >Terminal.app window navigate to the directory that contains all the >pbds that you want to view and type rasmol >3. in the window that was used to launch rasmol type load 1ADO.pdb >where 1ADO.pdb is the name of the file that you want to open. > >Chris > >On Sunday, March 2, 2003, at 07:35 AM, George Tzotzos wrote: > >> Hi there, >> >> I followed Harold's option 1. X11 properly installed, rasmol 2.7.2.1 >> and rasmol.help both downloaded from arcib.dowling.edu and moved to >> the /usr/local/bin directory. >> >> Encountered the following problems: >> >> 1. On trying to open files with .pdb extension rasmol is overriden by >> iMol (native OSX program). >> 2. On trying to open rasmol scripted files (.ras extension), system >> OS9 is fired up and the file is open by RasMol 2.6 for system 9. >> >> Both of the above even if I reboot and try to open files from the X11 >> window. >> >> Would be grateful for any suggestions. >> >> George >> >> Dr George Tzotzos >> UNIDO, Vienna, Austria >> >> Tel: +43-1-26026 4336 >> Fax: +43-1-26026 6810 >> email: g.tzotzos@unido.org >> >> >> >> On Saturday, February 22, 2003, at 07:01PM, Harold Schranz >> wrote: >> >>> On Friday, February 21, 2003, at 07:26 PM, adriano ceccarelli wrote: >>>> Dear Chris and all the ones who sent helpful suggestions, >>>> which I have followed the most carefully I could, I am afraid I still >>>> am in troubles. >>> >>> Dear Adriano >>> >>> Hopefully I correctly understand your predicament! >>> >>> A simple approach MIGHT be the following (assuming you have OS X 10.2 >>> or later): >>> >>> 1) In case the route involving getting the bits and pieces together as >>> in >>> Christopher Masi's post is too hard (at first) you could just download >>> one of the precompiled executables from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> Mac_OS_X_10.2.2_PPC/ >>> (e.g. the 32 bit one if your display covers that range) >>> and the corresponding help file from: >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> rasmol.hlp.gz >>> which I put both (after gunzipping) in /usr/local/bin >>> (a little less elegant than the full Fink install procedure but it >>> works). >>> (see >>> http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.2.1/ >>> for >>> details) >>> >>> Of course, you will still need (for example) X11 for Mac OS X Public >>> Beta, which >>> is an implementation of the X Window System that makes it possible to >>> run X11-based applications in Mac OS >>> http://www.apple.com/downloads/macosx/apple/x11formacosx.html (41.8MB) >>> >>> 2) Eventually, if you do get the energy, (as stated by others) the >>> following link is invaluable >>> http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html >>> to get all of the appropriate pieces together and use Fink for the >>> compile/install procedures >>> (rasmol executable will end up in /sw/bin/ and not overwrite >>> /usr/local/bin/). >>> Just a matter of being persistent and careful and a little patient. >>> >>> I've actually got Rasmol installed by both routes (but gave/linked >>> them >>> to unique names); >>> don't ask why I bothered ... just bored I guess. 8-) >>> >>> I hope this helps! >>> >>> Good Luck >>> Harry. >>> >>> ---------------------------------------------------------------------- >>> -- >>> ---- >>> Dr. Harold W. Schranz, Senior Research Associate Phone: +61 2 >>> 6268 >>> 8919 >>> School of Chemistry, University College (UNSW) Fax: +61 2 >>> 6268 >>> 8002 >>> Australian Defence Force Academy Fax: +61 2 >>> 6268 >>> 8017 >>> Canberra ACT 2600, Australia Email: >>> Harold.Schranz@adfa.edu.au >>> >>> Visiting Fellow, Biophysics Group, Department of Theoretical Physics >>> and ANU Supercomputer Facility and Research School of Chemistry >>> Australian National University, Canberra ACT 0200, Australia >>> Email: Harold.Schranz@anu.edu.au Phone: +61 2 >>> 6125 >>> 6533 >>> ---------------------------------------------------------------------- >>> -- >>> ---- >>> >>> >>> >>> >> >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> ---------------------------------------------------------------- >> rasmol-- >> > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: helgew@www.grajagan.net ++++------+------+------+------+------+------+------+------+------+------+ From: Helge Weissig Subject: book announcement: Structural Bioinformatics Date: Wed, 12 Mar 2003 09:53:47 -0800 (PST) To: Bioinformatics List: ; Dear Colleague, I am very pleased to announce the availability of a new text book with the title "Structural Bioinformatics" (Editors: P. E. Bourne and H. Weissig. Hoboken, NJ, John Wiley & Sons, Inc.). Chapters of interest to this list include "The Protein Data Bank", "Computational Aspects of High-throughput Crystallographic Macromolecular Structure Determination" and "Molecular Visualization." Other chapters cover areas such as Comparative Features, Structure and Functional Assignment, Proteins as Drug Targets and Structure Prediction. A full list of chapters together with the names of all authors and more is available at the book's companion web site http://www.structuralbioinformaticsbook.com We hope you will find this book of great relevance to your area of research and/or teaching and your comments and feedback are very welcome. Apologies in advance, should you have received this message multiple times. with best regards, h. /--------------------------------------------- / Helge Weissig, Ph.D. / Co-Editor, Structural Bioinformatics / http://www.structuralbioinformaticsbook.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: rasmol and 4cpa Date: Fri, 28 Mar 2003 12:40:05 +0000 To: rasmol Hi, I dont't know if you know pdb 4cpa - It has a weird format, having some null chain and some named chain. As far as I know this is the only pdb to mix null and named chains. In rasmol is there any way to select just the null chain? I am guessing that this feature was not implemented, as it is almost never necessary. I asked at the PDB about this file, but they said they could not update the record, which seems a bit strange to me. Thanks, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <3E8442A5.9030602@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: tiny bug Date: Fri, 28 Mar 2003 12:54:20 +0000 To: rasmol@lists.umass.edu I just saw that select not all and select ! all doesn't work like select not * and select !* ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: rasmol and 4cpa Date: Fri, 28 Mar 2003 08:14:45 -0500 To: "'rasmol@lists.umass.edu'" Dan, All that is needed is a little Boolean logic... Use the command "select not (*I and *G)" this will select just the enzyme and not the inhibitor or the glycine. You could modify this strategy to select a specific part of the enzyme. For example to select residue 7 in the enzyme without selecting residue 7 in the inhibitor you would use the command "select 7 and not 7I" Hope that this helps, --- Frank ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D. Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm -----Original Message----- Sent: Friday, March 28, 2003 7:40 AM From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] Subject: rasmol and 4cpa To: rasmol Hi, I dont't know if you know pdb 4cpa - It has a weird format, having some null chain and some named chain. As far as I know this is the only pdb to mix null and named chains. In rasmol is there any way to select just the null chain? I am guessing that this feature was not implemented, as it is almost never necessary. I asked at the PDB about this file, but they said they could not update the record, which seems a bit strange to me. Thanks, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: rasmol and 4cpa Date: Fri, 28 Mar 2003 09:05:24 -0500 To: rasmol@lists.umass.edu At 3/28/03, you wrote: >Hi, I dont't know if you know pdb 4cpa - It has a weird format, >having some null chain and some named chain. As far as I know >this is the only pdb to mix null and named chains. > >In rasmol is there any way to select just the null chain? > >I am guessing that this feature was not implemented, as it is almost >never necessary. > >I asked at the PDB about this file, but they said they could not update >the record, which seems a bit strange to me. > >Thanks, Dan. Frank Gorga's Boolean solution is a good one. Alternatively, one can use DeepView to rename the unnamed chain. The result with chains A, G, I is available at http://molvis.sdsc.edu/pdb/4cpa_agi.pdb The procedure is: -Preferences, Loading Protein, uncheck Ignore solvent (lower left in dialog). [Unnecessary for 4cpa since it has no water.] -In the Control Panel, select the unnamed chain by clicking in the blank leftmost column. -Holding down Ctrl, click to deselect ZN1. -Edit, Rename current layer. -In that dialog, enter "A" in Rename Chain of Selected Groups -Click OK. -File, Save, Layer. -Remove the SPDB records inserted at the end by DeepView (optional - I did). -Copy the original header into the DeepView result (optional - I did). DeepView makes at least one other change: Residue 2 in chain I is GLX. This is a legal residue name in PDB format meaning either GLU or GLN (http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_82.html#Anchor-Amino-36680). DeepView changes this residue from ATOM to HETATM. Dan, I would be interested in seeing a copy of your inquiry to the PDB and their reply. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <9F5E83E17008D31193DD0090274E75051319DCE9@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: rasmol and 4cpa Date: Fri, 28 Mar 2003 15:12:10 +0100 To: rasmol@lists.umass.edu Hi, you surelly meant "select not (*I or *G)" as *I and *G is empty. Paul ----- Original Message ----- Sent: Friday, March 28, 2003 2:14 PM From: "Gorga, Frank" Subject: RE: rasmol and 4cpa To: > Dan, > > All that is needed is a little Boolean logic... > > Use the command "select not (*I and *G)" this will select just the enzyme > and not the inhibitor or the glycine. > > You could modify this strategy to select a specific part of the enzyme. For > example to select residue 7 in the enzyme without selecting residue 7 in the > inhibitor you would use the command "select 7 and not 7I" > > Hope that this helps, > > --- Frank > > -------------------------------------------------------------------------- -- > - > Frank R. Gorga, Ph.D. > Department of Chemical Sciences > Bridgewater State College > Bridgewater, MA 02325 > 508-531-2827 / 508-531-1785 (fax) > fgorga@bridgew.edu > webhost.bridgew.edu/fgorga > -------------------------------------------------------------------------- -- > Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > > -----Original Message----- > From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] > Sent: Friday, March 28, 2003 7:40 AM > To: rasmol > Subject: rasmol and 4cpa > > > Hi, I dont't know if you know pdb 4cpa - It has a weird format, > having some null chain and some named chain. As far as I know > this is the only pdb to mix null and named chains. > > In rasmol is there any way to select just the null chain? > > I am guessing that this feature was not implemented, as it is almost > never necessary. > > I asked at the PDB about this file, but they said they could not update > the record, which seems a bit strange to me. > > Thanks, Dan. > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <9F5E83E17008D31193DD0090274E75051319DCE9@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: rasmol and 4cpa Date: Fri, 28 Mar 2003 14:57:55 +0000 To: rasmol@lists.umass.edu Perfect, I guess I am getting slow in my old age! Dan. Gorga, Frank wrote: >Dan, > >All that is needed is a little Boolean logic... > >Use the command "select not (*I and *G)" this will select just the enzyme >and not the inhibitor or the glycine. > >You could modify this strategy to select a specific part of the enzyme. For >example to select residue 7 in the enzyme without selecting residue 7 in the >inhibitor you would use the command "select 7 and not 7I" > >Hope that this helps, > >--- Frank > >---------------------------------------------------------------------------- >- >Frank R. Gorga, Ph.D. >Department of Chemical Sciences >Bridgewater State College >Bridgewater, MA 02325 >508-531-2827 / 508-531-1785 (fax) >fgorga@bridgew.edu >webhost.bridgew.edu/fgorga >---------------------------------------------------------------------------- >Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > >-----Original Message----- >From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] >Sent: Friday, March 28, 2003 7:40 AM >To: rasmol >Subject: rasmol and 4cpa > > >Hi, I dont't know if you know pdb 4cpa - It has a weird format, >having some null chain and some named chain. As far as I know >this is the only pdb to mix null and named chains. > >In rasmol is there any way to select just the null chain? > >I am guessing that this feature was not implemented, as it is almost >never necessary. > >I asked at the PDB about this file, but they said they could not update >the record, which seems a bit strange to me. > >Thanks, Dan. > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Original mail to PDB:[Fwd: Fwd: 4cpa - unique format.] Date: Fri, 28 Mar 2003 15:00:17 +0000 To: rasmol --Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ) -------- Original Message -------- ++++------+------+------+------+------+------+------+------+------+------+ From: Shri Jain Subject: Fwd: 4cpa - unique format. Date: Thu, 16 Jan 2003 14:36:52 -0500 To: dmb@mrc-dunn.cam.ac.uk, SJ_INFO , "Jain, Shri" Hi, This is a very old file. Under the data uniformity project, the older files were fixed and are available in mmCIF format from the pdb site. The information about how to get the file and translate it to pdb format is available at http://www.rcsb.org/pdb/uniformity/index.html Hope this helps, Shri >>You wrote: >Hi, I don't know if this molecule breaks >the format specification, but it is unique >in that it has both a 'null' chain and a >chain with an identifier. > >I had asumed that any null chain was itself >indicative of a single chain pdb, with all >multi chain pdbs having chain id's in all >instances. > >Using the scop domain definition I found that >4cpa is unique in this respect. > >Thanks for any help you can give in this matter. >Dan. -- =========================================================== Shri C Jain, Ph.D. RCSB Protein Data Bank Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email: sjain@rcsb.rutgers.edu Phone: (732) 445-0103 Fax: (732)-445-4320 =========================================================== --Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ)

-------- Original Message --------
Subject: Fwd: 4cpa - unique format.
Date: Thu, 16 Jan 2003 14:36:52 -0500
From: Shri Jain <sjain@rcsb.rutgers.edu>
To: dmb@mrc-dunn.cam.ac.uk, SJ_INFO <info@rcsb.org>, "Jain, Shri" <sjain@rcsb.rutgers.edu> 


Hi,

	This is a very old file. Under the data uniformity project, the older files
were fixed and are available in mmCIF format from the pdb site. The information
about how to get the file and translate it to pdb format is available at
 
http://www.rcsb.org/pdb/uniformity/index.html

	Hope this helps,
	Shri

	

>>You wrote:

>Hi, I don't know if this molecule breaks
>the format specification, but it is unique
>in that it has both a 'null' chain and a
>chain with an identifier.
>
>I had asumed that any null chain was itself
>indicative of a single chain pdb, with all
>multi chain pdbs having chain id's in all
>instances.
>
>Using the scop domain definition I found that
>4cpa is unique in this respect.
>
>Thanks for any help you can give in this matter.
>Dan.
-- 
===========================================================
Shri C Jain, Ph.D.
RCSB Protein Data Bank
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:  sjain@rcsb.rutgers.edu
Phone:  (732) 445-0103  
Fax:    (732)-445-4320
===========================================================
--Boundary_(ID_vkiRG+fml7gWFWwfqWEqZQ)-- boundary="Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Original reply to that mail:[Fwd: Re: Fwd: 4cpa - unique format.] Date: Fri, 28 Mar 2003 15:01:13 +0000 To: rasmol --Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q) I didn't get any reply... :( -------- Original Message -------- , SJ_INFO References: <3E2709D4.DF0F9F8C@rcsb.rutgers.edu> <32808.81.100.89.186.1042753284.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Shri Jain Subject: Re: Fwd: 4cpa - unique format. Date: Fri, 17 Jan 2003 09:34:58 -0500 To: Dan Bolser , "Jain, Shri" If the changes are in the coordinate section, we are not permitted to change. IF there are any corrections in the header section, we do make changes and the updated file is re-released to appear in public domain. Shri Jain Dan Bolser wrote: > > So there is no plan to replace / update the original PDB? > > The problem is that the pdb is classified a certain way by > scop. Updating my local copy isn't the problem. > > Please let me know, > > Thanks for the reply, > > Dan. > > Shri Jain said: > > Hi, > > > > This is a very old file. Under the data uniformity project, the older files > > were fixed and are available in mmCIF format from the pdb site. The information > > about how to get the file and translate it to pdb format is available at > > > > http://www.rcsb.org/pdb/uniformity/index.html > > > > Hope this helps, > > Shri > > > > > > > > > > > >>>You wrote: > > > > > >>Hi, I don't know if this molecule breaks > >>the format specification, but it is unique > >>in that it has both a 'null' chain and a > >>chain with an identifier. > >> > >>I had asumed that any null chain was itself > >>indicative of a single chain pdb, with all > >>multi chain pdbs having chain id's in all > >>instances. > >> > >>Using the scop domain definition I found that > >>4cpa is unique in this respect. > >> > >>Thanks for any help you can give in this matter. > >>Dan. > > -- > > =========================================================== > > Shri C Jain, Ph.D. > > RCSB Protein Data Bank > > Department of Chemistry and Chemical Biology > > Rutgers The State University of New Jersey > > 610 Taylor Road > > Piscataway, NJ 08854-8087 > > > > Email: sjain@rcsb.rutgers.edu > > Phone: (732) 445-0103 > > Fax: (732)-445-4320 > > =========================================================== -- =========================================================== Shri C Jain, Ph.D. RCSB Protein Data Bank Department of Chemistry and Chemical Biology Rutgers The State University of New Jersey 610 Taylor Road Piscataway, NJ 08854-8087 Email: sjain@rcsb.rutgers.edu Phone: (732) 445-0103 Fax: (732)-445-4320 =========================================================== --Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q) I didn't get any reply... :(

-------- Original Message --------
Subject: Re: Fwd: 4cpa - unique format.
Date: Fri, 17 Jan 2003 09:34:58 -0500
From: Shri Jain <sjain@rcsb.rutgers.edu>
To: Dan Bolser <dmb@mrc-dunn.cam.ac.uk>, "Jain, Shri" <sjain@rcsb.rutgers.edu>, SJ_INFO <info@rcsb.org>
References: <3E2709D4.DF0F9F8C@rcsb.rutgers.edu> <32808.81.100.89.186.1042753284.squirrel@www.mrc-dunn.cam.ac.uk> 


	If the changes are in the coordinate section, we are not permitted to change.
IF there are any corrections in the header section, we do make changes and the
updated file is re-released to appear in public domain.

	Shri Jain

Dan Bolser wrote:
> 
> So there is no plan to replace / update the original PDB?
> 
> The problem is that the pdb is classified a certain way by
> scop. Updating my local copy isn't the problem.
> 
> Please let me know,
> 
> Thanks for the reply,
> 
> Dan.
> 
> Shri Jain said:
> > Hi,
> >
> >       This is a very old file. Under the data uniformity project, the older files
> > were fixed and are available in mmCIF format from the pdb site. The information
> > about how to get the file and translate it to pdb format is available at
> >
> > http://www.rcsb.org/pdb/uniformity/index.html
> >
> >       Hope this helps,
> >       Shri
> >
> >
> >
> >
> >
> >>>You wrote:
> >
> >
> >>Hi, I don't know if this molecule breaks
> >>the format specification, but it is unique
> >>in that it has both a 'null' chain and a
> >>chain with an identifier.
> >>
> >>I had asumed that any null chain was itself
> >>indicative of a single chain pdb, with all
> >>multi chain pdbs having chain id's in all
> >>instances.
> >>
> >>Using the scop domain definition I found that
> >>4cpa is unique in this respect.
> >>
> >>Thanks for any help you can give in this matter.
> >>Dan.
> > --
> > ===========================================================
> > Shri C Jain, Ph.D.
> > RCSB Protein Data Bank
> > Department of Chemistry and Chemical Biology
> > Rutgers The State University of New Jersey
> > 610 Taylor Road
> > Piscataway, NJ 08854-8087
> >
> > Email:  sjain@rcsb.rutgers.edu
> > Phone:  (732) 445-0103
> > Fax:    (732)-445-4320
> > ===========================================================

-- 
===========================================================
Shri C Jain, Ph.D.
RCSB Protein Data Bank
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:  sjain@rcsb.rutgers.edu
Phone:  (732) 445-0103  
Fax:    (732)-445-4320
===========================================================
--Boundary_(ID_r0eUW1rcC03DF1cFqCqE8Q)-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: 4cpa Date: Fri, 28 Mar 2003 11:33:12 -0500 (EST) To: sjain@rcsb.rugers.edu Cc: jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu, rasmol@lists.umass.edu Hi, I saw the correspondence about 4cpa and am puzzled why it is not possible to correct the chain indentifier problem. This would not be a change to the coordinates but is rather a representation issue. Note that the format description (under SEQRES) indicates: Chain identifier. This may be any single legal character, including a blank which is used if there is only one chain. This implies that a blank cannot be used if there is more than one chain, which is the case in 4cpa. Thus the entry as it stands violates the PDB format. To take the argument about not changing coordinates to the extreme, would you not correct an entry with a misformatted ATOM record or with a spurious character in an ATOM record? Frances C. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: 4cpa Date: Fri, 28 Mar 2003 18:20:30 +0000 To: rasmol@lists.umass.edu Cc: sjain@rcsb.rugers.edu, jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu exactly! What if the structure turned out to be wrong? Frances C. Bernstein wrote: >Hi, > > I saw the correspondence about 4cpa and am puzzled >why it is not possible to correct the chain indentifier >problem. This would not be a change to the coordinates >but is rather a representation issue. Note that the format >description (under SEQRES) indicates: > > Chain identifier. This may be any single legal character, > including a blank which is used if there is only one chain. > >This implies that a blank cannot be used if there is more >than one chain, which is the case in 4cpa. Thus the >entry as it stands violates the PDB format. > > To take the argument about not changing coordinates >to the extreme, would you not correct an entry with a >misformatted ATOM record or with a spurious character in >an ATOM record? > > Frances C. Bernstein >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Frances C. Bernstein > * *** fcb@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 >===================================================== > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: Roy Carambula Subject: RE: 4cpa Date: Fri, 28 Mar 2003 13:50:30 -0500 To: "'rasmol@lists.umass.edu'" Hi list, It sounds like a "raw data" preservation-like concern. However I'm sure there must be a procedure to fix this, in any case this can't be the first time a mistake/error is found Roy Dan Bolser wrote: exactly! What if the structure turned out to be wrong? Frances C. Bernstein wrote: >Hi, > > I saw the correspondence about 4cpa and am puzzled >why it is not possible to correct the chain indentifier >problem. This would not be a change to the coordinates >but is rather a representation issue. Note that the format >description (under SEQRES) indicates: > > Chain identifier. This may be any single legal character, > including a blank which is used if there is only one chain. > >This implies that a blank cannot be used if there is more >than one chain, which is the case in 4cpa. Thus the >entry as it stands violates the PDB format. > > To take the argument about not changing coordinates >to the extreme, would you not correct an entry with a >misformatted ATOM record or with a spurious character in >an ATOM record? > > Frances C. Bernstein >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Frances C. Bernstein > * *** fcb@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 >===================================================== > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <3E84926E.5020204@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: 4cpa,... and 3cpa Date: Fri, 28 Mar 2003 19:50:51 +0100 To: rasmol@lists.umass.edu 3cpa has also a blank character as an identifier to the enzym chain, and a substrate chain identified by S Paul ----- Original Message ----- Sent: Friday, March 28, 2003 7:20 PM From: "Dan Bolser" Subject: Re: 4cpa To: Cc: ; ; > exactly! What if the structure turned out to be wrong? > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: 4cpa (fwd) Date: Fri, 28 Mar 2003 16:21:02 -0500 (EST) To: Shri Jain Cc: jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu, rasmol@lists.umass.edu Dear Shri, I have been involved with CIF and mmCIF since 1990 and think that mmCIF will eventually become the standard format. However, I recognize the reality that almost everyone in the world who currently uses the PDB wants entries in PDB format. Perhaps you could provide statistics on the number of entries retrieved per month in mmCIF format versus the number retrieved per month in PDB format. This would help to establish whether your decision not to correct 4cpa in PDB format is in the best interests of the user community. Frances ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 28 Mar 2003, Shri Jain wrote: > Dear Frances, > > Thank you for your email. The 4CPA file was fixed for chain id and is available > from the site BETAmmCIF site as mmcif file: > > ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/ > > Shri > > > > "Frances C. Bernstein" wrote: > > > > Sorry I mistyped your address the first time. > > > > Frances > > > > ===================================================== > > **** BERNSTEIN + SONS > > * * INFORMATION SYSTEMS CONSULTANTS > > **** P.O. BOX 177, BELLPORT, NY 11713-0177 > > * * *** > > **** * Frances C. Bernstein > > * *** fcb@bernstein-plus-sons.com > > *** * > > * *** 1-631-286-1339 FAX: 1-631-286-1999 > > ===================================================== > > > > ---------- Forwarded message ---------- > > Date: Fri, 28 Mar 2003 11:33:12 -0500 (EST) > > From: Frances C. Bernstein > > To: sjain@rcsb.rugers.edu > > Cc: jwest@rcsb.rutgers.edu, flippen@rcsb.rutgers.edu, rasmol@lists.umass.edu > > Subject: 4cpa > > Hi, > > > > I saw the correspondence about 4cpa and am puzzled > > why it is not possible to correct the chain indentifier > > problem. This would not be a change to the coordinates > > but is rather a representation issue. Note that the format > > description (under SEQRES) indicates: > > > > Chain identifier. This may be any single legal character, > > including a blank which is used if there is only one chain. > > > > This implies that a blank cannot be used if there is more > > than one chain, which is the case in 4cpa. Thus the > > entry as it stands violates the PDB format. > > > > To take the argument about not changing coordinates > > to the extreme, would you not correct an entry with a > > misformatted ATOM record or with a spurious character in > > an ATOM record? > > > > Frances C. Bernstein > > ===================================================== > > **** BERNSTEIN + SONS > > * * INFORMATION SYSTEMS CONSULTANTS > > **** P.O. BOX 177, BELLPORT, NY 11713-0177 > > * * *** > > **** * Frances C. Bernstein > > * *** fcb@bernstein-plus-sons.com > > *** * > > * *** 1-631-286-1339 FAX: 1-631-286-1999 > > ===================================================== > > -- > =========================================================== > Shri C Jain, Ph.D. > RCSB Protein Data Bank > Department of Chemistry and Chemical Biology > Rutgers The State University of New Jersey > 610 Taylor Road > Piscataway, NJ 08854-8087 > > Email: sjain@rcsb.rutgers.edu > Phone: (732) 445-0103 > Fax: (732)-445-4320 > =========================================================== > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <9F5E83E17008D31193DD0090274E75051319DCE9@mailhost.bridgew.edu> <000501c2f534$0f0d7580$0100a8c0@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: rasmol and 4cpa Date: Mon, 31 Mar 2003 09:54:29 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg) Cheers, Paul Pillot wrote: >Hi, > >you surelly meant "select not (*I or *G)" as *I and *G is empty. > >Paul >----- Original Message ----- >From: "Gorga, Frank" >To: >Sent: Friday, March 28, 2003 2:14 PM >Subject: RE: rasmol and 4cpa > > > > >>Dan, >> >>All that is needed is a little Boolean logic... >> >>Use the command "select not (*I and *G)" this will select just the enzyme >>and not the inhibitor or the glycine. >> >>You could modify this strategy to select a specific part of the enzyme. >> >> >For > > >>example to select residue 7 in the enzyme without selecting residue 7 in >> >> >the > > >>inhibitor you would use the command "select 7 and not 7I" >> >>Hope that this helps, >> >>--- Frank >> >>-------------------------------------------------------------------------- >> >> >-- > > >>- >>Frank R. Gorga, Ph.D. >>Department of Chemical Sciences >>Bridgewater State College >>Bridgewater, MA 02325 >>508-531-2827 / 508-531-1785 (fax) >>fgorga@bridgew.edu >>webhost.bridgew.edu/fgorga >>-------------------------------------------------------------------------- >> >> >-- > > >>Comfort the troubled; trouble the comfortable. >> -- Dietrich Bonhoeffer, 1906-1945 >> http://www.dbonhoeffer.org/who-was-db2.htm >> >> >>-----Original Message----- >>From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] >>Sent: Friday, March 28, 2003 7:40 AM >>To: rasmol >>Subject: rasmol and 4cpa >> >> >>Hi, I dont't know if you know pdb 4cpa - It has a weird format, >>having some null chain and some named chain. As far as I know >>this is the only pdb to mix null and named chains. >> >>In rasmol is there any way to select just the null chain? >> >>I am guessing that this feature was not implemented, as it is almost >>never necessary. >> >>I asked at the PDB about this file, but they said they could not update >>the record, which seems a bit strange to me. >> >>Thanks, Dan. >> >> >> >> >> >> > > > > --Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg) Cheers,

Paul Pillot wrote:
Hi,

you surelly meant "select not (*I or *G)" as *I and *G is empty.

Paul
----- Original Message -----
Sent: Friday, March 28, 2003 2:14 PM
From: "Gorga, Frank" <FGORGA@bridgew.edu>
Subject: RE: rasmol and 4cpa
To: <rasmol@lists.umass.edu>

  
Dan,

All that is needed is a little Boolean logic...

Use the command "select not (*I and *G)" this will select just the enzyme
and not the inhibitor or the glycine.

You could modify this strategy to select a specific part of the enzyme.
    
For
  
example to select residue 7 in the enzyme without selecting residue 7 in
    
the
  
inhibitor you would use the command "select 7 and not 7I"

Hope that this helps,

--- Frank

--------------------------------------------------------------------------
    
--
  
-
Frank R. Gorga, Ph.D.
Department of Chemical Sciences
Bridgewater State College
Bridgewater, MA 02325
508-531-2827 / 508-531-1785 (fax)
fgorga@bridgew.edu
webhost.bridgew.edu/fgorga
--------------------------------------------------------------------------
    
--
  
Comfort the troubled; trouble the comfortable.
       -- Dietrich Bonhoeffer, 1906-1945
          http://www.dbonhoeffer.org/who-was-db2.htm

-----Original Message-----
Sent: Friday, March 28, 2003 7:40 AM
From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk]
Subject: rasmol and 4cpa
To: rasmol

Hi, I dont't know if you know pdb 4cpa - It has a weird format,
having some null chain and some named chain. As far as I know
this is the only pdb to mix null and named chains.

In rasmol is there any way to select just the null chain?

I am guessing that this feature was not implemented, as it is almost
never necessary.

I asked at the PDB about this file, but they said they could not update
the record, which seems a bit strange to me.

Thanks, Dan.

--Boundary_(ID_wbyT9DRRWWCPYGumXPL7Gg)-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 31 Mar 2003 15:24:00.0348 (UTC) FILETIME=[8DF4C1C0:01C2F799] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Using chime with Yellowdog Linux Date: Mon, 31 Mar 2003 10:31:54 -0500 To: rasmol@lists.umass.edu Hi - Has anyone tried chime using Mac On Linux on Yellowdog linux (or any other linux)? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Using chime with Yellowdog Linux Date: Mon, 31 Mar 2003 11:16:10 -0600 (CST) To: rasmol@lists.umass.edu Hi, I think you will be out of luck with the combination of Linux and Mac. It might work if you can emulate the Mac OS under Linux in some way (eg Mac on Linux). The issues appear to relate to communication between the browser, chime and the OS. It would be easier to get the browser to run another viewer. Regards Bruce On Mon, 31 Mar 2003, Brian White wrote: > Hi - > Has anyone tried chime using Mac On Linux on Yellowdog linux (or any > other linux)? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: 4cpa Date: Tue, 01 Apr 2003 15:43:56 +0200 To: rasmol@lists.umass.edu Exactly. In addition, not 4cpa is the only file with blank or odd chain identifiers. Quite often the water molecules are marked with blank. It is not uncommon either that the identifier changes from one letter to another or to blank somewhere between TERs. Because column 22 in the pdb file is for the chain identifier - as FCB cites - its correctness should be checked more rigorously at PDB before the publication of an entry. How Rasmol & the others behave in this case? If between TERs the identifier changes from A to B, on selecting the second chain, atoms with identifier B are selected or from the appropriate TER until the next TER? Tamas E. Gunda ---------------------------- Dr. Tamas E. Gunda Department of Pharmaceutical Chemistry Medical and Health Center University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- Sent: Friday, March 28, 2003 18:33 From: "Frances C. Bernstein" Subject: 4cpa To: Cc: ; ; > Hi, > > I saw the correspondence about 4cpa and am puzzled > why it is not possible to correct the chain indentifier > problem. This would not be a change to the coordinates > but is rather a representation issue. Note that the format > description (under SEQRES) indicates: > > Chain identifier. This may be any single legal character, > including a blank which is used if there is only one chain. > > This implies that a blank cannot be used if there is more > than one chain, which is the case in 4cpa. Thus the > entry as it stands violates the PDB format. > > To take the argument about not changing coordinates > to the extreme, would you not correct an entry with a > misformatted ATOM record or with a spurious character in > an ATOM record? > > Frances C. Bernstein > ===================================================== > **** BERNSTEIN + SONS > * * INFORMATION SYSTEMS CONSULTANTS > **** P.O. BOX 177, BELLPORT, NY 11713-0177 > * * *** > **** * Frances C. Bernstein > * *** fcb@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 > ===================================================== > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20021120 Netscape/7.01 X-Accept-Language: en-us, en References: <001d01c2f854$bdf9a0f0$3b8506c1@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: 4cpa Date: Wed, 02 Apr 2003 10:46:50 +0100 To: rasmol@lists.umass.edu Any news on this entry? Can we expect it to change? Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: A little help with Rasmol and Protein Explorerer Date: Fri, 11 Apr 2003 11:41:41 -0400 To: Scott Pendley Cc: rasmol@lists.umass.edu At 4/11/03, Scott Pendley wrote:
Eric,
 
I have been playing around with Rasmol for a little while but am new to PE.  I was wondering if you could tell me if there is a command that will list that atoms that are currently selected.  To put this in context I am working on very large protein-protein interaction and am looking for hydrogen between the complexes using the select within.  Trying to find the bonded residues based on color alone is a little difficult.  Do you know of any commands that will help eithor with listing selected atoms or determining hbonds on quaternary structures?
 
Thank you,
 
Scott

Dear Scott:

There are three shortcuts for visualizing noncovalent bonds in PE. The resulting selected residues, atoms, or chains can easily be listed. In each case, the scripts employed are displayed in the message box so you can see how much of a shortcut these are.

1. In QuickViews, select e.g. one chain (or any moiety), then DISPLAY Contacts.
After doing this, at the very bottom of the long explanation in the middle help window are instructions for listing the contacting atoms. In addition to "show residue" you can also "show atom" or "show chain". These Chime commands are not implemented in RasMol 2.6; I don't know about RasMol 2.7.

2. In Advanced Explorer, Contact Surfaces, you have more control. For example if you "generate the surface on" ":a and not carbon" you will unclutter the display by excluding putative van der Waals interactions. The same commands can be used for listing residues or atoms.

3. In Advanced Explorer, use the NonCovalent Bond Finder. Again the "show" commands can be used to list the current shell. Click on the "Instruction" button and look under "Selectable terms defined by NCBF". For example, you can "select found" (all atoms found to date in all shells), then "show residue". Here, there are slots for "don't find" or "find only", so "don't find carbon" will find mostly hydrogen bonds or salt bridges.

"show atom" lists only atom serial numbers. You could inspect the PDB file to find out the complete information about each serial number listed. "show atom identify" lists only the element and position. These lists are not as useful as they could be since they don't show the residues containing the atoms. "show residue" lists only the residues containing selected atoms, but not the individual atoms selected. Of course you can click on any atom (in the graphic) for a full identification of that one atom, including its residue.

I have copied this to the email list because it may be of interest to some subscribers.
-Eric

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List:
      http://www.umass.edu/microbio/rasmol/raslist.htm

Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
              http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */
----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 boundary="Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Helios Chen Subject: help command can not work Date: Tue, 29 Apr 2003 21:56:42 +0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q) Hi, The message " Unable to find RasMol help file "occurs when I enter the "help" in the RasMol Command Line, could you tell me what's wrong or any path need to be set? Thanks a lot. --Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q)

Hi,
 
The message " Unable to find RasMol help file "occurs when I enter the "help" in the RasMol Command Line, could you tell me what's wrong or any path need to be set?  Thanks a lot.
--Boundary_(ID_EQTYqBZrIpx/8TtfXmG67Q)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Assessment of Protein Explorer by Classes Date: Wed, 30 Apr 2003 09:29:24 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org To All Educators Who Are Using Protein Explorer in Classes: As the semester wraps up, please hand out the short one-page Student Assessment of Learning Gains (SALG) form available at http://molvis.sdsc.edu/protexpl/evalppr.htm This will only take about 5 minutes of class time and the results will be useful for future funding and development priorities for Protein Explorer. This will be useful even if you used Protein Explorer only in lectures, or only for a single computer laboratory class or homework assignment. For those interested in electronic assessment, you can set up the SALG website for your students to fill out the above form in a web browser, and you can also use the SALG mechanism for evaluation of your entire course, including questions that you formulate or modify from the generic template available. Details at http://molvis.sdsc.edu/protexpl/eval.htm Thanks, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: pdb-l: Assessment of Protein Explorer by Classes Date: Wed, 30 Apr 2003 11:02:26 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org Please do not confuse the use of Protein Explorer with the use of RasMol. Please send reports of your classroom and research experience with RasMol to reports@rasmol.org Such reports will help us in setting priorities for RasMol development. Our thanks to the community for the continuing interest in RasMol and the steady stream of downloads. -- H. J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 30 Apr 2003, Eric Martz wrote: > To All Educators Who Are Using Protein Explorer in Classes: > > As the semester wraps up, please hand out the short one-page Student > Assessment of Learning Gains (SALG) form available at > http://molvis.sdsc.edu/protexpl/evalppr.htm > > This will only take about 5 minutes of class time and the results will be > useful for future funding and development priorities for Protein Explorer. > > This will be useful even if you used Protein Explorer only in lectures, or > only for a single computer laboratory class or homework assignment. > > For those interested in electronic assessment, you can set up the SALG > website for your students to fill out the above form in a web browser, and > you can also use the SALG mechanism for evaluation of your entire course, > including questions that you formulate or modify from the generic template > available. Details at http://molvis.sdsc.edu/protexpl/eval.htm > > Thanks, -Eric Martz > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Foley Subject: Multiple windows open? Prevent duplicate names of same object. Date: Thu, 01 May 2003 09:52:50 -0500 To: rasmol@lists.umass.edu Dear RasMol/CHIME users, Last night, as I was debugging some HTML/CHIME scripting used to make an online macromolecular "museum exhibit" (such as those at David Marcey's OMM http://www.clunet.edu/BioDev/omm/gallery.htm) I found out that if I have two windows open in my www browser that are both running CHIME and accessing the same (or even related) pages, CHIME can be confused by dealing with two object with the same name. Scripts called from one www browser window will operate on the object in to other window that has the same name as the "target" of the CHIME script. Eric Martz uses a nice technique to avoid this in Protein Explorer: --------- from Eric ---------- The solution to this, Brian, is to give the Chime's in each window different names. In Protein Explorer, concurrent sessions are possible because the parent window assigns a number to each new session, and uses that number as part of the Chime names to make each unique. You can see this by viewing the source of the Chime frame. In Netscape, it is sufficient if each window has a different name, even if the Chime's don't. However in IE, each Chime must have a different name to avoid the problem you describe. ---------------------------------- Brian Foley, PhD HIV Genetic Sequences and Immunology Databases btf@lanl.gov (505) 665-1970 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Darrell Brooks Subject: Chime & Windows XP Date: Wed, 07 May 2003 17:32:28 +0100 To: rasmol A naive question Our network is going over to Windows XP. This won't affect Chime will it? Darrell ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Chip Coward Subject: RE: Chime & Windows XP Date: Wed, 07 May 2003 12:51:37 -0400 To: rasmol@lists.umass.edu Darrell, We have just set up Protein Explorer on a Dell Workstation and Dell Laptop using Windows XP Professional and all I had to do was to download the latest version of Chime. Chip -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Darrell Brooks Sent: Wednesday, May 07, 2003 12:32 PM From: owner-rasmol@lists.umass.edu Subject: Chime & Windows XP To: rasmol A naive question Our network is going over to Windows XP. This won't affect Chime will it? Darrell ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul I. Reisberg" Subject: Chime & OSX Date: Wed, 07 May 2003 14:58:42 -0400 To: rasmol@lists.umass.edu Is using Netscape 4.79 in classic mode still the best option for those using OSX? Anyone have any success with an OSX browser, Safari or Opera perhaps? ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Chime & OSX Date: Wed, 07 May 2003 16:04:44 -0400 To: rasmol@lists.umass.edu Chime only works under OS X running netscape 4.x in Classic mode. It does not work in any native OS X browser. that being said, Chime still works just fine in Classic NS4. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 2:58 PM EDT on (Wednesday) 7 May 2003 Paul I. Reisberg said: > Is using Netscape 4.79 in classic mode still the best option for those > using OSX? > Anyone have any success with an OSX browser, Safari or Opera perhaps? > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 boundary="Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Helios Chen Subject: Chime script Date: Sat, 10 May 2003 09:38:16 +0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ) Dear Sir, The rotation command "spin on" in the Chime is too fast, could any script command adjust the speed? Best Regards. Helios Chen --Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ)
Dear Sir, The rotation command "spin on" in the Chime is too fast, could any script command adjust the speed?  Best Regards.
 
Helios Chen
--Boundary_(ID_genbFwy6DrIQZrPIOkwgWQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Chime script Date: Fri, 09 May 2003 22:02:02 -0400 To: rasmol@lists.umass.edu at 9:38 AM EDT on Saturday, May 10, 2003 Helios Chen said: > Dear Sir, The rotation command "spin on" in the Chime is too fast, could any > script command adjust the speed? Best Regards. > > Helios Chen from the Chime site at mdli: " Tag name: set spin fps Description: Sets the spin frames per second. This is equivalent to the spinfps embed tag Syntax: set spin fps ### ------------------------------------------------------------------------ Tag name: set spin x|y|z Description: Sets the speed of spin along the x, y, or z axis, in degrees per second. This is equivalent to the spinX, spinY, and spinZ embed tags. Syntax: set spin {x|y|z} ### ------------------------------------------------------------------------ " hope that helps! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Chime in OSX Date: Fri, 09 May 2003 22:10:06 -0400 To: LIST rasmol those of us "waiting" for an OSX-friendly version of Chime may do well to read the mdl faq: " When will you have a version of Chime for Macintosh OS-X or Linux? We don't have any current plans for an OS-X version of Macintosh or a Linux version. " I believe that means there is no X-friendly version of Chime forthcoming. how sad. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Helios Chen Subject: Re: Chime script Date: Sat, 10 May 2003 10:55:03 +0800 To: rasmol@lists.umass.edu Thanks for your help, colud any script command get the "spin" function in Rasmol?? I command the "spin on" on the Rasmol Command Line, but it can't work? If the first question could execute, are ther any command adjust the speed in Rasmol? ----- Original Message ----- Sent: Saturday, May 10, 2003 10:02 AM From: "timothy driscoll" Subject: Re: Chime script To: > > at 9:38 AM EDT on Saturday, May 10, 2003 Helios Chen said: > > > Dear Sir, The rotation command "spin on" in the Chime is too fast, could any > > script command adjust the speed? Best Regards. > > > > Helios Chen > > > from the Chime site at mdli: > > " > Tag name: set spin fps > Description: Sets the spin frames per second. This is equivalent to the > spinfps embed tag > Syntax: set spin fps ### > > ------------------------------------------------------------------------ > > Tag name: set spin x|y|z > Description: Sets the speed of spin along the x, y, or z axis, in degrees per > second. This is equivalent to the spinX, spinY, and spinZ embed tags. > Syntax: set spin {x|y|z} ### > > ------------------------------------------------------------------------ > " > > > hope that helps! > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVbu7tfnfi9UNHMnFEicc/lc+eVdLm1FJfG18Eew5CEMXKUs4mKtPDU+ ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: Chime in OSX Date: Fri, 09 May 2003 23:06:23 -0400 To: rasmol@lists.umass.edu That makes me sad. I am guessing that it would not be trivial to convert the Rasmol source to a plug-in. So, is there a cross platform way of creating web pages that can display molecules? I have used Chemical Applet but this page seems to have _recently_ disappeared. The developer, John Purvis, was associated with the CAChe molecular modeling system, and the Applet displayed molecules and surfaces generated by the CAChe molecular modeling system. I have also created QuickTIme Virtual Reality Objects of molecules and orbital surfaces, but QTVR Objects are limited in options and large in size. Thanks, Chris On Friday, May 9, 2003, at 10:10 PM, timothy driscoll wrote: > those of us "waiting" for an OSX-friendly version of Chime may do well > to read > the mdl faq: > > " > When will you have a version of Chime for Macintosh OS-X or Linux? > > We don't have any current plans for an OS-X version of Macintosh or a > Linux > version. > " > > > I believe that means there is no X-friendly version of Chime > forthcoming. how > sad. > > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime script Date: Sat, 10 May 2003 13:32:57 -0400 To: rasmol@lists.umass.edu At 5/10/03, Helios Chen wrote: >Thanks for your help, colud any script command get the "spin" function in >Rasmol?? I command the "spin on" on the Rasmol Command Line, but it can't >work? If the first question could execute, are ther any command adjust the >speed in Rasmol? The 'spin', 'move', and 'delay' commands are some of the many that Tim Maffett (of MDL) added to Chime that are not implemented in RasMol, at least in RasMol 2.6 beta-2a. I'm not sure about RasMol 2.7. Maffett spent a lot of time making movements in Chime be relatively independent of the hardware computer speed. In RasMol 2.6, there is no way to do that. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: ChimeShim "pbd" bug in Chime 2.6 SP4 Installer Date: Mon, 12 May 2003 17:10:55 -0400 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com There is a bug in the Chime 2.6 SP4 installer as follows. In Internet Explorer (but not Netscape) when trying to display a PDB file directly in Chime (e.g. http://www.umass.edu/microbio/chime/atp.pdb) you sometimes get this spurious file download dialog: File Download: File Name: atp.pbd [NOTE THE TYPO, SHOULD BE .pdb] File Type: ChimeShimLibrary Object (open or save?) Clicking Open fails to invoke Chime. The bug is the typographical error "pbd" instead of "pdb" in the Windows Registry, put there by the Chime installer. The Chime 2.6 SP3 installer does not insert the incorrect ".pbd" extension in the registry, so the bug seems to be new with SP4. This bug was reported on this email list by Robley Light on January 24, but none of the responses identified the problem in the registry. Robert Lancashire recently told me about the typo in the registry, and said that MDL is aware of the problem. Shortly after that, it happened on my computer for the first time, and I investigated further. I have seen the spurious ChimeShim message occur in Internet Explorer 6.0 in Win98 and Win2000, but not consistently, even on the same machine (different boots). So far I have no explanation for why it occurs sometimes and not others. I have seen the error in the registry on WinXP but in my limited tests, the spurious ChimeShim message did not occur (the ATP molecule loaded correctly). However, since it occurs inconsistently in Win98 and Win2000, it won't surprise me if it sometimes occurs on WinXP also. If you need to correct this problem, Start, Run, RegEdit. In the left panel of the Registry Editor, be sure to highlight the top entry, My Computer, so your search will start at the top. Searching the Registry for "pbd" (the wrong spelling) finds two instances. The first is the one that needs fixing. The second involves "MSPBDE40.DLL" which must not be changed. Specifically, the incorrect registry entry is under My Computer HKEY_CLASSES_ROOT MIME Database Content Type chemical/x-pdb Extension ".pbd" ["chemical/x-pdb" occurs 13 times in my registry. ".pdb" occurs close to 30 times.] To correct the incorrect Extension ".pbd": right click, Modify, change to ".pdb", and exit (careful! the registry is automatically saved when you change it in RegEdit). This appears to fix the problem. You don't have to reboot, but you have to close IE and re-open it for the registry change to take effect in IE. I also tried uninstalling Chime 2.6 SP4 (from both IE 6 and Netscape 4) on Windows 2000, and then installing Chime 2.6 SP3. This did not fix the problem. Instead, Chime 2.6 SP3 failed to work at all in IE 6 (but worked in Netscape 4). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: SYBYL on LINUX? Date: Wed, 14 May 2003 21:20:12 +0200 To: rasmol@lists.umass.edu The most recent issue of Biosilico magazine (www.drugdiscoverytoday.com) has an advertisement saying that Tripos Inc. (www.tripos.com) has made Sybil available on the Linux platform. I was curious how many people on this mailing list use Sybyl or have access to it via their respective institutions? Any feedback would be appreciated. Next, one of the reasons I mention Biosilico in terms of the question listed above is due to an article in this issue written by Brian Donnelly, "Data integration technologies: an unfulfilled revolution in the drug discovery process?" pp. 59-63 ... The plug for his own company on page 60 made me immediately think "infomercial", but as I read on much of what was said paralleled my own thoughts developing in the years since first hearing the term "bioinformatics" in 1998. Does Brian Donnelly know about this list? Does he subscribe? How much interaction is there between commercial software developers and those using the technology? The Verity House group comes to mind when I think about software manufacturers with both biomedical skills and programming skills under the same roof. Is there a distance between the "bio" and the "informatic" still? What level of cooperation do each of you see between your research/educational group and commercial software developers? Is there any central developmental organization concerning integration of services for the bioinformatics industry? I subscribe to an IBM software developer's list. I subscribe to databank and cluster-server tech lists. I get info regularly from Cisco, Sun Microsystems, etc. I cannot do more than just dip my finger in any particular pie, because I am a hardware specialist that just happened to get a medical core curriculum in a program that was cancelled about the time I finished the bachelor's level prerequisites. My interest in computer hardware drove my interest in other disciplines because one needs to have a finger on the pulse of various industries in order to anticipate the next shift in hardwar demands. While this reader list is focused on a particular software, I find so many different issues being brought up concerning how to do this, or that, as to feel that most persons on this list would be interested in the Biosilico magazine and in software using open-code operating systems. If any of you know of a user list or shared-topic discussion group where these questions would be more appropriate, I would appreciate that information. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 19 May 2003 14:11:34.0700 (UTC) FILETIME=[8DFD3EC0:01C31E10] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Open-source chime project? Date: Mon, 19 May 2003 10:20:05 -0400 To: "rasmol@lists.umass.edu" With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:07:09 -0400 To: rasmol@lists.umass.edu hi Brian, Rob Lue at Harvard and I have initiated an ambitious project to create a modern mol vis authoring environment; we should have a demo ready by the end of this summer. it is not a browser plug-in, though it will be fully compatible with Chime. instead, our software tool will be a platform to develop mol vis animations and figures and combine them with other media types. it will provide a lot of mol vis tools, all based on sound scientific principles, but very little true modeling. OTOH, you will be able to import various types of media (2D and 3D) created in other software and merge everything into a single module. We thought a lot about making a plug-in "viewer" to go with it, ala the Flash model (stand-alone authoring tool, plug-in viewer). we decided against it for various reasons, opting instead to make our tool Internet-savvy on its own. of course, it is still pre-demo so YNK... ;-) anyway, our software will be free, open-source, and aimed primarily at educators. if you (or anyone) are interested in contributing, drop me a line. currently, we are especially interested in lining up mol vis users to provide feedback on our demo once it comes out. we plan to use the demo (and the accompanying tech specs) to apply for significant grant money to acutally build, distribute, and support the thing. anyone who wants to be part of this project, feel free to email me offlist and I can provide more details. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:13:59 -0400 (EDT) To: brian.white@umb.edu, rasmol@lists.umass.edu Dear Prof. White, I am all in favor of an open source Chime project, and, as the maintainer of RasMol, would be happy to collaborate in a funding proposal for such a project. It would be best if MDL were to release the source for this purpose, but if they will not do so, then the safest approach to avoid legal tangles is a "clean-room" project in which a person who has never used chime works from the RasMol source and a set of external specifications to produce the desired functionality. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Brian White wrote: > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_kFyeyPxHH9snEVJg946Cbg)" ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:23:06 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_kFyeyPxHH9snEVJg946Cbg) Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo. Malcolm On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote: > hi Brian, > > Rob Lue at Harvard and I have initiated an ambitious project to create > a > modern mol vis authoring environment; we should have a demo ready by > the end > of this summer. it is not a browser plug-in, though it will be fully > compatible with Chime. instead, our software tool will be a platform > to > develop mol vis animations and figures and combine them with other > media > types. it will provide a lot of mol vis tools, all based on sound > scientific > principles, but very little true modeling. OTOH, you will be able to > import > various types of media (2D and 3D) created in other software and merge > everything into a single module. > > We thought a lot about making a plug-in "viewer" to go with it, ala > the Flash > model (stand-alone authoring tool, plug-in viewer). we decided > against it for > various reasons, opting instead to make our tool Internet-savvy on its > own. > of course, it is still pre-demo so YNK... ;-) > > anyway, our software will be free, open-source, and aimed primarily at > educators. if you (or anyone) are interested in contributing, drop me > a line. > currently, we are especially interested in lining up mol vis users to > provide > feedback on our demo once it comes out. we plan to use the demo (and > the > accompanying tech specs) to apply for significant grant money to > acutally > build, distribute, and support the thing. > > anyone who wants to be part of this project, feel free to email me > offlist and > I can provide more details. > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: > >> With all this talk of 'no plans for an OS-X chime' and other platform >> issues, it seemes to me that what we _really_ need is an open-source >> chime. I don't know about the software or legal issues, but I'd be >> willing to look into grant funding posibilities - it seems like it >> would >> be very useful. Does anyone out there know whether this is possible >> or >> not? Has anyone tried? Is anyone interested in working with me to get >> the grant? >> >> Brian >> >> -- >> Prof. Brian White >> Biology Department >> University of Massachusetts, Boston >> 100 Morrissey Blvd >> Boston MA 02125 >> (617) 287-6630 >> fax:(617) 287-6650 >> brian.white@umb.edu >> http://intro.bio.umb.edu/BW/ >> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_kFyeyPxHH9snEVJg946Cbg) Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo. Malcolm On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote: hi Brian, Rob Lue at Harvard and I have initiated an ambitious project to create a modern mol vis authoring environment; we should have a demo ready by the end of this summer. it is not a browser plug-in, though it will be fully compatible with Chime. instead, our software tool will be a platform to develop mol vis animations and figures and combine them with other media types. it will provide a lot of mol vis tools, all based on sound scientific principles, but very little true modeling. OTOH, you will be able to import various types of media (2D and 3D) created in other software and merge everything into a single module. We thought a lot about making a plug-in "viewer" to go with it, ala the Flash model (stand-alone authoring tool, plug-in viewer). we decided against it for various reasons, opting instead to make our tool Internet-savvy on its own. of course, it is still pre-demo so YNK... ;-) anyway, our software will be free, open-source, and aimed primarily at educators. if you (or anyone) are interested in contributing, drop me a line. currently, we are especially interested in lining up mol vis users to provide feedback on our demo once it comes out. we plan to use the demo (and the accompanying tech specs) to apply for significant grant money to acutally build, distribute, and support the thing. anyone who wants to be part of this project, feel free to email me offlist and I can provide more details. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization < usa:north carolina:wake forest at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ Helvetica ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_kFyeyPxHH9snEVJg946Cbg)-- Importance: Normal References: <3EC8E810.1631FF46@umb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 17:27:38 +0200 (CEST) To: rasmol@lists.umass.edu Cc: brian.white@umb.edu, jmol-developers@lists.sourceforge.net Brian, The good news ------------- The newest version of Jmol (http://jmol.sourceforge.net) offers support for RasMol/Chime scripts in both the java application and the applet. I encourage all RasMol/Chime users to take a look at Jmol, tell us what you think, tell us where it falls short of your needs, and help us make it better. The bad news ------------ Jmol currently has performance problems with larger molecules ... like the protein molecules that most of you are probably interested in :( The Jmol rendering engine is currently unable to support isosurfaces, cartoons, ribbons, and other protein-visualization methods ... the kind of thing that most of you are probably interested in :( Detail ------ I only subscribed to this mailing list last week, so I am not familiar with a lot of the discussions which have gone on in the past. I am one of the contributing developers on the Jmol project, a java based open-source viewer based at http://jmol.sourceforge.net My plan was to make an announcement next week, but since you raised this question I felt I should respond a little earlier :) We are in the process of releasing Jmol v6, and will have the packaging done this week. I joined the Jmol project explicitly to write an open-source RasMol/Chime interpreter. I have worked on it for for the past 6 months, and believe that the interpreter engine is very solid. It now supports most RasMol/Chime scripting commands and atom expressions. Unfortunately, it *does* fall short in some important protein-specific areas. The rendering engine currently does not support intersecting shapes nor any protein-specific visualization shapes, like cartoons, ribbons, etc. However, some development prototyping has been done in this area. In addition, the core chemistry classes are quite heavy-weight and somewhat sluggish for larger molecules. More than 1K atoms and things start to slow down. The code is now ready for some 'real world' testing ... that is why I joined this mailing list :) So, if you have some scripts that work on smaller molecules, we would very much like to work with you. I would very much like for the readership to take a look at jmol (http://jmol.sourceforge.net), tell us what you think, tell us where it falls short of your needs, and help us make it better. Miguel > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > -------------------------------------------------- Miguel Howard miguel@howards.org c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:35:34 -0400 To: rasmol@lists.umass.edu a clarification on my last post: full compatibility with Chime means not only the command language, but also as mnay existing Chime resources as possible. this includes javascript-based buttons, interfaces, and the like. my goal is to have our software tool accept full web sites without a hiccup, if you want to incoporate them in a module. it was 11:07 am EDT on (Monday) 19 May 2003 when timothy driscoll said: >hi Brian, > >Rob Lue at Harvard and I have initiated an ambitious project to create >a modern mol vis authoring environment; we should have a demo ready by >the end of this summer. it is not a browser plug-in, though it will >be fully compatible with Chime. instead, our software tool will be a >platform to develop mol vis animations and figures and combine them >with other media types. it will provide a lot of mol vis tools, all >based on sound scientific principles, but very little true modeling. >OTOH, you will be able to import various types of media (2D and 3D) >created in other software and merge everything into a single module. > >We thought a lot about making a plug-in "viewer" to go with it, ala >the Flash model (stand-alone authoring tool, plug-in viewer). we >decided against it for various reasons, opting instead to make our >tool Internet-savvy on its own. of course, it is still pre-demo so >YNK... ;-) > >anyway, our software will be free, open-source, and aimed primarily at >educators. if you (or anyone) are interested in contributing, drop me >a line. currently, we are especially interested in lining up mol vis >users to provide feedback on our demo once it comes out. we plan to >use the demo (and the accompanying tech specs) to apply for >significant grant money to acutally build, distribute, and support the >thing. > >anyone who wants to be part of this project, feel free to email me >offlist and I can provide more details. > > >regards, > >:tim > >-- timothy driscoll molvisions - molecular graphics & visualization > usa:north carolina:wake forest > > > >at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: > >> With all this talk of 'no plans for an OS-X chime' and other >> platform issues, it seemes to me that what we _really_ need is an >> open-source chime. I don't know about the software or legal issues, >> but I'd be willing to look into grant funding posibilities - it >> seems like it would be very useful. Does anyone out there know >> whether this is possible or not? Has anyone tried? Is anyone >> interested in working with me to get the grant? >> >> Brian >> >> -- Prof. Brian White Biology Department University of Massachusetts, >> Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) >> 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ >> >> >> >> > >----------------------------------------------------------------rasmol >-+ > >To change your address, unsubscribe, view previous messages/history, >receive messages as weekly digests, or for any other information about >the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > >----------------------------------------------------------------rasmol >-- > > :tim - timothy driscoll molvisions molecular graphics and visualization ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:39:13 -0400 To: rasmol@lists.umass.edu in all deference to Rasmol, and to Roger Sayle, I have also been impressed with John Moreland's Java-based Molecular Biology Toolkit. I saw him demo a simple viewer app that took just a few lines of Java on top of his MBT core, and looked very promising. worth considering... it was 11:13 am EDT on (Monday) 19 May 2003 when Herbert J. Bernstein said: >Dear Prof. White, > > I am all in favor of an open source Chime project, and, as the >maintainer of RasMol, would be happy to collaborate in a funding proposal >for such a project. It would be best if MDL were to release the source >for this purpose, but if they will not do so, then the safest approach >to avoid legal tangles is a "clean-room" project in which a person >who has never used chime works from the RasMol source and a set of >external specifications to produce the desired functionality. > > Regards, > Herbert J. Bernstein >===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu >===================================================== > >On Mon, 19 May 2003, Brian White wrote: > >> With all this talk of 'no plans for an OS-X chime' and other platform >> issues, it seemes to me that what we _really_ need is an open-source >> chime. I don't know about the software or legal issues, but I'd be >> willing to look into grant funding posibilities - it seems like it would >> be very useful. Does anyone out there know whether this is possible or >> not? Has anyone tried? Is anyone interested in working with me to get >> the grant? >> >> Brian >> >> -- >> Prof. Brian White >> Biology Department >> University of Massachusetts, Boston >> 100 Morrissey Blvd >> Boston MA 02125 >> (617) 287-6630 >> fax:(617) 287-6650 >> brian.white@umb.edu >> http://intro.bio.umb.edu/BW/ >> >> >> >> > > > :tim - timothy driscoll molvisions molecular graphics and visualization ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 11:39:54 -0400 To: rasmol@lists.umass.edu it was 11:23 am EDT on (Monday) 19 May 2003 when A.Malcolm Campbell said: >Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can >get the drivers so your new program could project in stereo. > >Malcolm > :tim - timothy driscoll molvisions molecular graphics and visualization ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 boundary="Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ)" Thread-Topic: Open-source chime project? Thread-Index: AcMeGzY9VnrssKEeQvO3/ebbjeuhSAAAOPEw content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: David Cassinelli Subject: RE: Open-source chime project? Date: Mon, 19 May 2003 11:34:53 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ) James River Technical has a Passive Stereo 3D visualization system that Robert Lue at Harvard has seen personally. For more information go to www.jrti.com/vew Sorry about the commercial but this is a fantastic affordable solution perfect for education and research. David Cassinelli James River Technical 120 Quarry Dr Milford, MA 01757 508-381-6311 Office 508-667-3311 Cell 508-381-6981 Fax www.jrti.com -----Original Message----- Sent: Monday, May 19, 2003 11:23 AM From: A.Malcolm Campbell [mailto:macampbell@davidson.edu] Subject: Re: Open-source chime project? To: rasmol@lists.umass.edu Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo. Malcolm On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote: hi Brian, Rob Lue at Harvard and I have initiated an ambitious project to create a modern mol vis authoring environment; we should have a demo ready by the end of this summer. it is not a browser plug-in, though it will be fully compatible with Chime. instead, our software tool will be a platform to develop mol vis animations and figures and combine them with other media types. it will provide a lot of mol vis tools, all based on sound scientific principles, but very little true modeling. OTOH, you will be able to import various types of media (2D and 3D) created in other software and merge everything into a single module. We thought a lot about making a plug-in "viewer" to go with it, ala the Flash model (stand-alone authoring tool, plug-in viewer). we decided against it for various reasons, opting instead to make our tool Internet-savvy on its own. of course, it is still pre-demo so YNK... ;-) anyway, our software will be free, open-source, and aimed primarily at educators. if you (or anyone) are interested in contributing, drop me a line. currently, we are especially interested in lining up mol vis users to provide feedback on our demo once it comes out. we plan to use the demo (and the accompanying tech specs) to apply for significant grant money to acutally build, distribute, and support the thing. anyone who wants to be part of this project, feel free to email me offlist and I can provide more details. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 10:20 AM EDT on Monday, May 19, 2003 Brian White said: With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ)
James River Technical has a Passive Stereo 3D visualization system that Robert Lue at Harvard has seen personally.  For more information go to www.jrti.com/vew
Sorry about the commercial but this is a fantastic affordable solution perfect for education and research.
 

David Cassinelli
James River Technical
120 Quarry Dr
Milford, MA  01757

508-381-6311 Office
508-667-3311 Cell
508-381-6981 Fax
www.jrti.com

-----Original Message-----
From: A.Malcolm Campbell [mailto:macampbell@davidson.edu]
Sent: Monday, May 19, 2003 11:23 AM
To: rasmol@lists.umass.edu
Subject: Re: Open-source chime project?

Oh yeah, one other thing. CrystalEyes now works with OSX. I bet you can get the drivers so your new program could project in stereo.

Malcolm

On Monday, May 19, 2003, at 11:07 AM, timothy driscoll wrote:

hi Brian,

Rob Lue at Harvard and I have initiated an ambitious project to create a
modern mol vis authoring environment; we should have a demo ready by the end
of this summer. it is not a browser plug-in, though it will be fully
compatible with Chime. instead, our software tool will be a platform to
develop mol vis animations and figures and combine them with other media
types. it will provide a lot of mol vis tools, all based on sound scientific
principles, but very little true modeling. OTOH, you will be able to import
various types of media (2D and 3D) created in other software and merge
everything into a single module.

We thought a lot about making a plug-in "viewer" to go with it, ala the Flash
model (stand-alone authoring tool, plug-in viewer). we decided against it for
various reasons, opting instead to make our tool Internet-savvy on its own.
of course, it is still pre-demo so YNK... ;-)

anyway, our software will be free, open-source, and aimed primarily at
educators. if you (or anyone) are interested in contributing, drop me a line.
currently, we are especially interested in lining up mol vis users to provide
feedback on our demo once it comes out. we plan to use the demo (and the
accompanying tech specs) to apply for significant grant money to acutally
build, distribute, and support the thing.

anyone who wants to be part of this project, feel free to email me offlist and
I can provide more details.


regards,

:tim

--
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/>
usa:north carolina:wake forest



at 10:20 AM EDT on Monday, May 19, 2003 Brian White said:

With all this talk of 'no plans for an OS-X chime' and other platform
issues, it seemes to me that what we _really_ need is an open-source
chime. I don't know about the software or legal issues, but I'd be
willing to look into grant funding posibilities - it seems like it would
be very useful. Does anyone out there know whether this is possible or
not? Has anyone tried? Is anyone interested in working with me to get
the grant?

Brian

--
Prof. Brian White
Biology Department
University of Massachusetts, Boston
100 Morrissey Blvd
Boston MA 02125
(617) 287-6630
fax:(617) 287-6650
brian.white@umb.edu
http://intro.bio.umb.edu/BW/








________________________________________________________
A. Malcolm Campbell, Ph.D.
Associate Professor of Biology
Davidson College
Director of GCAT (www.bio.davidson.edu/GCAT)
Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org)

PO Box 7118 (US Mail)
209 Ridge Road (shipping)
Davidson College
Davidson, NC 28035
704-894-2692 (phone)
704-894-2512 (fax)
www.bio.davidson.edu/campbell
--Boundary_(ID_7r5ljpJUU1yq6PR0g+bUeQ)-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 13:18:48 -0300 To: rasmol@lists.umass.edu Hello, I'm glad because you bring forward a Open Source Chime project. Months ago, this subject received treatment. But, I think that "a Open Chime project" needs evolution like everything in the life. A hard work will be necesary to build a open source software "full compatible" with Chime. To walk a road we need to take a first step. Andrej Sali from Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University has developed the SkyMol plug-in, but it works only with Netscape 4.X under Linux (http://salilab.org/modview/news.shtml). A Open Source Chime software could be builded with other programming others language like tk/tcl, etc. Regards, timothy driscoll wrote: > a clarification on my last post: > > full compatibility with Chime means not only the command language, but also as > mnay existing Chime resources as possible. this includes javascript-based > buttons, interfaces, and the like. my goal is to have our software tool accept > full web sites without a hiccup, if you want to incoporate them in a module. > > Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 13:05:17 -0500 (CDT) To: rasmol@lists.umass.edu Hi, Has anybody officially contacted MDL regarding this? Or know how MDL actually stands on this (officially or unofficially)? I think that is best to directly include MDL in any discussions. Since Chime is currently a 'free' download then it would be nice to hear their side. Clearly based on the Rasmol situation there are numerous problems involved that need to be clarified. There are many forms of 'Open Source' that can be used that may not conflict with their commercial interests and intellectual property. The General Public License of GNU is probably not suitable but www.opensource.org lists a number of examples. (However it is NOT my right to determine the 'fate' of code that I didn't write.) As only a suggestion (I do have some understanding of what is involved), perhaps those who are creating 'Open Source' should try to see if they can combine their projects. Just my thoughts, Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_He60lACWscc7MOoxTIYt4A)" ++++------+------+------+------+------+------+------+------+------+------+ From: Barry E Rowe Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 22:22:37 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_He60lACWscc7MOoxTIYt4A) I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll see if we can find a programmer who would be interested. Is the source of chime public domain? barry On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it > would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_He60lACWscc7MOoxTIYt4A) I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll see if we can find a programmer who would be interested. Is the source of chime public domain? barry On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: With all this talk of 'no plans for an OS-X chime' and other platform issues, it seemes to me that what we _really_ need is an open-source chime. I don't know about the software or legal issues, but I'd be willing to look into grant funding posibilities - it seems like it would be very useful. Does anyone out there know whether this is possible or not? Has anyone tried? Is anyone interested in working with me to get the grant? Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lucida Grande "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_He60lACWscc7MOoxTIYt4A)-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 02:21:30 -0300 To: rasmol@lists.umass.edu Hi, When I think in Open Source Chime I think in a General Public License for Chime. It's my opinion. I believe that is the best way to make a educational software for any OS. Obviously, if MDL make not free the source code to scientific comunity, we will to need starting from zero using the RasMol algorithms and the Pluging Tutorial from Netscape or Mozilla web site. If anybody wants read about GNU Licenses: http://www.gnu.org/licenses/licenses.html Regards, southey@ux1.cso.uiuc.edu wrote: > Hi, > Has anybody officially contacted MDL regarding this? Or know how MDL > actually stands on this (officially or unofficially)? > > I think that is best to directly include MDL in any discussions. Since > Chime is currently a 'free' download then it would be nice to hear their > side. Clearly based on the Rasmol situation there are numerous problems > involved that need to be clarified. There are many forms of 'Open Source' > that can be used that may not conflict with their commercial interests and > intellectual property. The General Public License of GNU is probably not > suitable but www.opensource.org lists a number of examples. (However it is > NOT my right to determine the 'fate' of code that I didn't write.) > > As only a suggestion (I do have some understanding of what is involved), > perhaps those who are creating 'Open Source' should try to see if they can > combine their projects. > > Just my thoughts, > Bruce > > > -- Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Open-source chime project? Date: Mon, 19 May 2003 23:43:05 -0700 To: rasmol@lists.umass.edu I agree with you Bruce and I suggested some times ago in a private discussion that we should release the central part of RasMol code under the LGPL. But before all, it is important to give to RasMol all the means to be a project where everybody wants to contribute. In that regards, I am surprised that RasMol be still under an exotic license and not under the GPL. I think it is time for the contributors to take position so that we could move forward quickly. Personnally, I authorize the release of RasMol derivative works containing code contributed by myself under the GPL. Of course, all contributors must agree before any change can occur. Philippe Valadon ----- Original Message ----- Sent: Monday, May 19, 2003 11:05 AM From: Subject: Re: Open-source chime project? To: > Hi, > Has anybody officially contacted MDL regarding this? Or know how MDL > actually stands on this (officially or unofficially)? > > I think that is best to directly include MDL in any discussions. Since > Chime is currently a 'free' download then it would be nice to hear their > side. Clearly based on the Rasmol situation there are numerous problems > involved that need to be clarified. There are many forms of 'Open Source' > that can be used that may not conflict with their commercial interests and > intellectual property. The General Public License of GNU is probably not > suitable but www.opensource.org lists a number of examples. (However it is > NOT my right to determine the 'fate' of code that I didn't write.) > > As only a suggestion (I do have some understanding of what is involved), > perhaps those who are creating 'Open Source' should try to see if they can > combine their projects. > > Just my thoughts, > Bruce > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 11:30:07 +0200 To: rasmol@lists.umass.edu I still have not gotten any positive feedback concerning the issues discussed in Biosilico magazine. I would encourage all persons interested in projects such as this topic most recently being kicked around this user list avail themselves of this publication. For those of you who do not keep up with corporate structures, MDL is a subsidiary of Elsevier Science Company. Biosilico is a publication from the same source. Complaints concerning the nature of the Chime licensing, etc. turn into conversation on this list regularly suggesting alternative platforms. Want to tap into the motherload (?) or do as Mr. Bernstein, et al, suggest and find a virgin programmer in terms of the current software subjected to debate and thus capable of re-inventing the wheel without anyone claiming contamination from the MDL (etc.) world. It seems to me that is something akin to looking for the immaculate conception. I seem to recall that certain lower forms of like can accomplish this, but they don't make good programmers. The persons agreeing to take responsibility for the editorial board of Biosilico include Craig Vetter and a host of other high-profile specialists with the reputation of getting things done. A goldmine of contact information is available via this magazine. Two readers of this user-list responded privately to my last email query and neither commented on the magazine, so I assume that the readers of this list are quite busy - hence responding to something like my query is a low priority. Still leaves me wondering how many people found the time to go the the website and ask for a free copy of the journal. Of that number, who actually had the time to read an issue, and does the number of persons reading the material correspond to a smaller number actually understanding the implications of the material discussed? So why am I pushing this magazine so hard? There are issues to consider like establishing rules for processing before creation of the 3D generator, establishing rules for structural attachments based on chemistry/physics, etc. The basic information is the bear and not the actual programming. I can give you an analogy that I think is appropriate for the sort of responses I see in this group. This concerns MIDI files, which are a means of making musical information logical to a computer. While one person would think, "well yes, this is a no brainer", in terms of the process of evolving a solution for presenting a 3D representation of a molecule or a MIDI representation of J. S. Bach's Imprivisation #9, another person would not understand this sort of analytical process until a explanation like: "A MIDI file allows a computer to use a well defined functional set and parameters for the audible presentation of data related to instrument dynamics, timing, etc. allowing a very small input of data to be translated into audible output, which by comparison recording a directly digital expression of the analog when compared to MIDI information is a logarithmically multiplied output in terms of space occupied on the storage medium." Yet another person would need an explanation like: "I just finished encoding a 45 minute CD album in MIDI format. The program running the MIDI to audio output conversion fits on a 1.44MB floppy disk. 650MB of data corresponds to 74 minutes of audio in standard format as read by your audio CD player. The entire 45 minutes consisted of 343KB of data in MIDI format." At this point most people would want to know why the format used for consumer audio CD takes the space-hungry format it does. Then the brain kicks in... hmmm 45 minutes is 343kb in MIDI, perhaps my whole record collection could be put on one CD-ROM. Next synaptic burst would (hopefully) come up with the marketing nightmare of selling an entire musical collection on a single CD-ROM disk with the corresponding price compared to conventional formatting. ECONOMICS! Asleep yet? OK, back to contacts with persons who know what your up against in reinventing the wheel - as it would be a non-MDL wheel that everyone could take for a spin at the same time and would work on everything from the baby-buggy to the space shuttle. IF anyone is still with me, I suggest you look for a 3D programmer ala Duke Nuke-um or Wolfenstein. I can recall when these were freebie programs written when the biggest question was, programming's done - now can we make it run on a 286? Those same guys that pioneered the 3D gaming phenomenon are still out there. Are any of you guys reading this user list? If so, have you absolutely no idea what MDL was up to (wink, wink, nod) when they constructed the MDL Chime? We have an offer not unlike Uncle Sam when he says, "Join the Navy and see the world!" Now I have to do some real work. (Make lunch) Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 10:59:48 +0100 To: rasmol@lists.umass.edu I tried to get a free copy, but I don't know if my subscription will be accepted as I am a lowly phd student. I too am interested in developing open source systems for 'open science'. I feel like I am banging my head against a wall when I talk about integrated systems. My idea is based around an integrated database a la SRS (only better, as I have a better understanding of what data modeling in the biological domain really means). I have not found any comfort in the vast array of different licenses that different db's use, nor the willingness of the biological community to work together on standards for data integration. It is getting better, but the committee road is a hard one to walk. Can you post the relevant article in its entirety? Cheers, Dan. Lewis Edgel wrote: >I still have not gotten any positive feedback concerning the issues >discussed in Biosilico magazine. I would encourage all persons interested in >projects such as this topic most recently being kicked around this user list >avail themselves of this publication. For those of you who do not keep up >with corporate structures, MDL is a subsidiary of Elsevier Science Company. >Biosilico is a publication from the same source. Complaints concerning the >nature of the Chime licensing, etc. turn into conversation on this list >regularly suggesting alternative platforms. Want to tap into the motherload >(?) or do as Mr. Bernstein, et al, suggest and find a virgin programmer in >terms of the current software subjected to debate and thus capable of >re-inventing the wheel without anyone claiming contamination from the MDL >(etc.) world. It seems to me that is something akin to looking for the >immaculate conception. I seem to recall that certain lower forms of like can >accomplish this, but they don't make good programmers. > >The persons agreeing to take responsibility for the editorial board of >Biosilico include Craig Vetter and a host of other high-profile specialists >with the reputation of getting things done. A goldmine of contact >information is available via this magazine. Two readers of this user-list >responded privately to my last email query and neither commented on the >magazine, so I assume that the readers of this list are quite busy - hence >responding to something like my query is a low priority. Still leaves me >wondering how many people found the time to go the the website and ask for a >free copy of the journal. Of that number, who actually had the time to read >an issue, and does the number of persons reading the material correspond to >a smaller number actually understanding the implications of the material >discussed? > >So why am I pushing this magazine so hard? There are issues to consider like >establishing rules for processing before creation of the 3D generator, >establishing rules for structural attachments based on chemistry/physics, >etc. The basic information is the bear and not the actual programming. I can >give you an analogy that I think is appropriate for the sort of responses I >see in this group. This concerns MIDI files, which are a means of making >musical information logical to a computer. While one person would think, >"well yes, this is a no brainer", in terms of the process of evolving a >solution for presenting a 3D representation of a molecule or a MIDI >representation of J. S. Bach's Imprivisation #9, another person would not >understand this sort of analytical process until a explanation like: "A MIDI >file allows a computer to use a well defined functional set and parameters >for the audible presentation of data related to instrument dynamics, timing, >etc. allowing a very small input of data to be translated into audible >output, which by comparison recording a directly digital expression of the >analog when compared to MIDI information is a logarithmically multiplied >output in terms of space occupied on the storage medium." > >Yet another person would need an explanation like: "I just finished encoding >a 45 minute CD album in MIDI format. The program running the MIDI to audio >output conversion fits on a 1.44MB floppy disk. 650MB of data corresponds to >74 minutes of audio in standard format as read by your audio CD player. The >entire 45 minutes consisted of 343KB of data in MIDI format." At this point >most people would want to know why the format used for consumer audio CD >takes the space-hungry format it does. Then the brain kicks in... hmmm 45 >minutes is 343kb in MIDI, perhaps my whole record collection could be put on >one CD-ROM. Next synaptic burst would (hopefully) come up with the marketing >nightmare of selling an entire musical collection on a single CD-ROM disk >with the corresponding price compared to conventional formatting. ECONOMICS! > >Asleep yet? OK, back to contacts with persons who know what your up against >in reinventing the wheel - as it would be a non-MDL wheel that everyone >could take for a spin at the same time and would work on everything from the >baby-buggy to the space shuttle. IF anyone is still with me, I suggest you >look for a 3D programmer ala Duke Nuke-um or Wolfenstein. I can recall when >these were freebie programs written when the biggest question was, >programming's done - now can we make it run on a 286? Those same guys that >pioneered the 3D gaming phenomenon are still out there. Are any of you guys >reading this user list? If so, have you absolutely no idea what MDL was up >to (wink, wink, nod) when they constructed the MDL Chime? We have an offer >not unlike Uncle Sam when he says, "Join the Navy and see the world!" > >Now I have to do some real work. (Make lunch) > >Lewis Edgel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Thread-Topic: MDL/Biosilico/open source solutions for 3D molecular visualization Thread-Index: AcMes0Xo9kjDlyNsT1OF2Ui6ToVq1gAEpLvg content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Robin Forder Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 12:51:49 +0100 To: rasmol@lists.umass.edu Dear Lewis Edgel, Re. the motherload (?): motherlode, probably. >From Robin Forder. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Jmol offers RasMol/Chime scripting Date: Tue, 20 May 2003 13:53:32 +0200 (CEST) To: rasmol@lists.umass.edu Cc: egonw@sci.kun.nl Forwarded to this mailing list on behalf of egonw@sci.kun.nl > The good news > ------------- > The newest version of Jmol (http://jmol.sourceforge.net) offers support > for RasMol/Chime scripts in both the java application and the applet. I > encourage all RasMol/Chime users to take a look at Jmol, tell us what you > think, tell us where it falls short of your needs, and help us make it > better. I would like to add this to it: More good news ------------- Jmol works on all browsers going back and including IE5.0 and Netscape4.5 on a number of platforms, including several GNU/Linux, Windows95/98, and SunOS. In addition, the Jmol applet does not require anythings else than a Java plugin, i.e. no Java3D required. kind regards, Egon Willighagen jmol.sf.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id h4L47Fj27492 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 09:11:02 -0400 (EDT) To: rasmol@lists.umass.edu Cc: brian.white@umb.edu, jmol-developers@lists.sourceforge.net Jmol is a very nice program and the feature/performance issues for macromolecules can be solved. While applets are not a perfect solution, they now cause far less grief in multi-platform porting than do plug-ins. I am all in favor achieving full RasMol functionality and better in a java environment. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Miguel wrote: > Brian, > > The good news > ------------- > The newest version of Jmol (http://jmol.sourceforge.net) offers support > for RasMol/Chime scripts in both the java application and the applet. I > encourage all RasMol/Chime users to take a look at Jmol, tell us what you > think, tell us where it falls short of your needs, and help us make it > better. > > > The bad news > ------------ > Jmol currently has performance problems with larger molecules ... like the > protein molecules that most of you are probably interested in :( > The Jmol rendering engine is currently unable to support isosurfaces, > cartoons, ribbons, and other protein-visualization methods ... the kind of > thing that most of you are probably interested in :( > > > Detail > ------ > I only subscribed to this mailing list last week, so I am not familiar > with a lot of the discussions which have gone on in the past. > > I am one of the contributing developers on the Jmol project, a java based > open-source viewer based at http://jmol.sourceforge.net > > My plan was to make an announcement next week, but since you raised this > question I felt I should respond a little earlier :) > > We are in the process of releasing Jmol v6, and will have the packaging > done this week. > > I joined the Jmol project explicitly to write an open-source RasMol/Chime > interpreter. I have worked on it for for the past 6 months, and believe > that the interpreter engine is very solid. It now supports most > RasMol/Chime scripting commands and atom expressions. > > Unfortunately, it *does* fall short in some important protein-specific areas. > > The rendering engine currently does not support intersecting shapes nor > any protein-specific visualization shapes, like cartoons, ribbons, etc. > However, some development prototyping has been done in this area. > > In addition, the core chemistry classes are quite heavy-weight and > somewhat sluggish for larger molecules. More than 1K atoms and things > start to slow down. > > The code is now ready for some 'real world' testing ... that is why I > joined this mailing list :) > > So, if you have some scripts that work on smaller molecules, we would very > much like to work with you. > > I would very much like for the readership to take a look at jmol > (http://jmol.sourceforge.net), tell us what you think, tell us where it > falls short of your needs, and help us make it better. > > Miguel > > > With all this talk of 'no plans for an OS-X chime' and other platform > > issues, it seemes to me that what we _really_ need is an open-source > > chime. I don't know about the software or legal issues, but I'd be > > willing to look into grant funding posibilities - it seems like it would > > be very useful. Does anyone out there know whether this is possible or > > not? Has anyone tried? Is anyone interested in working with me to get > > the grant? > > > > Brian > > > > -- > > Prof. Brian White > > Biology Department > > University of Massachusetts, Boston > > 100 Morrissey Blvd > > Boston MA 02125 > > (617) 287-6630 > > fax:(617) 287-6650 > > brian.white@umb.edu > > http://intro.bio.umb.edu/BW/ > > > > > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 08:22:55 -0400 (EDT) To: rasmol@lists.umass.edu With respect to licenses: The current RasMol license is GPL-like (not LGPL-like). A future version of RasMol _will_ be released under the the GPL. We have approval from Richard Stallman in our handling of the conflict between using the GPL and dealing with code that involves software patents. However, in order to prevent a repeat of the problems with Chime (which is a closed-source derivative of RasMol), please note that the current license and the GPL are infectious. All code derived from RasMol is and will be covered by the same infectious open-source license. Some people feel that this inhibits commercial development, and hope for some sort of license that will allow then to develop a closed-source derivative of RasMol. I disagree. You are free to develop commercial open-source derivatives of RasMol. Doing science with closed-source software leaves its users with a serious gap in their understanding of how they have obtained their results, making closed-source software of questionable value for scientific applications. For those who are interested in statistics, please note that RasMol enjoys a steady stream of downloads of the latest releases of RasMol (i.e. RasWin, RasMac and Rasmol) -- more than 1000 a week from the primary site alone. The current license does not seem to be inhibiting the widespread use of RasMol. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Philippe wrote: > I agree with you Bruce and I suggested some times ago in a private > discussion that we should release the central part of RasMol code under the > LGPL. But before all, it is important to give to RasMol all the means to be > a project where everybody wants to contribute. In that regards, I am > surprised that RasMol be still under an exotic license and not under the > GPL. I think it is time for the contributors to take position so that we > could move forward quickly. Personnally, I authorize the release of RasMol > derivative works containing code contributed by myself under the GPL. Of > course, all contributors must agree before any change can occur. > > Philippe Valadon > > > ----- Original Message ----- > From: > To: > Sent: Monday, May 19, 2003 11:05 AM > Subject: Re: Open-source chime project? > > > > Hi, > > Has anybody officially contacted MDL regarding this? Or know how MDL > > actually stands on this (officially or unofficially)? > > > > I think that is best to directly include MDL in any discussions. Since > > Chime is currently a 'free' download then it would be nice to hear their > > side. Clearly based on the Rasmol situation there are numerous problems > > involved that need to be clarified. There are many forms of 'Open Source' > > that can be used that may not conflict with their commercial interests and > > intellectual property. The General Public License of GNU is probably not > > suitable but www.opensource.org lists a number of examples. (However it is > > NOT my right to determine the 'fate' of code that I didn't write.) > > > > As only a suggestion (I do have some understanding of what is involved), > > perhaps those who are creating 'Open Source' should try to see if they can > > combine their projects. > > > > Just my thoughts, > > Bruce > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 20 May 2003 15:09:27.0164 (UTC) FILETIME=[CE26F3C0:01C31EE1] References: <4E92C217-8A72-11D7-A7B4-000502931696@mac.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Re: Open-source chime project? Date: Tue, 20 May 2003 11:18:10 -0400 To: rasmol@lists.umass.edu Barry - No, it is not public domain - RasMol is. Many people have responded with various info on the legal issues. I need to contact MDL to see what 's up. I'll be in touch if it looks like I can work something out. Brian Barry E Rowe wrote: > I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll see if we can find a programmer who would be interested. > > Is the source of chime public domain? > > barry > On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: > > With all this talk of 'no plans for an OS-X chime' and other platform > issues, it seemes to me that what we _really_ need is an open-source > chime. I don't know about the software or legal issues, but I'd be > willing to look into grant funding posibilities - it seems like it would > be very useful. Does anyone out there know whether this is possible or > not? Has anyone tried? Is anyone interested in working with me to get > the grant? > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > Barry Rowe O- farquasi@mac.com > Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team > > "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." > Nobel Peace Prize Laureate Jimmy Carter -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Tue, 20 May 2003 23:39:38 +0200 To: rasmol@lists.umass.edu Perhaps I could have been more succinct in offering my viewpoint. MDL is not the devil incarnate. When others have tried to replicate the MDL product the results have been rather inferior in comparison. While people talk of funding a "me-too" product, I think it would be better to raise money and fund MDL to produce the various flavours of Chime, etc. meeting user's needs. The MDL product is a mature technology. MY earlier reference to MIDI relates to an industry-wide concensus about how to proceed with digital music processes and based on this agreed framework standardization became possible. One has to decide - Am I, and my coworkers the end-user (consumer)? The end-user for commercial music products do not get the same quality of product as a person with sufficient training to access a more "geek-chic" product. An industry needs to have a certifying body. That body assumes responsibility for standardization for the benefit of all members in the industry. MDL Chime has been the de facto standard for many years for educational 3D molecular representation AND that product is free of charge. Dissatisfaction with that product should not result in conversation to replace the MDL product until it is clear that a progressive relationship with the patent-holder for this de facto product cannot be developed. If funding can be arranged, I think those funds would get the most "bang for the buck" in the hands of MDL. Biosilico magazine can be a platform for informed discussion in the subject of standardization within the industry. Biosilico is free at this point. Elsevier is in the business of making money, so if you can put two and two together, you get: MDL + Biosilico = moving toward standardization within an industry. It might not be too hard to understand YOUR benefits from taking part in the standardization process. I use Free/OpenBSD for a lot of things. These UNIX type operating systems have been around for a long long time. Myriad free programs are available to run on this OS. Still, people insist on spending money when free alternatives have been in place since the infancy of computer science. Why? Imagine this scenario: You have a problem with the free lunch I just gave you. Perhaps, the meat was cooked too little or too much for your liking. Compare that to a lunch you paid good money for - dissatisfaction can be remedied via the legal process. I say where the issue is: MDL or not to MDL - I say the money is better spent continuing the MDL relationship and providing concerted maintenance-funding for this mature technology. I apologise to anyone who could not follow my obtuse opinions as presented in the previous message to the Chime/Rasmol user-group list Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: rasmol@lists.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: Open-source chime project? Date: Wed, 21 May 2003 10:33:03 +0200 To: rasmol@lists.umass.edu Cc: jmol-developers@lists.sourceforge.net I agree with Mr. Bersteins comments concerning Java applets' future role in providing a solution to Internet-based problems when an educator wishes to place a 3D generator inside an HTML application. I tried several different applets over the years and as standardization in web-browsers' interpretation of the java code came into being - so also came JS as an effective solution. I also think that careful consideration of the form licensing takes in any project as being currently suggested is a very important topic. Comparison between the MDL approach to an Internet based interface and Rasmol's does provide one with some insight into the future one can expect if there is a divergence between the technologies. I wonder how compatible is a product specifically written for Rasmol when it is placed in the Chime environment? As I understand it there are just minor timing issues that come up. As I understand some of the past comments in this user's group discussion, several people began documenting problems related to cross-platform compatibility issues, etc. It might be a good idea for a central collection site for all pertinent information on the subject to be established, before the project feasibility study is begun. A third point Mr. Bernstein made concerns the problems arising when a macromolecule is attempted in Jmol. Has anyone tried consecutively more complex molecules in the Jmol environment with the intent of forming a body of information that can be used to categorize the relationship between molecule complexity and the problems in manipulating such inside the Jmol environment? Such a project would go far in allowing one to suggest solutions to that problem. I found from personal use, that JS is great for "passing off" information to another programming body and then returning the completed product back to the HTML-GUI. It sometimes happens that JS consumes too much time in internal processes and that results in some timing problems. My gut-feeling is that might be a structural limitation in JS, but I am far from an authority on any programming subject. Most of what I know of programming is a result of being the poor slob that is stuck with the task of proving that an issue is NOT a hardware problem. What I know of programming is an evolution of the need to route problems to those who could provide a solution. Too many times I had software problems sent to me because the end-user had experienced past problems that WERE hardware related and based on the user's level of expertise the new problem had the same characteristics. Other than that, my experience with programming is "hobby-class". A close friend was working on a project that required a flexible transfer medium. He found that the "C" programming language was best for certain parts of his project while Fortran accomplished a solution to other parts of the problem fastest. His nightmare arose when he reached a point where he needed to integrate the various functions. He had to shelve the project for a time. When JS finally was sorted out, he was able to construct the interface required to pass information back and forth within the prescribed time limits. My conclusion is that if it becomes a concensus that MDL cannot respond to user needs, the most viable solution in terms of cross-platform compatibility is the use of Java scripting. I still think at this point that offering to fund MDL to develop more flexible and user friendly products ala Chime is the most reasonable because it is already here, and already effective. Oh, and thanks to Robin Forder for pointing out my spelling error... I got a good laugh out of that! My wife would say I had made a Freudian slip as she often views my commentary as being a "load". I hope this message to which he (or she) refers was not viewed by the majority of readers as being the "mother of all loads." (grin) Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Herbert J. Bernstein Sent: Tuesday, May 20, 2003 3:11 PM From: owner-rasmol@lists.umass.edu Subject: Re: Open-source chime project? To: rasmol@lists.umass.edu Cc: brian.white@umb.edu; jmol-developers@lists.sourceforge.net Jmol is a very nice program and the feature/performance issues for macromolecules can be solved. While applets are not a perfect solution, they now cause far less grief in multi-platform porting than do plug-ins. I am all in favor achieving full RasMol functionality and better in a java environment. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 19 May 2003, Miguel wrote: > Brian, > > The good news > ------------- > The newest version of Jmol (http://jmol.sourceforge.net) offers support > for RasMol/Chime scripts in both the java application and the applet. I > encourage all RasMol/Chime users to take a look at Jmol, tell us what you > think, tell us where it falls short of your needs, and help us make it > better. > > > The bad news > ------------ > Jmol currently has performance problems with larger molecules ... like the > protein molecules that most of you are probably interested in :( > The Jmol rendering engine is currently unable to support isosurfaces, > cartoons, ribbons, and other protein-visualization methods ... the kind of > thing that most of you are probably interested in :( > > > Detail > ------ > I only subscribed to this mailing list last week, so I am not familiar > with a lot of the discussions which have gone on in the past. > > I am one of the contributing developers on the Jmol project, a java based > open-source viewer based at http://jmol.sourceforge.net > > My plan was to make an announcement next week, but since you raised this > question I felt I should respond a little earlier :) > > We are in the process of releasing Jmol v6, and will have the packaging > done this week. > > I joined the Jmol project explicitly to write an open-source RasMol/Chime > interpreter. I have worked on it for for the past 6 months, and believe > that the interpreter engine is very solid. It now supports most > RasMol/Chime scripting commands and atom expressions. > > Unfortunately, it *does* fall short in some important protein-specific areas. > > The rendering engine currently does not support intersecting shapes nor > any protein-specific visualization shapes, like cartoons, ribbons, etc. > However, some development prototyping has been done in this area. > > In addition, the core chemistry classes are quite heavy-weight and > somewhat sluggish for larger molecules. More than 1K atoms and things > start to slow down. > > The code is now ready for some 'real world' testing ... that is why I > joined this mailing list :) > > So, if you have some scripts that work on smaller molecules, we would very > much like to work with you. > > I would very much like for the readership to take a look at jmol > (http://jmol.sourceforge.net), tell us what you think, tell us where it > falls short of your needs, and help us make it better. > > Miguel > > > With all this talk of 'no plans for an OS-X chime' and other platform > > issues, it seemes to me that what we _really_ need is an open-source > > chime. I don't know about the software or legal issues, but I'd be > > willing to look into grant funding posibilities - it seems like it would > > be very useful. Does anyone out there know whether this is possible or > > not? Has anyone tried? Is anyone interested in working with me to get > > the grant? > > > > Brian > > > > -- > > Prof. Brian White > > Biology Department > > University of Massachusetts, Boston > > 100 Morrissey Blvd > > Boston MA 02125 > > (617) 287-6630 > > fax:(617) 287-6650 > > brian.white@umb.edu > > http://intro.bio.umb.edu/BW/ > > > > > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Wed, 21 May 2003 06:31:49 -0400 To: rasmol@lists.umass.edu hi Lewis, thanks for your comments. may I suggest that you post the link to biosilico again? some of us (esp new subscribers) may not have your earlier message. at 11:39 PM EDT on Tuesday, May 20, 2003 Lewis Edgel said: > Perhaps I could have been more succinct in offering my viewpoint. MDL is not > the devil incarnate. When others have tried to replicate the MDL product the > results have been rather inferior in comparison. While people talk of > funding a "me-too" product, I think it would be better to raise money and > fund MDL to produce the various flavours of Chime, etc. meeting user's > needs. The MDL product is a mature technology. > the free version of Chime is not a mature product at all, just underdeveloped and undersupported. look around the video game industry and see the possibilities for 3D molecular visualization. also check out "mainstream" 3D modelers like Amapi 3D, Maya, 3ds max, etc. Director now has a 3D component, too, although I have never seen it in action. MDL has its own agenda regarding Chime development. it is wonderful when this runs in conjunction with (or at least does not oppose) the needs of the educational community. it sucks when the two apparently diverge. we are not MDL's user base. this does not make them the devil incarnate. (I am allowed to complain loudly about them, however, since this is an open forum.) > MY earlier reference to MIDI relates to an industry-wide concensus about how > to proceed with digital music processes and based on this agreed framework > standardization became possible. One has to decide - Am I, and my coworkers > the end-user (consumer)? The end-user for commercial music products do not > get the same quality of product as a person with sufficient training to > access a more "geek-chic" product. An industry needs to have a certifying > body. That body assumes responsibility for standardization for the benefit > of all members in the industry. > are you suggesting that MDL be a certifying body for mol vis? certainly the Protein Data Bank does most, if not all, of that work now, and is in a better position to handle it. in any case, there are standards already in place, and being refined. isn't pdb is a standard file format? your ref to MIDI is apt. it may reflect a consensus, but it is certainly not the only type of music file in widespread use. and it does not include a definition of what software to use, or who can develop that software. you may prefer Media Player or Real Audio; I like iTunes. no standardization body should tell either of us to use a specific software product. > MDL Chime has been the de facto standard for many years for educational 3D > molecular representation AND that product is free of charge. Dissatisfaction > with that product should not result in conversation to replace the MDL > product until it is clear that a progressive relationship with the > patent-holder for this de facto product cannot be developed. If funding can > be arranged, I think those funds would get the most "bang for the buck" in > the hands of MDL. > there have been many efforts to develop a "public" relationship between MDL and the edu mol vis community. I have not seen any positive results. there has always been some level of behind-the-scenes communication with individual programmers at MDL, but my general impression is that the entity that is MDL has no official policy of supporting Chime development for emv. and frankly, I doubt we could gather enough funding to divert MDL from its customer base even if we wanted to. I can't see that grant proposal sailing through the NSF ;-) as far as complaining about Chime, well, if my healthcare is free, but they're still using leeches, don't I have a right to speak up? I think the dissatisfaction is not with Chime per se, but rather with the lack of development, support, and open communication about it from MDL - again, from the perspective of the emv community. at least, that is my complaint. others may differ. > Biosilico magazine can be a platform for informed discussion in the subject > of standardization within the industry. Biosilico is free at this point. > Elsevier is in the business of making money, so if you can put two and two > together, you get: MDL + Biosilico = moving toward standardization within an > industry. It might not be too hard to understand YOUR benefits from taking > part in the standardization process. > again, standardization of what? the software to use for mol vis? Elsevier, to be more specific, is in the business of making money by selling scientific materials (i.e., textbooks). so Elsevier + Chime + control over standards in mol vis = monopoly. > I use Free/OpenBSD for a lot of things. These UNIX type operating systems > have been around for a long long time. Myriad free programs are available to > run on this OS. Still, people insist on spending money when free > alternatives have been in place since the infancy of computer science. Why? > you have to ask? ease of use. comfort level. ease of use. advertising. ease of use. wider base of general programs. my mom likes it. it has a cool color. ease of use. etc. I could go out in my yard, catch a rabbit, clean it, cook it over an open fire, and eat it, but honestly - I'd rather pay a couple bucks and buy a hamburger. for one thing, I could spend the extra hours with my family, or working - and I'll make more money working those hours than I'll save by killing my own dinner. one of the wonderful aspects about computers is that I can find what I want, and you can find what you want. I use a lot of free software, and a lot of commercial stuff. it lets me tinker with things when I want, and not spend time trying to learn everything about everything just to use my computer. > Imagine this scenario: You have a problem with the free lunch I just gave > you. Perhaps, the meat was cooked too little or too much for your liking. > Compare that to a lunch you paid good money for - dissatisfaction can be > remedied via the legal process. I say where the issue is: MDL or not to > MDL - I say the money is better spent continuing the MDL relationship and > providing concerted maintenance-funding for this mature technology. I > apologise to anyone who could not follow my obtuse opinions as presented in > the previous message to the Chime/Rasmol user-group list > 1. the relationship between MDL and the emv is one-sided, publicly at least, and IMHO it has become a lodestone on progress in the field. 2. I am not aware of any successful precedent for suing a company because you paid for their software and didn't like it. 3. Chime is not mature; it is going in a direction that does not seem to coincide with needs of the emv community. the time has come to provide software designed for this audience, by institutions that respond directly to feedback from this user base. besides, a group of us already tried throwing money at MDL to fix a bug in Chime, and nothing came of it. ;-) politics is a nasty business. I appreciate your comments; please continue to contribute to the list, and repost the link to biosilico. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > > Lewis Edgel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Open-source chime project? Date: Wed, 21 May 2003 08:22:16 -0400 (EDT) To: rasmol@lists.umass.edu The RasMol 2.7 series is _not_ public domain, it is open source. There is an important difference -- you can make copies and base new programs on RasMol, but the copies you make and the programs you derive are also covered by the same license and are open source as well. This hopefully will keep us from ever getting into the difficulties we have now with MDL's derivative of RasMol ever again. There is an older version of RasMol which is in the public domain, but it is half a decade out of date. -- H. J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 20 May 2003, Brian White wrote: > Barry - > No, it is not public domain - RasMol is. Many people have responded > with various info on the legal issues. I need to contact MDL to see > what 's up. I'll be in touch if it looks like I can work something out. > > Brian > > Barry E Rowe wrote: > > > I'm interested. I am a consultant at NCSA in Champaign Urbana Il. I'll > > see if we can find a programmer who would be interested. > > > > Is the source of chime public domain? > > > > barry > > On Monday, May 19, 2003, at 09:20 AM, Brian White wrote: > > > > With all this talk of 'no plans for an OS-X chime' and other platform > > issues, it seemes to me that what we _really_ need is an open-source > > chime. I don't know about the software or legal issues, but I'd be > > willing to look into grant funding posibilities - it seems like it would > > be very useful. Does anyone out there know whether this is possible or > > not? Has anyone tried? Is anyone interested in working with me to get > > the grant? > > > > Brian > > > > -- > > Prof. Brian White > > Biology Department > > University of Massachusetts, Boston > > 100 Morrissey Blvd > > Boston MA 02125 > > (617) 287-6630 > > fax:(617) 287-6650 > > brian.white@umb.edu > > http://intro.bio.umb.edu/BW/ > > > > Barry Rowe O- farquasi@mac.com > > Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team > > > > "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." > > Nobel Peace Prize Laureate Jimmy Carter > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: computer virus warning Date: Wed, 21 May 2003 14:31:13 +0200 To: rasmol@lists.umass.edu I received an email to my in-box supposedly from support@microsoft.com having the subject "Approved (Ref: 38406-263)" With the body holding a statement: "All necessary information is contained in the attachment." The attachment was labeled "approved.pif". I checked the attachment characteristics to see if it had the proper author ID such as a legit file from Microsoft would have. It did not have this. I searched the "known virus" database and found it is a variant worm of the "W32/palyh". If you have received something like this and opened it, do a system search for files named "msccn32.exe", "hnks.ini", and "mdbrr.ini". If any of these are found, you have been infected with a computer virus that can potentially steal password and credit card information. As well, my firewall has been taking hits all day. (but that is normal...) Lucky me, I crushed the little worm before it could wiggle into my system (grin). I'm sending this message to everyone with addresses in my mailer. If such is not appreciated, I apologise in advance. I do not have time to prune my mailer tree at the moment. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RE: MDL/Biosilico/open source solutions for 3D molecular visualization Date: Wed, 21 May 2003 08:52:43 -0400 (EDT) To: rasmol@lists.umass.edu Actually, one could just as well claim that RasMol been the de facto "standard", of which Chime is just one of many variants. Fortunately for the progress of science there is no body which attempts to stifle the creativity of the community in exploring new and useful ways to approach molecular visualization, and there are many powerful and useful programs available. It is unfortunate that there are now problems for the potential users of Chime that MDL has not yet effectively addressed. There is no reason why we cannot have a robust competition of ideas, with MDL doing what they can to make Chime attractive to users and the open source proponents doing what they can to provide alternatives, whether creating something from scratch or making something based on RasMol, Jmol, or some other program. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 20 May 2003, Lewis Edgel wrote: > Perhaps I could have been more succinct in offering my viewpoint. MDL is not > the devil incarnate. When others have tried to replicate the MDL product the > results have been rather inferior in comparison. While people talk of > funding a "me-too" product, I think it would be better to raise money and > fund MDL to produce the various flavours of Chime, etc. meeting user's > needs. The MDL product is a mature technology. > > MY earlier reference to MIDI relates to an industry-wide concensus about how > to proceed with digital music processes and based on this agreed framework > standardization became possible. One has to decide - Am I, and my coworkers > the end-user (consumer)? The end-user for commercial music products do not > get the same quality of product as a person with sufficient training to > access a more "geek-chic" product. An industry needs to have a certifying > body. That body assumes responsibility for standardization for the benefit > of all members in the industry. > > MDL Chime has been the de facto standard for many years for educational 3D > molecular representation AND that product is free of charge. Dissatisfaction > with that product should not result in conversation to replace the MDL > product until it is clear that a progressive relationship with the > patent-holder for this de facto product cannot be developed. If funding can > be arranged, I think those funds would get the most "bang for the buck" in > the hands of MDL. > > Biosilico magazine can be a platform for informed discussion in the subject > of standardization within the industry. Biosilico is free at this point. > Elsevier is in the business of making money, so if you can put two and two > together, you get: MDL + Biosilico = moving toward standardization within an > industry. It might not be too hard to understand YOUR benefits from taking > part in the standardization process. > > I use Free/OpenBSD for a lot of things. These UNIX type operating systems > have been around for a long long time. Myriad free programs are available to > run on this OS. Still, people insist on spending money when free > alternatives have been in place since the infancy of computer science. Why? > > Imagine this scenario: You have a problem with the free lunch I just gave > you. Perhaps, the meat was cooked too little or too much for your liking. > Compare that to a lunch you paid good money for - dissatisfaction can be > remedied via the legal process. I say where the issue is: MDL or not to > MDL - I say the money is better spent continuing the MDL relationship and > providing concerted maintenance-funding for this mature technology. I > apologise to anyone who could not follow my obtuse opinions as presented in > the previous message to the Chime/Rasmol user-group list > > > Lewis Edgel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: On having choices.... (etc.) Date: Thu, 22 May 2003 10:11:44 +0200 To: rasmol@lists.umass.edu First, for those who might have missed the link for Biosilico, it is: www.drugdiscoverytoday.com (the last time I looked)... I cannot verify for today, as my direct link to the Internet is not available. On to next items for debate. Some time ago I endorsed the idea of using a java-scripted solution for 3D modeling internal to HTML because of the cross-platform functionality Java has to offer. People reading this list might wonder if I have "flip-flopped" in supporting the idea that funding be offered to MDL to continue the development of the Chime Internet-based interface. As Mr. Bernstein points out these options are not mutually exclusive. Just as competition in the natural world ensures robust species, so does populating every available niche in the world of technology produce a comparably healthy working environment for users of the technology. Again, Mr. Berstein has made clear the importance of formulating a policy dictating what may or may not be done with the charitable products variously called freeware, GNU, etc. I have not researched the matter, but as Mr. Bernstein infers - the change of status concerning Rasmol from public domain to such as it exists today, could well be directly related to the evolving relationship as seen in how Chime used the technology without seeming to endorse the spirit of sharing inherent in the milieu from which came Rasmol. When a public-domain product does not have a legally-binding statement of use dictating how that product may be adapted for other uses, etc., the result can be a limiting of the open-sharing of ideas. After looking at the evolution of the debate over some months, I began to see that the immediate solution to the problem of cross-platform compatibility was well on the way of being addressed. It was at this point that I began to see a parallel between the biological evolution in our natural world and that taking place in the world of computer-based technologies. Since so many of you are struggling with genomic research and need to look at myriad complex molecules, I began to think of this biological model in terms of computer science. The "standardization" of the DNA-RNA complex should be considered as a model for the standardization of the technology used to study the material of life itself. There is bound to be a lot of nonsense-code carried along as baggage while we move forward, but just as it was eventually possible to conclude that there are mandatory base-pairs for functionality - the binary code of computer science has achieved a wonderful complexity based on the number pair (0,1). I think the same ethical concerns debated when it became possible to consider that patent-right for genetic material could eventually evolve into the legal right to own a life form similar to a human-being. Most people would not question the right to ownership of a pet cat, or for a farmer to own a herd of cattle. The essential matter that I think concerned bio-ethics specialists was the possibility that if an open-forum for debate was not initiated a legal decision could be made that was short-sighted with implications that could limit public access to information of great personal concern to all. After all, regardless of one's religious-ethical ideals - the role of DNA is at the core of all known life. Corresponding to this is the very real and finite function of how elements interact with one another. When the variety of ways a carbon atom can interact with other elements has been reduced to a mathematical formula and thus rendered accessible to a computer, the person or persons doing the work deserve payment for their analytic skills. But this formula does, in a sense, become public domain because the research is directly tied to the natural world. Imagine Pythagoras being alive today and arriving at the conclusion of his theorem, picking up his phone and calling a patent-attorney. I do not think this matter of reaching a concensus concerning how the basic research allowing 3D visualization is to go forward and how this research is to be shared has been discussed sufficiently. User groups are very important, but the platform for debate is by nature limited. The good people at U.Mass kindly support this forum, but without industry-wide funding it would not be possible for the finite facilities housing this debate to serve as a clearinghouse for this sort of issue. Are bioinformatics professionals ready for an international symposium dedicated to discussing standards? How long after the invention of the automobile before the Society of Automotive Engineers was formed? How much longer after that was the SAE standard for nuts and bolts established? I think it is overdue for bioinformatics professionals to consider the "nuts and bolts" of their industry. When I endorse Biosilico, it is because of the sort of concerns discussed within the bounds of the journal - the use of the silicon chip for the study of biology. I am not endorsing putting the public debate under the control of a private corporation. The issue of funding is never far away for any researcher. I would have to say that a large proportion of at-home crisis in my household are the product of a demanding work schedule followed by at- home work trying to write a grant-proposal at the same time as the teenager thinks it appropriate to test the limits of the speaker system attached to the home stereo. Every time basic research is assigned a price tag, there is the constant concern that the price will limit the possibility of future research. (Not to mention the cost in frayed nerves and un-paid overtime!) I was glad to see how many people offered services and funding for the development of visualization software. Can we ask U.Mass to provide some hard-drive space for a separate forum where people separated by physical distance can have a place to unite in cyberspace? I tend to spiral out into outerspace when a birdseye view would be sufficient, so to return to a functional level: Having a separate forum would allow this user group to remain focused on the immediate issues related to Rasmol. (Not to mention allowing debate that is not mediated by a corporate body.) Well, the morning "fika" is over... Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: On having choices.... (etc.) Date: Thu, 22 May 2003 11:29:44 -0400 To: rasmol@lists.umass.edu it was 10:11 am EDT on (Thursday) 22 May 2003 when Lewis Edgel said: >First, for those who might have missed the link for Biosilico, it is: >www.drugdiscoverytoday.com (the last time I looked)... I cannot verify for >today, as my direct link to the Internet is not available. > yes, that link works. thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: On having more choices.... (etc.) Date: Thu, 22 May 2003 17:49:00 +0100 To: rasmol@lists.umass.edu Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? > I think it is overdue for bioinformatics >professionals to consider the "nuts and bolts" of their industry. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: SVG annual developer's meeting Date: Thu, 22 May 2003 20:20:01 +0200 To: rasmol@lists.umass.edu http://www.svgopen.org/2003/registration.html SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser Sent: Thursday, May 22, 2003 6:49 PM From: owner-rasmol@lists.umass.edu Subject: Re: On having more choices.... (etc.) To: rasmol@lists.umass.edu Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? > I think it is overdue for bioinformatics >professionals to consider the "nuts and bolts" of their industry. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg)" ++++------+------+------+------+------+------+------+------+------+------+ From: Barry E Rowe Subject: Re: SVG annual developer's meeting Date: Thu, 22 May 2003 14:25:24 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg) Will it run on a mac? In OSX? barry On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: > http://www.svgopen.org/2003/registration.html > > SVG developer's meeting in Vancouver, Canada from July 13th to 18th, > 2003. > > > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser > Sent: Thursday, May 22, 2003 6:49 PM > To: rasmol@lists.umass.edu > Subject: Re: On having more choices.... (etc.) > > > Just a quick question, > > Has anyone explored the possibility of using SVG > (Scalable Vector Graphics) to build a molecular viewer? > > I like the idea of SVG, being a standard dialect of XML, > images of molecules can easily be created by an apache > web server with access to relational PDB DB and an > appropriate XMLST. > > The beauty of such an image is that even though it is being > rendered by your browser in all the ways you might want > to render a molecule, it would also contain all the original > molecular data for you to save / analyse separatly. > > I have heard that the RDB PDB is well under way, and this > would seem like a natural extension to that project. > > Mozilla is developing an SVG viewer, as well as netscape > and several other java iniatives, so soon it should be widely > supported just like flash. > > The power of an XML 'flash like' language is that any well > organized DB (such as a DB of molecular motions) could > potentially be dumped using an appropriate XMLST to create > an image with standard navigation / display features. > > SVG is about as open as a format can get, so, any plans? > >> I think it is overdue for bioinformatics >> professionals to consider the "nuts and bolts" of their industry. >> > > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg) Will it run on a mac? In OSX? barry On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: http://www.svgopen.org/2003/registration.html SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. -----Original Message----- From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser Sent: Thursday, May 22, 2003 6:49 PM To: rasmol@lists.umass.edu Subject: Re: On having more choices.... (etc.) Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? I think it is overdue for bioinformatics professionals to consider the "nuts and bolts" of their industry. Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lucida Grande "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_SnWbiB4XnpWP6dCBLUN3Eg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 boundary="Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: SVG annual developer's meeting Date: Thu, 22 May 2003 22:00:26 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q) Go to http://www.w3.org/ and you will find most of the pertinent information concerning current and future plans for the world wide web (hence the name). Specific information is in the collumn to the left. Scroll down to SVG - one mouse click, and PRESTO! All the basic need to know info (such as compatibility issues). Lewis Edgel -----Original Message----- From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Barry E Rowe Sent: Thursday, May 22, 2003 9:25 PM To: rasmol@lists.umass.edu Subject: Re: SVG annual developer's meeting Will it run on a mac? In OSX? barry On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: http://www.svgopen.org/2003/registration.html SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. -----Original Message----- From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser Sent: Thursday, May 22, 2003 6:49 PM To: rasmol@lists.umass.edu Subject: Re: On having more choices.... (etc.) Just a quick question, Has anyone explored the possibility of using SVG (Scalable Vector Graphics) to build a molecular viewer? I like the idea of SVG, being a standard dialect of XML, images of molecules can easily be created by an apache web server with access to relational PDB DB and an appropriate XMLST. The beauty of such an image is that even though it is being rendered by your browser in all the ways you might want to render a molecule, it would also contain all the original molecular data for you to save / analyse separatly. I have heard that the RDB PDB is well under way, and this would seem like a natural extension to that project. Mozilla is developing an SVG viewer, as well as netscape and several other java iniatives, so soon it should be widely supported just like flash. The power of an XML 'flash like' language is that any well organized DB (such as a DB of molecular motions) could potentially be dumped using an appropriate XMLST to create an image with standard navigation / display features. SVG is about as open as a format can get, so, any plans? I think it is overdue for bioinformatics professionals to consider the "nuts and bolts" of their industry. Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team "War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children." Nobel Peace Prize Laureate Jimmy Carter --Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q)
Go to http://www.w3.org/ and you will find most of the pertinent information concerning current and future plans for the world wide web (hence the name). Specific information is in the collumn to the left. Scroll down to SVG - one mouse click, and PRESTO! All the basic need to know info (such as compatibility issues).
Lewis Edgel
-----Original Message-----
From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Barry E Rowe
Sent: Thursday, May 22, 2003 9:25 PM
To: rasmol@lists.umass.edu
Subject: Re: SVG annual developer's meeting

Will it run on a mac? In OSX?

barry
On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote:

http://www.svgopen.org/2003/registration.html

SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003.



-----Original Message-----
From: owner-rasmol@lists.umass.edu
[mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser
Sent: Thursday, May 22, 2003 6:49 PM
To: rasmol@lists.umass.edu
Subject: Re: On having more choices.... (etc.)


Just a quick question,

Has anyone explored the possibility of using SVG
(Scalable Vector Graphics) to build a molecular viewer?

I like the idea of SVG, being a standard dialect of XML,
images of molecules can easily be created by an apache
web server with access to relational PDB DB and an
appropriate XMLST.

The beauty of such an image is that even though it is being
rendered by your browser in all the ways you might want
to render a molecule, it would also contain all the original
molecular data for you to save / analyse separatly.

I have heard that the RDB PDB is well under way, and this
would seem like a natural extension to that project.

Mozilla is developing an SVG viewer, as well as netscape
and several other java iniatives, so soon it should be widely
supported just like flash.

The power of an XML 'flash like' language is that any well
organized DB (such as a DB of molecular motions) could
potentially be dumped using an appropriate XMLST to create
an image with standard navigation / display features.

SVG is about as open as a format can get, so, any plans?

I think it is overdue for bioinformatics
professionals to consider the "nuts and bolts" of their industry.







Barry Rowe O- farquasi@mac.com
Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team

"War may sometimes be a necessary evil, but no matter how necessary, it is always evil, never good. We will not learn how to live together in peace by killing each other's children."
Nobel Peace Prize Laureate Jimmy Carter
--Boundary_(ID_k2R4/mfpcBMxgPNFXfVS9Q)-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVZ9t9UYpsmNRT4cz8GDOobr9lOIF2xQny5fomf87a5ZCSzqjDWCUpZ0 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: SVG annual developer's meeting Date: Thu, 22 May 2003 16:51:42 -0400 To: rasmol@lists.umass.edu Yes. Yes. There may be others, but here is one implementation of an SVG viewer for the Mac. http://www.adobe.com:80/svg/svgOSX.html http://www.adobe.com:80/support/downloads/ product.jsp?product=46&platform=Macintosh Chris On Thursday, May 22, 2003, at 03:25 PM, Barry E Rowe wrote: > Will it run on a mac? In OSX? > > barry > On Thursday, May 22, 2003, at 01:20 PM, Lewis Edgel wrote: > >> http://www.svgopen.org/2003/registration.html >> >> SVG developer's meeting in Vancouver, Canada from July 13th to 18th, >> 2003. >> >> >> >> -----Original Message----- >> From: owner-rasmol@lists.umass.edu >> [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser >> Sent: Thursday, May 22, 2003 6:49 PM >> To: rasmol@lists.umass.edu >> Subject: Re: On having more choices.... (etc.) >> >> >> Just a quick question, >> >> Has anyone explored the possibility of using SVG >> (Scalable Vector Graphics) to build a molecular viewer? >> >> I like the idea of SVG, being a standard dialect of XML, >> images of molecules can easily be created by an apache >> web server with access to relational PDB DB and an >> appropriate XMLST. >> >> The beauty of such an image is that even though it is being >> rendered by your browser in all the ways you might want >> to render a molecule, it would also contain all the original >> molecular data for you to save / analyse separatly. >> >> I have heard that the RDB PDB is well under way, and this >> would seem like a natural extension to that project. >> >> Mozilla is developing an SVG viewer, as well as netscape >> and several other java iniatives, so soon it should be widely >> supported just like flash. >> >> The power of an XML 'flash like' language is that any well >> organized DB (such as a DB of molecular motions) could >> potentially be dumped using an appropriate XMLST to create >> an image with standard navigation / display features. >> >> SVG is about as open as a format can get, so, any plans? >> >>> I think it is overdue for bioinformatics >>> professionals to consider the "nuts and bolts" of their industry. >>> >> >> >> >> >> >> > Barry Rowe O- > farquasi@mac.com > Chemistry / Physics Teacher > http://roweba.com Champaign Centennial High > School NCSA ChemViz Team > > "War may sometimes be a necessary evil, but no matter how necessary, > it is always evil, never good. We will not learn how to live together > in peace by killing each other's children." > Nobel Peace Prize Laureate Jimmy Carter ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3ECCFF7C.6010902@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: SVG annual developer's meeting Date: Thu, 22 May 2003 22:32:02 +0100 (BST) To: rasmol@lists.umass.edu ;) Lewis Edgel said: > http://www.svgopen.org/2003/registration.html > > SVG developer's meeting in Vancouver, Canada from July 13th to 18th, 2003. > > > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Dan Bolser > Sent: Thursday, May 22, 2003 6:49 PM > To: rasmol@lists.umass.edu > Subject: Re: On having more choices.... (etc.) > > > Just a quick question, > > Has anyone explored the possibility of using SVG > (Scalable Vector Graphics) to build a molecular viewer? > > I like the idea of SVG, being a standard dialect of XML, > images of molecules can easily be created by an apache > web server with access to relational PDB DB and an > appropriate XMLST. > > The beauty of such an image is that even though it is being > rendered by your browser in all the ways you might want > to render a molecule, it would also contain all the original > molecular data for you to save / analyse separatly. > > I have heard that the RDB PDB is well under way, and this > would seem like a natural extension to that project. > > Mozilla is developing an SVG viewer, as well as netscape > and several other java iniatives, so soon it should be widely > supported just like flash. > > The power of an XML 'flash like' language is that any well > organized DB (such as a DB of molecular motions) could > potentially be dumped using an appropriate XMLST to create > an image with standard navigation / display features. > > SVG is about as open as a format can get, so, any plans? > >> I think it is overdue for bioinformatics >>professionals to consider the "nuts and bolts" of their industry. >> > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: pymol question Date: Fri, 23 May 2003 09:07:02 -0400 To: LIST rasmol hi folks, anyone out there using PyMOL? I want to zoom, which is normally right-click. but I am on a powerbook with only one mouse button. I can't figure out the correct syntax for zoom from the cmd line. any PyMOL gurus that can help? thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Re: pymol question Date: Fri, 23 May 2003 07:58:58 -0600 To: rasmol@lists.umass.edu Zoom is a move command along the z axis. A positive argument zooms in. move z, +10 move z, -4 Dave Fahrney Professor of Biochemistry timothy driscoll wrote: > > hi folks, > > anyone out there using PyMOL? I want to zoom, which is normally right-click. > but I am on a powerbook with only one mouse button. I can't figure out the > correct syntax for zoom from the cmd line. any PyMOL gurus that can help? > > thanks, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: pymol question Date: Fri, 23 May 2003 10:12:58 -0400 To: rasmol@lists.umass.edu at 7:58 AM EDT on Friday, May 23, 2003 David Fahrney said: > Zoom is a move command along the z axis. > A positive argument zooms in. > > move z, +10 > move z, -4 > > Dave Fahrney > Professor of Biochemistry > thanks Dave, and all offlist responders, too. (quick note - move in PyMOL is incremental and not absolute like Chime and RasMol.) :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > timothy driscoll wrote: > > > > hi folks, > > > > anyone out there using PyMOL? I want to zoom, which is normally > > right-click. but I am on a powerbook with only one mouse button. I > > can't figure out the correct syntax for zoom from the cmd line. any > > PyMOL gurus that can help? > > > > thanks, > > > > :tim > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew W. Maverick" Subject: Re: RASMOL digest 282 Date: Sun, 25 May 2003 14:54:37 +0200 To: rasmol@lists.umass.edu Dear Colleagues, I wasn't going to send this, but now that we've had one comment on "motherlode": We have been reminded once again that, like immaculate conception and virgin birth, open source and public domain are not the same thing. Andy Maverick Andrew W. Maverick Department of Chemistry Louisiana State University Baton Rouge LA 70803-1804 USA (225)LSU-4415 (578-4415) Fax: (225)LSU-3458 (578-3458) maverick@lsu.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: <5.1.0.14.2.20030525144938.00b23218@mail031.lsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: RASMOL digest 282 Date: Sun, 25 May 2003 13:50:54 -0300 To: rasmol@lists.umass.edu Hi, It is obvious, if you know the licenses. You earn money developing open source applications: you sell the program and you have to give the source. I believe that the development of a Open Chime software have to be Open Source and GPL. Regards, Andrew W. Maverick wrote: > Dear Colleagues, > I wasn't going to send this, but now that we've had one comment on > "motherlode": > We have been reminded once again that, like immaculate conception and > virgin birth, open source and public domain are not the same thing. > Andy Maverick > > Andrew W. Maverick > Department of Chemistry > Louisiana State University > Baton Rouge LA 70803-1804 > USA > (225)LSU-4415 (578-4415) > Fax: (225)LSU-3458 (578-3458) > maverick@lsu.edu > > > -- Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication X-Trace: UmFuZG9tSVYbpQVsYJKreCyUDsgjFxS4WnuhggcUK/52YdLUOst81tWOXNPsNLrk ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: pymol question Date: Sun, 25 May 2003 20:23:57 -0400 To: rasmol@lists.umass.edu Tim, Did someone point out that zoom is a "command+up/down mouse drag". Chris On Friday, May 23, 2003, at 10:12 AM, timothy driscoll wrote: > at 7:58 AM EDT on Friday, May 23, 2003 David Fahrney said: > >> Zoom is a move command along the z axis. >> A positive argument zooms in. >> >> move z, +10 >> move z, -4 >> >> Dave Fahrney >> Professor of Biochemistry >> > > thanks Dave, and all offlist responders, too. (quick note - move in > PyMOL is > incremental and not absolute like Chime and RasMol.) > > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > >> timothy driscoll wrote: >>> >>> hi folks, >>> >>> anyone out there using PyMOL? I want to zoom, which is normally >>> right-click. but I am on a powerbook with only one mouse button. I >>> can't figure out the correct syntax for zoom from the cmd line. any >>> PyMOL gurus that can help? >>> >>> thanks, >>> >>> :tim >>> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: select element in chime Date: Mon, 26 May 2003 09:07:37 -0400 To: LIST rasmol greetings, regarding selection by element in Chime, is select *.[element symbol] the most consistent syntax? because as far as I can tell, support for select [element name] and select [element symbol] is inconsistent, and these are the only three variations that I know. for example, I can "select carbon" but I can not "select magnesium" (I can, however, "select mg"). before I test the various flavors of select, I thought someone might know the answer already. thanks! :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- RASter display of MOLecular structure X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Re: Open-source chime project? Date: Mon, 26 May 2003 12:27:32 -0700 To: Brian White Cc: timothy driscoll , Hello Brian: Thank you for the discussion on developing an Open Source version of Chime. I tried to initiate interest in this topic at the GRC at Mt Hollyoke two years ago, with little success. In fact, I had proposed a mini-grant to investigate a combination Flash animation-Chime-like package. I don't think anyone at NSF knew what Flash was (or was capable of) at the time, so the proposal was turned down. ( See p. 7 of IEEE Multimedia, 2001: http://home.earthlink.net/~shalpine/gallery/CGA/halpine.pdf) Tim Driscoll and Rob Lue's software sound very similar to my initial proposal. Tim - as you know, I am very interested in the development of this type of software. Please keep me in the loop. Some solution is long overdue. Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 239 Sunridge Street Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair American Chemical Society, Southern California Section ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Originator-info: login-token=Mulberry:01WMHWp88uBhdqL14tn0IGBOshUdTj9U/FNgQMjkE=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: will mcclure Subject: Re: select element in chime Date: Mon, 26 May 2003 20:18:55 -0400 To: rasmol@lists.umass.edu Tim, 'select elemno=##' always works . . . but you may have to check a periodic table. 'symbol' works when the HETERO in the PDB file is defined that way (eg CA, MG, etc), but they often have other names (eg. MGO). -Will McClure --On Monday, May 26, 2003 9:07 AM -0400 timothy driscoll wrote: > greetings, > > regarding selection by element in Chime, is > > select *.[element symbol] > > the most consistent syntax? because as far as I can tell, support > for > > select [element name] > > and > > select [element symbol] > > is inconsistent, and these are the only three variations that I > know. for example, I can "select carbon" but I can not "select > magnesium" (I can, however, "select mg"). > > before I test the various flavors of select, I thought someone > might know the answer already. > > > thanks! > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------ras > mol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------ras > mol-- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: select element in chime Date: Mon, 26 May 2003 20:53:08 -0400 To: rasmol@lists.umass.edu at 8:18 PM EDT on Monday, May 26, 2003 will mcclure said: > Tim, > > 'select elemno=##' always works . . . but you may have to check a > periodic table. > > 'symbol' works when the HETERO in the PDB file is defined that way > (eg CA, MG, etc), but they often have other names (eg. MGO). > > -Will McClure > ah ha - forgot about elemno. thanks, Will! :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > --On Monday, May 26, 2003 9:07 AM -0400 timothy driscoll > wrote: > > > greetings, > > > > regarding selection by element in Chime, is > > > > select *.[element symbol] > > > > the most consistent syntax? because as far as I can tell, support > > for > > > > select [element name] > > > > and > > > > select [element symbol] > > > > is inconsistent, and these are the only three variations that I > > know. for example, I can "select carbon" but I can not "select > > magnesium" (I can, however, "select mg"). > > > > before I test the various flavors of select, I thought someone > > might know the answer already. > > > > > > thanks! > > > > :tim > > > > -- > > timothy driscoll > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > ----------------------------------------------------------------ras > > mol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ----------------------------------------------------------------ras > > mol-- > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3ECE0F9A.6080403@mrc-dunn.cam.ac.uk> <3ECFD8E2.3020207@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Strange format for PDB 1cm4 Date: Tue, 27 May 2003 11:53:07 +0100 To: info@rcsb.org Cc: Wan Kyu Kim , rasmol The following atom line section for 1cm4 looks a little wrong, having a stray atom from residue 293 of chain F in between the TER and HETATM lines of chain E. I always asumed that all the atoms for a residue should be sequential. Is this correct? Cheers, Dan. ATOM 3641 N THR E 146 31.312 61.978 75.234 0.25 36.30 N ATOM 3642 CA THR E 146 32.587 61.624 75.853 0.25 38.50 C ATOM 3643 C THR E 146 32.984 62.653 76.912 0.25 39.10 C ATOM 3644 O THR E 146 32.170 62.973 77.780 0.25 38.90 O ATOM 3645 CB THR E 146 33.768 61.528 74.820 0.25 39.70 C ATOM 3646 OG1 THR E 146 33.927 62.815 74.234 0.25 41.30 O ATOM 3647 CG2 THR E 146 33.545 60.456 73.753 0.25 39.30 C TER 3648 THR E 146 ATOM 3649 CB PHE F 293 11.275 70.102 78.942 0.25 40.50 C <---- ?? HETATM 3650 CA CA E 401 8.040 46.688 78.529 0.25 18.20 CA HETATM 3651 CA CA E 402 14.450 40.835 85.677 0.25 28.00 CA HETATM 3652 CA CA E 403 22.542 69.262 59.236 0.25130.40 CA HETATM 3653 CA CA E 404 28.059 73.861 66.193 0.25 7.60 CA ATOM 3654 N PHE F 293 10.703 69.598 81.261 0.25 40.10 N ATOM 3655 CA PHE F 293 11.610 69.258 80.181 0.25 38.30 C ATOM 3656 C PHE F 293 13.054 69.496 80.591 0.25 36.70 C ATOM 3657 O PHE F 293 13.390 70.501 81.221 0.25 38.80 O ATOM 3658 CG PHE F 293 12.212 69.884 77.755 0.25 42.50 C ATOM 3659 CD1 PHE F 293 12.147 68.699 77.016 0.25 42.80 C ATOM 3660 CD2 PHE F 293 13.154 70.866 77.422 0.25 42.80 C ATOM 3661 CE1 PHE F 293 13.023 68.500 75.948 0.25 42.80 C ATOM 3662 CE2 PHE F 293 14.026 70.657 76.355 0.25 43.40 C ATOM 3663 CZ PHE F 293 13.963 69.475 75.619 0.25 43.20 C ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.1 X-Spam-Status: No, hits=-104.5 required=5.8 tests=BAYES_10,DATE_IN_FUTURE_12_24,USER_AGENT_KMAIL, USER_IN_WHITELIST version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: saving in gif format Date: Wed, 28 May 2003 14:02:19 +0300 To: rasmol@lists.umass.edu Hello, Sorry, but I couldn't find anywere how to solve this problem: I have a linux version of Rasmol (on Redhat 7.3) that was compiled with 16 bit depth. When trying to save gif images, i get "Output Error: Only 8-bit GIF files supported!", When I try to run 8-bit version, on rasmol invoking I get: "No suitable display detected!" message So currently, I cannot use a single file for both viewing molecules and exporting images: for viewing I use rasmol (the 16 bit version), and for exporting I use "rasmol_8BIT -nodisplay". Is there any better way to perform these tasks? Thanks in advance Boris Gorelik ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <200305281402.19699.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: saving in gif format Date: Tue, 27 May 2003 16:42:04 +0200 (CEST) To: rasmol@lists.umass.edu Cc: bgbg@pob.huji.ac.il Boris, I don't have a lot of rasmol experience ... so this may not be the best answer ... but, I would save the images in a format that works. Then convert them to .gif if necessary. Or, you can do screen captures of the rasmol window using xwd. Then convert to whatever format you want. For image conversion on linux/unix systems go to www.imagemagick.org. On RedHat install from the imagemagick rpm. Miguel > Hello, > Sorry, but I couldn't find anywere how to solve this problem: > I have a linux version of Rasmol (on Redhat 7.3) that was compiled > with 16 bit depth. > When trying to save gif images, i get > "Output Error: Only 8-bit GIF files supported!", > When I try to run 8-bit version, on rasmol invoking I get: > "No suitable display detected!" message > So currently, I cannot use a single file for both viewing molecules and > exporting images: for viewing I use rasmol (the 16 bit version), and for > exporting I use "rasmol_8BIT -nodisplay". > > Is there any better way to perform these tasks? > > Thanks in advance > Boris Gorelik > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.1 X-Spam-Status: No, hits=-103.7 required=5.8 tests=BAYES_20,DATE_IN_FUTURE_12_24,EMAIL_ATTRIBUTION,IN_REP_TO, QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_KMAIL,USER_IN_WHITELIST version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) References: <200305281402.19699.bgbg@pob.huji.ac.il> <60335.80.58.16.170.1054046524.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: Re: saving in gif format Date: Wed, 28 May 2003 18:09:34 +0300 To: rasmol@lists.umass.edu On Tuesday 27 May 2003 17:42, Miguel wrote: > I would save the images in a format that works. Then convert them to .gif > if necessary. It appears that no export works with "non 8bit" versions. > > Or, you can do screen captures of the rasmol window using xwd. Then > convert to whatever format you want. This option won't be good for scripts etc, and in any case is harder than keeping 2 binaries > Thanks ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.1 X-Spam-Status: No, hits=-104.0 required=5.8 tests=AWL,BAYES_10,DATE_IN_FUTURE_12_24,EMAIL_ATTRIBUTION, USER_AGENT_KMAIL,USER_IN_WHITELIST version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: Fwd: Re: saving in gif format Date: Wed, 28 May 2003 20:28:20 +0300 To: rasmol@lists.umass.edu This solution works pretty well, except for some color distorsions. Thanks dr. Michael Sternberg for the tip ---------- Forwarded Message ---------- ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg Subject: Re: saving in gif format Date: Tue, 27 May 2003 13:20:41 -0500 To: Boris Gorelik Hello Boris, Due to issues with our mail server I cannot currently post to the list, so here's my suggestion, which you may pass on if you wish: On Wed, May 28, 2003 at 02:02:19PM +0300, Boris Gorelik wrote: > I have a linux version of Rasmol (on Redhat 7.3) that was compiled with > 16 bit depth. When trying to save gif images, i get > "Output Error: Only 8-bit GIF files supported!", > When I try to run 8-bit version, on rasmol invoking I get: > "No suitable display detected!" message If you wish to save directly what you see, you can save in ppm format from a 16-bit viewer and convert later: RasMol> write ppm foo.ppm RasMol> exit shell> ppmtogif foo.ppm > foo.gif shell> rm foo.ppm "ppmtogif" is part of the package netpbm-progs, which comes with RedHat. Pixmap images created this way are fine for certain things like web use. However, for print, they are far too low in resolution. I prefer to use postscript as intermediate format: RasMol> set vectps on RasMol> write vectps foo.ps RasMol> exit This ps output is suitable for printing directly, and can be converted to a pixmap for online use. Note, however, that only basic visualisation elements are supported for vectps output (ball & stick), which is just fine for solid state physics :-) Regards, -- Michael Sternberg, Ph.D.; Argonne National Laboratory; sternberg.at.anl.gov ------------------------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <3ECE0F9A.6080403@mrc-dunn.cam.ac.uk> <3ECFD8E2.3020207@mrc-dunn.cam.ac.uk> <3ED34393.9000509@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Strange format for PDB 1cm4 Date: Wed, 28 May 2003 10:00:38 +0200 To: rasmol@lists.umass.edu This is a strange pdb file, as it contains 9 chains separated by TERs (the last unnamed chain is that of waters). It is a four-in-one structure, four different representations of the same molecule in one. These should be be separated by MODELs, I don't why has the file been created such way. You should use an applications which can separately handle separately or browse the chains, (such as Mol2mol) and cut the parts you need. Best regards Tamas Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tamasgunda*AT*tigris.klte.hu ----- Original Message ----- Sent: Tuesday, May 27, 2003 12:53 PM From: "Dan Bolser" Subject: Strange format for PDB 1cm4 To: Cc: "Wan Kyu Kim" ; "rasmol" > The following atom line section for 1cm4 looks a little wrong, having a > stray atom from > residue 293 of chain F in between the TER and HETATM lines of chain E. > > I always asumed that all the atoms for a residue should be sequential. > Is this correct? > > Cheers, Dan. > > ATOM 3641 N THR E 146 31.312 61.978 75.234 0.25 > 36.30 N > ATOM 3642 CA THR E 146 32.587 61.624 75.853 0.25 > 38.50 C > ATOM 3643 C THR E 146 32.984 62.653 76.912 0.25 > 39.10 C > ATOM 3644 O THR E 146 32.170 62.973 77.780 0.25 > 38.90 O > ATOM 3645 CB THR E 146 33.768 61.528 74.820 0.25 > 39.70 C > ATOM 3646 OG1 THR E 146 33.927 62.815 74.234 0.25 > 41.30 O > ATOM 3647 CG2 THR E 146 33.545 60.456 73.753 0.25 > 39.30 C > TER 3648 THR E > 146 > ATOM 3649 CB PHE F 293 11.275 70.102 78.942 0.25 > 40.50 C <---- ?? > HETATM 3650 CA CA E 401 8.040 46.688 78.529 0.25 > 18.20 CA > HETATM 3651 CA CA E 402 14.450 40.835 85.677 0.25 > 28.00 CA > HETATM 3652 CA CA E 403 22.542 69.262 59.236 > 0.25130.40 CA > HETATM 3653 CA CA E 404 28.059 73.861 66.193 0.25 > 7.60 CA > ATOM 3654 N PHE F 293 10.703 69.598 81.261 0.25 > 40.10 N > ATOM 3655 CA PHE F 293 11.610 69.258 80.181 0.25 > 38.30 C > ATOM 3656 C PHE F 293 13.054 69.496 80.591 0.25 > 36.70 C > ATOM 3657 O PHE F 293 13.390 70.501 81.221 0.25 > 38.80 O > ATOM 3658 CG PHE F 293 12.212 69.884 77.755 0.25 > 42.50 C > ATOM 3659 CD1 PHE F 293 12.147 68.699 77.016 0.25 > 42.80 C > ATOM 3660 CD2 PHE F 293 13.154 70.866 77.422 0.25 > 42.80 C > ATOM 3661 CE1 PHE F 293 13.023 68.500 75.948 0.25 > 42.80 C > ATOM 3662 CE2 PHE F 293 14.026 70.657 76.355 0.25 > 43.40 C > ATOM 3663 CZ PHE F 293 13.963 69.475 75.619 0.25 > 43.20 C > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_RB7tzAs8uc5gbpdo9qEzvg)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3ECE0F9A.6080403@mrc-dunn.cam.ac.uk> <3ECFD8E2.3020207@mrc-dunn.cam.ac.uk> <3ED34393.9000509@mrc-dunn.cam.ac.uk> <006001c324ef$39fc0ff0$6c8506c1@youngcthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Strange format for PDB 1cm4 Date: Wed, 28 May 2003 10:19:47 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_RB7tzAs8uc5gbpdo9qEzvg) I thought it was the case that MODEL lines are used in these instances. I can view one chain at a time in rasmol though. Tamas E. Gunda wrote: >This is a strange pdb file, as it contains 9 chains separated by TERs (the >last unnamed chain is that of waters). It is a four-in-one structure, four >different representations of the same molecule in one. These should be be >separated by MODELs, I don't why has the file been created such way. You >should use an applications which can separately handle separately or browse >the chains, (such as Mol2mol) and cut the parts you need. > >Best regards > >Tamas > >Dr. Tamas E. Gunda >University of Debrecen >Medical and Health Science Center >Dept. of Pharmaceutical Chemistry >POBox 36 >H-4010 Debrecen >Hungary >e-mail: tamasgunda*AT*tigris.klte.hu > > >----- Original Message ----- >From: "Dan Bolser" >To: >Cc: "Wan Kyu Kim" ; "rasmol" > >Sent: Tuesday, May 27, 2003 12:53 PM >Subject: Strange format for PDB 1cm4 > > > > >>The following atom line section for 1cm4 looks a little wrong, having a >>stray atom from >>residue 293 of chain F in between the TER and HETATM lines of chain E. >> >>I always asumed that all the atoms for a residue should be sequential. >>Is this correct? >> >>Cheers, Dan. >> >>ATOM 3641 N THR E 146 31.312 61.978 75.234 0.25 >>36.30 N >>ATOM 3642 CA THR E 146 32.587 61.624 75.853 0.25 >>38.50 C >>ATOM 3643 C THR E 146 32.984 62.653 76.912 0.25 >>39.10 C >>ATOM 3644 O THR E 146 32.170 62.973 77.780 0.25 >>38.90 O >>ATOM 3645 CB THR E 146 33.768 61.528 74.820 0.25 >>39.70 C >>ATOM 3646 OG1 THR E 146 33.927 62.815 74.234 0.25 >>41.30 O >>ATOM 3647 CG2 THR E 146 33.545 60.456 73.753 0.25 >>39.30 C >>TER 3648 THR E >>146 >>ATOM 3649 CB PHE F 293 11.275 70.102 78.942 0.25 >>40.50 C <---- ?? >>HETATM 3650 CA CA E 401 8.040 46.688 78.529 0.25 >>18.20 CA >>HETATM 3651 CA CA E 402 14.450 40.835 85.677 0.25 >>28.00 CA >>HETATM 3652 CA CA E 403 22.542 69.262 59.236 >>0.25130.40 CA >>HETATM 3653 CA CA E 404 28.059 73.861 66.193 0.25 >>7.60 CA >>ATOM 3654 N PHE F 293 10.703 69.598 81.261 0.25 >>40.10 N >>ATOM 3655 CA PHE F 293 11.610 69.258 80.181 0.25 >>38.30 C >>ATOM 3656 C PHE F 293 13.054 69.496 80.591 0.25 >>36.70 C >>ATOM 3657 O PHE F 293 13.390 70.501 81.221 0.25 >>38.80 O >>ATOM 3658 CG PHE F 293 12.212 69.884 77.755 0.25 >>42.50 C >>ATOM 3659 CD1 PHE F 293 12.147 68.699 77.016 0.25 >>42.80 C >>ATOM 3660 CD2 PHE F 293 13.154 70.866 77.422 0.25 >>42.80 C >>ATOM 3661 CE1 PHE F 293 13.023 68.500 75.948 0.25 >>42.80 C >>ATOM 3662 CE2 PHE F 293 14.026 70.657 76.355 0.25 >>43.40 C >>ATOM 3663 CZ PHE F 293 13.963 69.475 75.619 0.25 >>43.20 C >> >> >> >> >> >> > > > --Boundary_(ID_RB7tzAs8uc5gbpdo9qEzvg) I thought it was the case that MODEL lines are used in these instances.

I can view one chain at a time in rasmol though.

Tamas E. Gunda wrote:
This is a strange pdb file, as it contains 9 chains separated by TERs (the
last unnamed chain is that of waters). It is a four-in-one structure, four
different representations of the same molecule in one. These should be be
separated by MODELs, I don't why has the file been created such way. You
should use an applications which can separately handle separately or browse
the chains, (such as Mol2mol) and cut the parts you need.

Best regards

Tamas

Dr. Tamas E. Gunda
University of Debrecen
Medical and Health Science Center
Dept. of Pharmaceutical Chemistry
POBox 36
H-4010 Debrecen
Hungary
e-mail: tamasgunda*AT*tigris.klte.hu

----- Original Message ----- 
<rasmol@lists.umass.edu>
Sent: Tuesday, May 27, 2003 12:53 PM
From: "Dan Bolser" <dmb@mrc-dunn.cam.ac.uk>
Subject: Strange format for PDB 1cm4
To: <info@rcsb.org>
Cc: "Wan Kyu Kim" <wan@mrc-dunn.cam.ac.uk>; "rasmol"

  
The following atom line section for 1cm4 looks a little wrong, having a
stray atom from
residue 293 of chain F in between the TER and HETATM lines of chain E.

I always asumed that all the atoms for a residue should be sequential.
Is this correct?

Cheers, Dan.

ATOM   3641  N   THR E 146      31.312  61.978  75.234  0.25
36.30           N
ATOM   3642  CA  THR E 146      32.587  61.624  75.853  0.25
38.50           C
ATOM   3643  C   THR E 146      32.984  62.653  76.912  0.25
39.10           C
ATOM   3644  O   THR E 146      32.170  62.973  77.780  0.25
38.90           O
ATOM   3645  CB  THR E 146      33.768  61.528  74.820  0.25
39.70           C
ATOM   3646  OG1 THR E 146      33.927  62.815  74.234  0.25
41.30           O
ATOM   3647  CG2 THR E 146      33.545  60.456  73.753  0.25
39.30           C
TER    3648      THR E
146
ATOM   3649  CB  PHE F 293      11.275  70.102  78.942  0.25
40.50           C  <---- ??
HETATM 3650 CA    CA E 401       8.040  46.688  78.529  0.25
18.20          CA
HETATM 3651 CA    CA E 402      14.450  40.835  85.677  0.25
28.00          CA
HETATM 3652 CA    CA E 403      22.542  69.262  59.236
0.25130.40          CA
HETATM 3653 CA    CA E 404      28.059  73.861  66.193  0.25
7.60          CA
ATOM   3654  N   PHE F 293      10.703  69.598  81.261  0.25
40.10           N
ATOM   3655  CA  PHE F 293      11.610  69.258  80.181  0.25
38.30           C
ATOM   3656  C   PHE F 293      13.054  69.496  80.591  0.25
36.70           C
ATOM   3657  O   PHE F 293      13.390  70.501  81.221  0.25
38.80           O
ATOM   3658  CG  PHE F 293      12.212  69.884  77.755  0.25
42.50           C
ATOM   3659  CD1 PHE F 293      12.147  68.699  77.016  0.25
42.80           C
ATOM   3660  CD2 PHE F 293      13.154  70.866  77.422  0.25
42.80           C
ATOM   3661  CE1 PHE F 293      13.023  68.500  75.948  0.25
42.80           C
ATOM   3662  CE2 PHE F 293      14.026  70.657  76.355  0.25
43.40           C
ATOM   3663  CZ  PHE F 293      13.963  69.475  75.619  0.25
43.20           C

--Boundary_(ID_RB7tzAs8uc5gbpdo9qEzvg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 boundary="Boundary_(ID_3uCO1FEodzz5zhQPyoOK1A)" X-MSMail-priority: Normal References: <3ECE0F9A.6080403@mrc-dunn.cam.ac.uk> <3ECFD8E2.3020207@mrc-dunn.cam.ac.uk> <3ED34393.9000509@mrc-dunn.cam.ac.uk> <006001c324ef$39fc0ff0$6c8506c1@youngcthulhu> <3ED47F33.4050102@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Strange format for PDB 1cm4 Date: Wed, 28 May 2003 12:53:16 +0200 To: rasmol@lists.umass.edu, dmb@mrc-dunn.cam.ac.uk This is a multi-part message in MIME format. --Boundary_(ID_3uCO1FEodzz5zhQPyoOK1A) Dan, I could reformat the file using MODELs, is it OK? Do you need the water molecules as well? Tamas ----- Original Message ----- From: Dan Bolser To: rasmol@lists.umass.edu Sent: Wednesday, May 28, 2003 11:19 AM Subject: Re: Strange format for PDB 1cm4 I thought it was the case that MODEL lines are used in these instances. I can view one chain at a time in rasmol though. Tamas E. Gunda wrote: This is a strange pdb file, as it contains 9 chains separated by TERs (the last unnamed chain is that of waters). It is a four-in-one structure, four different representations of the same molecule in one. These should be be separated by MODELs, I don't why has the file been created such way. You should use an applications which can separately handle separately or browse the chains, (such as Mol2mol) and cut the parts you need. Best regards Tamas Dr. Tamas E. Gunda University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tamasgunda*AT*tigris.klte.hu ----- Original Message ----- Sent: Tuesday, May 27, 2003 12:53 PM From: "Dan Bolser" Subject: Strange format for PDB 1cm4 To: Cc: "Wan Kyu Kim" ; "rasmol" The following atom line section for 1cm4 looks a little wrong, having a stray atom from residue 293 of chain F in between the TER and HETATM lines of chain E. I always asumed that all the atoms for a residue should be sequential. Is this correct? Cheers, Dan. ATOM 3641 N THR E 146 31.312 61.978 75.234 0.25 36.30 N ATOM 3642 CA THR E 146 32.587 61.624 75.853 0.25 38.50 C ATOM 3643 C THR E 146 32.984 62.653 76.912 0.25 39.10 C ATOM 3644 O THR E 146 32.170 62.973 77.780 0.25 38.90 O ATOM 3645 CB THR E 146 33.768 61.528 74.820 0.25 39.70 C ATOM 3646 OG1 THR E 146 33.927 62.815 74.234 0.25 41.30 O ATOM 3647 CG2 THR E 146 33.545 60.456 73.753 0.25 39.30 C TER 3648 THR E 146 ATOM 3649 CB PHE F 293 11.275 70.102 78.942 0.25 40.50 C <---- ?? HETATM 3650 CA CA E 401 8.040 46.688 78.529 0.25 18.20 CA HETATM 3651 CA CA E 402 14.450 40.835 85.677 0.25 28.00 CA HETATM 3652 CA CA E 403 22.542 69.262 59.236 0.25130.40 CA HETATM 3653 CA CA E 404 28.059 73.861 66.193 0.25 7.60 CA ATOM 3654 N PHE F 293 10.703 69.598 81.261 0.25 40.10 N ATOM 3655 CA PHE F 293 11.610 69.258 80.181 0.25 38.30 C ATOM 3656 C PHE F 293 13.054 69.496 80.591 0.25 36.70 C ATOM 3657 O PHE F 293 13.390 70.501 81.221 0.25 38.80 O ATOM 3658 CG PHE F 293 12.212 69.884 77.755 0.25 42.50 C ATOM 3659 CD1 PHE F 293 12.147 68.699 77.016 0.25 42.80 C ATOM 3660 CD2 PHE F 293 13.154 70.866 77.422 0.25 42.80 C ATOM 3661 CE1 PHE F 293 13.023 68.500 75.948 0.25 42.80 C ATOM 3662 CE2 PHE F 293 14.026 70.657 76.355 0.25 43.40 C ATOM 3663 CZ PHE F 293 13.963 69.475 75.619 0.25 43.20 C --Boundary_(ID_3uCO1FEodzz5zhQPyoOK1A)
Dan,
 
I could reformat the file using MODELs, is it OK? Do you need the water molecules as well?
 
Tamas 
----- Original Message -----
From: Dan Bolser
Sent: Wednesday, May 28, 2003 11:19 AM
Subject: Re: Strange format for PDB 1cm4

I thought it was the case that MODEL lines are used in these instances.

I can view one chain at a time in rasmol though.

Tamas E. Gunda wrote:
This is a strange pdb file, as it contains 9 chains separated by TERs (the
last unnamed chain is that of waters). It is a four-in-one structure, four
different representations of the same molecule in one. These should be be
separated by MODELs, I don't why has the file been created such way. You
should use an applications which can separately handle separately or browse
the chains, (such as Mol2mol) and cut the parts you need.

Best regards

Tamas

Dr. Tamas E. Gunda
University of Debrecen
Medical and Health Science Center
Dept. of Pharmaceutical Chemistry
POBox 36
H-4010 Debrecen
Hungary
e-mail: tamasgunda*AT*tigris.klte.hu

----- Original Message ----- 
<rasmol@lists.umass.edu>
Sent: Tuesday, May 27, 2003 12:53 PM
From: "Dan Bolser" <dmb@mrc-dunn.cam.ac.uk>
Subject: Strange format for PDB 1cm4
To: <info@rcsb.org>
Cc: "Wan Kyu Kim" <wan@mrc-dunn.cam.ac.uk>; "rasmol"

  
The following atom line section for 1cm4 looks a little wrong, having a
stray atom from
residue 293 of chain F in between the TER and HETATM lines of chain E.

I always asumed that all the atoms for a residue should be sequential.
Is this correct?

Cheers, Dan.

ATOM   3641  N   THR E 146      31.312  61.978  75.234  0.25
36.30           N
ATOM   3642  CA  THR E 146      32.587  61.624  75.853  0.25
38.50           C
ATOM   3643  C   THR E 146      32.984  62.653  76.912  0.25
39.10           C
ATOM   3644  O   THR E 146      32.170  62.973  77.780  0.25
38.90           O
ATOM   3645  CB  THR E 146      33.768  61.528  74.820  0.25
39.70           C
ATOM   3646  OG1 THR E 146      33.927  62.815  74.234  0.25
41.30           O
ATOM   3647  CG2 THR E 146      33.545  60.456  73.753  0.25
39.30           C
TER    3648      THR E
146
ATOM   3649  CB  PHE F 293      11.275  70.102  78.942  0.25
40.50           C  <---- ??
HETATM 3650 CA    CA E 401       8.040  46.688  78.529  0.25
18.20          CA
HETATM 3651 CA    CA E 402      14.450  40.835  85.677  0.25
28.00          CA
HETATM 3652 CA    CA E 403      22.542  69.262  59.236
0.25130.40          CA
HETATM 3653 CA    CA E 404      28.059  73.861  66.193  0.25
7.60          CA
ATOM   3654  N   PHE F 293      10.703  69.598  81.261  0.25
40.10           N
ATOM   3655  CA  PHE F 293      11.610  69.258  80.181  0.25
38.30           C
ATOM   3656  C   PHE F 293      13.054  69.496  80.591  0.25
36.70           C
ATOM   3657  O   PHE F 293      13.390  70.501  81.221  0.25
38.80           O
ATOM   3658  CG  PHE F 293      12.212  69.884  77.755  0.25
42.50           C
ATOM   3659  CD1 PHE F 293      12.147  68.699  77.016  0.25
42.80           C
ATOM   3660  CD2 PHE F 293      13.154  70.866  77.422  0.25
42.80           C
ATOM   3661  CE1 PHE F 293      13.023  68.500  75.948  0.25
42.80           C
ATOM   3662  CE2 PHE F 293      14.026  70.657  76.355  0.25
43.40           C
ATOM   3663  CZ  PHE F 293      13.963  69.475  75.619  0.25
43.20           C

--Boundary_(ID_3uCO1FEodzz5zhQPyoOK1A)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Erroneous statement in recent Bioinformatics paper Date: Wed, 28 May 2003 15:00:53 -0400 To: tcan@cs.ucsb.edu Cc: rasmol@lists.umass.edu Dear Dr. Can: I wish to point out an error in your recent Bioinformatics paper on FPV (http://bioinformatics.oupjournals.org/cgi/content/abstract/19/8/913). You say "RasMol is now being developed under the name of Protein Explorer." That is incorrect. In fact, RasMol 2.7 is now being developed as OpenRasMol (www.openrasmol.org), with an open-source team led by Herbert Bernstein. Protein Explorer is built around the plugin MDL Chime (www.mdlchime.com), which in turn incorporates some of the public domain RasMol version 2.6 source code. Chime has a great deal of functionality lacking in RasMol, and in turn, Protein Explorer adds a great deal more. Although they are built upon portions of Roger Sayle's superb RasMol source code, they are not "RasMol". I have copied this to the Molecular Visualization Freeware (originally "RasMol") email list to help avoid further confusion. You are welcome to subscribe to this list (see URL below). Incidentally, Duane Sears at your institution (UCSB) is a local expert on these visualization tools. Sincerely, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: stereo from RasMol Date: Wed, 28 May 2003 15:54:19 -0400 To: LIST rasmol greetings, can RasMol output an active stereo signal? if not, does anyone know of a patch to convert left-right stereo pairs into active stereo? thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Erroneous statement in recent Bioinformatics paper Date: Wed, 28 May 2003 17:57:18 -0400 (EDT) To: rasmol@lists.umass.edu Cc: tcan@cs.ucsb.edu Just to correct a mistunderstanding in Dr. Martz's recent message: The RasMol 2.7 series is the current main line of RasMol development. We had to use www.OpenRasMol.org as the name for the RasMol home page for a while because the holder of RasMol.org was not willing to release the domain name in a tmely manner. They have since done so, and you can find the RasMol 2.7 series releases at www.RasMol.org, the home page for RasMol, as well as at www.OpenRasMol.org which is simply an alias for www.RasMol.org. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 28 May 2003, Eric Martz wrote: > Dear Dr. Can: > > I wish to point out an error in your recent Bioinformatics paper on FPV > (http://bioinformatics.oupjournals.org/cgi/content/abstract/19/8/913). > > You say "RasMol is now being developed under the name of Protein Explorer." > That is incorrect. > > In fact, RasMol 2.7 is now being developed as OpenRasMol > (www.openrasmol.org), with an open-source team led by Herbert Bernstein. > > Protein Explorer is built around the plugin MDL Chime (www.mdlchime.com), > which in turn incorporates some of the public domain RasMol version 2.6 > source code. Chime has a great deal of functionality lacking in RasMol, and > in turn, Protein Explorer adds a great deal more. Although they are built > upon portions of Roger Sayle's superb RasMol source code, they are not > "RasMol". > > I have copied this to the Molecular Visualization Freeware (originally > "RasMol") email list to help avoid further confusion. You are welcome to > subscribe to this list (see URL below). > > Incidentally, Duane Sears at your institution (UCSB) is a local expert on > these visualization tools. > > Sincerely, -Eric Martz > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Alexander Koval Subject: saving transparent gif Date: Wed, 28 May 2003 23:15:58 +0300 To: rasmol@lists.umass.edu Dear rasmol listers, Can somebody here help me how to export transparent gif. grom Rasmol. The command "set transparent on" does not have any effect. What wrong I do? Thanks in advance. With Best Regards Alexander Koval kovalj@rambler.ru ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: <000301c32593$0ea943a0$70cd9ec2@bg> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: saving transparent gif Date: Wed, 28 May 2003 22:31:00 -0700 To: rasmol@lists.umass.edu Alexander wrote: > Can somebody here help me how to export transparent gif. grom Rasmol. The > command "set transparent on" does not have any effect. What wrong I do? Nothing wrong. The actual command does not have any significant action in the code. Fix the transparency in another software, Photoshop for example. Regards, Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Scripting command manuals and resources for RasMol and Chime Date: Thu, 29 May 2003 12:29:07 -0400 To: Joan Slonczewski Cc: rasmol@lists.umass.edu At 5/28/03, Joan Slonczewski wrote: Eric, How much of RasMol 2.7.2 applies to Chime? Do the updated RasMol 2.7.2 commands work for scripting with the current MDL Chime? I think it's understandable that authors get confused in citing these things; it's all still confusing to me. Thanks, Joan Dear Joan: I sympathize! I don't think this information has been summarized for awhile, so I'll copy this to the list. MDL Chime incorporates all of the RasMol 2.6 commands except for 'write'/'save' (files to disk). RasMol 2.6 commands are documented at http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual . MDL was able to incorporate a large portion of the RasMol 2.6 source code into MDL Chime because Roger Sayle, the author of RasMol 2.6, generously put its source code in the public domain without any restrictions on its use, including for commercial purposes. Commands added to RasMol in 2.7.x are documented at http://www.rasmol.org, but I'm not clear whether there is a separate list of post-2.6-beta2a features there. (Herb -- is there?) Chime does not include any of the RasMol 2.7.x enhancements (added after RasMol 2.6) because they were relased under an open source policy requiring that all derivatives be open source. (See Note 1.) Commands added to Chime, beyond the RasMol 2.6 commands, are documented at http://www.mdl.com/chime/chimerasmol.html For many years, MDL failed to document many of the new commands, but at this point in time, I think nearly all of them are documented to some extent, although for some the documentation is only partial. (See Note 2.) As a plugin, Chime added "embed tags" (actually parameters within the embed tag) that are documented at http://www.mdl.com/chime/chimeembed.html. (See Note 3.) The previous two links can be accessed through the easier to remember http://www.mdlchime.com, clicking on "Learn and Develop". * * * * * * * The above documents are reference manuals, not tutorials that explain how to get started. My suggestion is that the easiest way to learn RasMol scripting is to use Protein Explorer. There you can watch the script commands emitted by buttons and menus, then try entering them manually. Protein Explorer in Netscape can also run script files (*.spt) when you set a project folder. There are many tutorials at the original RasMol 2.6 "Home Page" (http://www.umass.edu/microbio/rasmol/), listed at http://www.umass.edu/microbio/rasmol/rastut.htm. There are also tutorials on "Select commands in RasMol and Chime" (http://www.umass.edu/microbio/rasmol/seleccmd.htm) and use of colors in RasMol and Chime (http://www.umass.edu/microbio/rasmol/rascolor.htm). Finally, there are FAQ by Roger Sayle, and by myself (http://www.umass.edu/microbio/rasmol/faq.htm) (http://molvis.sdsc.edu/protexpl/faq.htm). Turning to Chime tutorials, there is one on making Chime websites from scratch at my Chime Resources site (http://www.umass.edu/microbio/chime/), namely http://www.umass.edu/microbio/chime/chimehow/chimake.htm. A downloadable template for making presentations in Chime is available at http://www.umass.edu/microbio/chime/prsswc/template.htm. Additional resources for authors of Chime websites are indexed at http://molvisindex.org under the category "How to create new tutorials with Chime". Protein Explorer adds 'aliases' to the script language (click on 'Show Aliases' below the message box). Most of these are abbreviations for commands, for example "s l" expands to "select ligand", "bs" expands to a series of commands that produce ball and stick rendering, "coe" expands to "color cpk" ("e" for "element"), and "coh ff8000" expands to "color [xff8000]" (the "h" in "coh" stands for hexadecimal). These save typing and reduce typographical errors. The aliases can be easily changed or added to simply by editing a text file. There are also "commands to Protein Explorer" (click on the ? near the command input slot) that are not passed to Chime, for example to jump to another control page, recall a previous command, or execute commands in both molecules in Protein Comparator. -Eric ------------- Note 1: One can only speculate what would have happened had RasMol 2.6 been open source (requiring that all derivatives be open source). Either we wouldn't have Chime at all, or it would be open source. MDL has repeatedly refused to open the source of Chime, as recently discussed on this list. Note 2: One Chime feature that isn't documented by MDL enables scripts to be written that will run in both RasMol or Chime, using capabilities specific to each. Commands preceded by '#' are ignored by both RasMol and Chime. Commands preceded by '##' are executed in Chime but not RasMol. Commands FOLLOWED by '#!" are executed in RasMol but not Chime. These are used in the animation scripts generated by Protein Explorer, which can be run in Chime to display animations, and in RasMol to create a series of GIF files that can later be combined into an animated multi-GIF (see http://molvis.sdsc.edu/protexpl/animgif.htm). Note 3: A design flaw, in my opinion, is that some Chime features are accessible through embed tags but not through script commands, for example debugscript. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3ED52D2A.17D9FA8C@kenyon.edu> <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Inhibitor Date: Thu, 29 May 2003 23:25:33 +0100 (BST) To: rasmol@lists.umass.edu Hello, I have found problems with PDB 1nsa and 1pca, and several others. These PDB files use the alt code (or is it the insert code) to specify an enzyme inhibitor complex on the same chain. The problem is they use the same residue numbers to start each from 1. How can I select 1A and 1 differently in rasmol? NB, A isn't a chain, it is an alt code. Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> <3ED52D2A.17D9FA8C@kenyon.edu> <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Inhibitor (Insertions, Alternate conformations) Date: Fri, 30 May 2003 14:32:57 -0400 To: rasmol@lists.umass.edu At 5/29/03, Dan Bolser wrote: >Hello, > >I have found problems with PDB 1nsa and 1pca, >and several others. These PDB files use the >alt code (or is it the insert code) to specify >an enzyme inhibitor complex on the same chain. > >The problem is they use the same residue numbers >to start each from 1. > >How can I select 1A and 1 differently in rasmol? > >NB, A isn't a chain, it is an alt code. > >Cheers, >Dan. A short answer: run the command "renumber" before selecting, but then you will be using a differently numbered sequence. A longer answer: 1NSA uses insertion codes. It has residues numbered 7A-95A followed by 4-308 (including 188 and 188A). My understanding is that this means that another homologous reference protein has sequence 1-308, whereas the protein in 1NSA has an additional 95 N-terminal residues, and one extra serine inserted after position 188. All 404 residues are in separate positions along the chain. Insertion codes are explained in detail at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html under 9. Coordinate Section, ATOM record. Alternate position codes (not used in 1NSA) are used when more than one position is resolved for a group of atoms. According to Steve Bryant of NCBI, the majority of X-ray structures in the PDB have some alternate sidechain conformations. An example is 5HVP (L297, L97, N298, N98, T212, E65, D60, L63, and others?). Neither of these situations are handled well by RasMol 2.6 or Chime. I believe Cn3D does a much better job, at least for alternate positions. The RasMol "renumber [-][start_value]" command works in both RasMol and Chime, renumbering amino acids from N to C terminus. After running "renumber" in Chime, the C terminal residue of 1NSA is reported as 395 instead of 308. Furthermore, "select 1-95" now selects 95 residues rather than 181, and "color group" now used one blue-red series instead of two. If you run "renumber" BEFORE you first display Sequences or Seq3D in Protein Explorer, you can use the Seq3D display to select ranges of residues without confusion. Note that Chime unconditionally always saves a PDB file exactly as it received it, unmodified (so with the original numbering even if you ran "renumber"). In contrast, RasMol 2.6 always unconditionally recenters the entire coordinate system (so you can't combine blocks of residues saved separately by RasMol!), and saves only the currently selected residues. If you run "renumber", and select all, RasMol will save with renumbered residues. The properties of saving from Chime and RasMol 2.6 are summarized at http://www.umass.edu/microbio/rasmol/pdbtools.htm DeepView can also be used to renumber residues: Edit, Rename Current Layer. The resulting (surprising) "Rename Layer Components" dialog supports renaming chains and renumbering selected residues from a specified starting number. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> <3ED52D2A.17D9FA8C@kenyon.edu> <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> <5.2.0.9.2.20030530134657.0266f7b0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Inhibitor (Insertions, Alternate conformations) Date: Tue, 03 Jun 2003 10:27:50 +0100 To: rasmol@lists.umass.edu Sorry for my ignorance, but can I ask how insert codes are handled by the mmCIF? I would guess that you could number each chain from 1, and provide separate allignment details with an appropriate DB reference? Is the XML format an encoding of the mmCIF, or a new format? Cheers, Dan. Eric Martz wrote: > At 5/29/03, Dan Bolser wrote: > >> Hello, >> >> I have found problems with PDB 1nsa and 1pca, >> and several others. These PDB files use the >> alt code (or is it the insert code) to specify >> an enzyme inhibitor complex on the same chain. >> >> The problem is they use the same residue numbers >> to start each from 1. >> >> How can I select 1A and 1 differently in rasmol? >> >> NB, A isn't a chain, it is an alt code. >> >> Cheers, >> Dan. > > > > A short answer: run the command "renumber" before selecting, but then > you will be using a differently numbered sequence. > > A longer answer: > > 1NSA uses insertion codes. It has residues numbered 7A-95A followed by > 4-308 (including 188 and 188A). My understanding is that this means > that another homologous reference protein has sequence 1-308, whereas > the protein in 1NSA has an additional 95 N-terminal residues, and one > extra serine inserted after position 188. All 404 residues are in > separate positions along the chain. Insertion codes are explained in > detail at > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html > under 9. Coordinate Section, ATOM record. > > Alternate position codes (not used in 1NSA) are used when more than > one position is resolved for a group of atoms. According to Steve > Bryant of NCBI, the majority of X-ray structures in the PDB have some > alternate sidechain conformations. An example is 5HVP (L297, L97, > N298, N98, T212, E65, D60, L63, and others?). > > Neither of these situations are handled well by RasMol 2.6 or Chime. I > believe Cn3D does a much better job, at least for alternate positions. > > The RasMol "renumber [-][start_value]" command works in both RasMol > and Chime, renumbering amino acids from N to C terminus. After running > "renumber" in Chime, the C terminal residue of 1NSA is reported as 395 > instead of 308. Furthermore, "select 1-95" now selects 95 residues > rather than 181, and "color group" now used one blue-red series > instead of two. If you run "renumber" BEFORE you first display > Sequences or Seq3D in Protein Explorer, you can use the Seq3D display > to select ranges of residues without confusion. > > Note that Chime unconditionally always saves a PDB file exactly as it > received it, unmodified (so with the original numbering even if you > ran "renumber"). In contrast, RasMol 2.6 always unconditionally > recenters the entire coordinate system (so you can't combine blocks of > residues saved separately by RasMol!), and saves only the currently > selected residues. If you run "renumber", and select all, RasMol will > save with renumbered residues. The properties of saving from Chime and > RasMol 2.6 are summarized at > http://www.umass.edu/microbio/rasmol/pdbtools.htm > > DeepView can also be used to renumber residues: Edit, Rename Current > Layer. The resulting (surprising) "Rename Layer Components" dialog > supports renaming chains and renumbering selected residues from a > specified starting number. > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: Submited (004756-3463) Date: Tue, 03 Jun 2003 17:22:26 +0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_aAb371iIh+h2HCyM7Tf5cg) Please see the attached file. --Boundary_(ID_aAb371iIh+h2HCyM7Tf5cg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Trina Valencich Subject: Re: Submited (004756-3463) Date: Tue, 03 Jun 2003 17:56:46 -0600 To: rasmol@lists.umass.edu HB & Sons, No file was attached, trina At 05:22 PM 6/3/2003 +0400, you wrote: >Please see the attached file. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.0.20030603175622.00af0748@selway.umt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: The PDB and Education Date: Tue, 03 Jun 2003 20:26:05 -0400 To: rasmol@lists.umass.edu Dear Rasmol Colleagues, I'm on the Advisory Board for the Protein Data Bank and the sole representative of the undergraduate education community. I'd like to be of as much service to that community as I can and so would like to set up an email discussion group concerned with how the PDB can best serve educational users. I don't want to fill Rasmolers email boxes unnecessarily, so if you are interested in being part of such a discussion group please email me back directly (jvoet1@swarthmore.edu) and I'll set up an email list for us to use. Thanks for your potential interest. Judy Voet ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Submited (004756-3463) Date: Tue, 03 Jun 2003 20:56:28 -0400 To: rasmol@lists.umass.edu at 5:56 PM EDT on (Tuesday) 3 June 2003 Trina Valencich said: > HB & Sons, No file was attached, trina > > At 05:22 PM 6/3/2003 +0400, you wrote: > >Please see the attached file. > please be advised that this kind of cryptic message is characteristic of an email worm circulating the net: it is generally uncommon for list members to send attachments to the list, especially without explanation, so it is good practice to be wary of such messages. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Originating-IP: [128.111.200.225] X-Originating-Email: [sigmanuelder@hotmail.com] X-OriginalArrivalTime: 04 Jun 2003 01:00:37.0744 (UTC) FILETIME=[B60C6F00:01C32A34] ++++------+------+------+------+------+------+------+------+------+------+ From: Scott Thompson Subject: Re: The PDB and Education Date: Tue, 03 Jun 2003 18:00:37 -0700 To: rasmol@lists.umass.edu I would like to be included in this email listserve for PDB and Education. Thanks, Scott E. Thompson _________________________________________________________________ Protect your PC - get McAfee.com VirusScan Online http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Submited (004756-3463) Date: Wed, 04 Jun 2003 04:10:00 -0400 (EDT) To: rasmol@lists.umass.edu To my colleagues on the list, I am deeply distressed that some spammer is spoofing my email address to trick people into accepting worms. I do not send messages to any list with attachments, and you may safely delete any message purporting to come from me to this list that has an attachment or is formatted as html. Regards, Herbert J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 3 Jun 2003, Trina Valencich wrote: > HB & Sons, No file was attached, trina > > At 05:22 PM 6/3/2003 +0400, you wrote: > >Please see the attached file. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Submited (004756-3463) Date: Wed, 04 Jun 2003 10:19:16 +0200 To: rasmol@lists.umass.edu Unfortunetely not you are the only one; I get regularly worms and viruses masked as rasmol list, ccl list etc. Regards Tamas Gunda ----- Original Message ----- Sent: Wednesday, June 04, 2003 10:10 AM From: "Herbert J. Bernstein" Subject: Re: Submited (004756-3463) To: > To my colleagues on the list, > I am deeply distressed that some spammer is spoofing my email address > to trick people into accepting worms. I do not send messages to any > list with attachments, and you may safely delete any message purporting > to come from me to this list that has an attachment or is formatted as > html. > Regards, > Herbert J. Bernstein > > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Tue, 3 Jun 2003, Trina Valencich wrote: > > > HB & Sons, No file was attached, trina > > > > At 05:22 PM 6/3/2003 +0400, you wrote: > > >Please see the attached file. > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Submited (004756-3463) Date: Wed, 04 Jun 2003 07:29:13 -0400 To: rasmol@lists.umass.edu at 4:10 AM EDT on (Wednesday) 4 June 2003 Herbert J. Bernstein said: > To my colleagues on the list, > I am deeply distressed that some spammer is spoofing my email address > to trick people into accepting worms. I do not send messages to any > list with attachments, and you may safely delete any message purporting > to come from me to this list that has an attachment or is formatted as > html. > Regards, > Herbert J. Bernstein > hi Herb, no apology is necessary, I believe, because I don't think you could have done anything. according to the description at this worm culls email addresses from various types of documents, including html docs. so I imagine if your email address is anywhere on a public Web page, you are fair game. I have even received this particular worm from my own address, as well as from someone's long-defunct (but still obviously published) email address, both of which are Mac-based and thus unaffected. IIRC, the worm is scheduled to expire on 08 june. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Tue, 3 Jun 2003, Trina Valencich wrote: > > > HB & Sons, No file was attached, trina > > > > At 05:22 PM 6/3/2003 +0400, you wrote: > > >Please see the attached file. > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Spam sent to list Date: Wed, 04 Jun 2003 11:23:52 -0400 To: rasmol@lists.umass.edu This list currently has 617 subscribers. Junk mail sent to the list is rejected automatically unless sent by a subscriber. I get several messages each day from the listproc reporting such rejections. I approve all subscriptions manually, thereby avoiding obvious spam. It is possible that by spoofing the address of a subscriber as the sender, yesterday's junk/virus email got through. To my knowledge, it is the first. I am attempting to trace the true sender. All subscribers should have virus detection software installed and keep their virus definitions up to date. I will remove the subscription of any subscriber whose computer is suspected of sending spam to the list more than once (presumably as a result of being infected with a virus). We have tried in the past to block any attachments from being broadcast to the list but this turns out to be problematic. The virus-blocking gates at my campus may have stripped the attachment from yesterday's message. Did anyone actually receive an attachment with the message spoofed from yaya@bernstein-plus-sons.com with subject "Re: Submited (004756-3463)"? Of course you should never open any attachment that you don't trust. Opening a virus-infected attachment will infect your computer. Our campus strongly discourages using Outlook Express for email because, by default, it automatically opens attachments. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> <3ED52D2A.17D9FA8C@kenyon.edu> <5.2.0.9.2.20030529100718.02a0cec0@marlin.bio.umass.edu> <5.2.0.9.2.20030530134657.0266f7b0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: mmCIF and XML Date: Wed, 04 Jun 2003 11:45:42 -0400 To: rasmol@lists.umass.edu At 6/3/03, Dan Bolser wrote: >Is the XML format an encoding of the mmCIF, >or a new format? mmCIF is a data format for atomic coordinates and related information, expected to supercede the PDB format. XML is a more general way of identifying data content (in any discipline) for information transferred through the Internet. mmCIF can be encoded in XML (http://pdb.rutgers.edu/mmcif/). Neither is in wide use at this time, I believe, although the expectation is that both will become increasingly important and predominant. Information on mmCIF is available from the PDB: http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards Below is the XML entry I wrote for a forthcoming Dictionary of Bioinformatics (Wiley). Henry Rzepa and Peter Murray-Rust helped a lot with this XML entry. XML (eXtensible Markup Language) XML is a markup language that identifies data elements within a document. It is widely considered the universal format for structured documents and data on the Web. Its power is that the recipient of a document can recognize the contained data elements following a worldwide standard, and can therefore more easily utilize and display the data in any desired manner. XML annotates content, while, in contrast, HTML (HyperText Markup Language) annotates primarily appearance. HTML has a fixed set of tags, while XML (the X stands for eXtensible) is designed to accomodate an ever-growing set of discipline-specific tags. XML is an emerging standard, whereas HTML is a standard already in universal use for annotating information on the web. HTML specifies a static appearance for a document when displayed in a web browser. HTML alone does not enable the recipient web browser to identify the types of data elements contained in the document. For example, HTML can specify that a particular phrase be displayed centered in a large red bold font, but tells nothing about the kind of information in the phrase. In contrast, XML identifies the type of information. For example, XML tags could identify a certain portion of a document as the amino acid sequence for a specified protein. Presently, the content of a document that is of interest to a user must usually be selected by non-standard methods that are often inadequately automated. Once the desired information is extracted in computer-readable form, the format employed is often understood by only a subset of the programs in the world that deal with that type of information. XML provides a worldwide standard for content identification. XML itself is set of rules for writing discipline-specific implementations. The specifications for XML are managed by the World-Wide Web consortium in the form of W3C Recommendations. Each subject discipline must develop its own a "Document Type Definition" (DTD) or "XML Schema" (see examples below). Discipline-specific content within a document is identified by a "namespace". A document can contain mixtures of types of content, that is, multiple namespaces. Within each namespace, the allowed content-identifying tags, and the nesting relationships of the tags, are specified by the corresponding Schema or DTD. For example, in the Chemical Markup Language (CML) Schema or DTD, one element is "cml:molecule". It can have child elements such as "cml:atomArray" and "cml:bondArray". The cml:bondArray element has "cml:atom" elements as its children. The XML Schema for a particular discipline, such as CML, is enforced by a validation process. Each Schema has a primary website, where the discipline-specific tags and and rules for validation are defined. Examples of well defined XML languages for common generic use include: 1. XHTML (a general document markup language derived from HTML), 2. SVG (scalable vector graphics) for expressing diagrams and visual information 3. MathML (Mathematical markup language). Specific scientific, technical and medical (STM) namespaced applications of XML include: 1. STMML (for description of scientific units and quantities), 2. CML (Chemical markup language) for expressing molecular content, 3. CellML for computer-based biological models, 4. GAME (Genome annotation markup elements), 5. MAGE-ML (MicroArray and Gene Expression Markup Language ), 6. Molecular Dynamics [Markup] Language (MoDL), 7. StarDOM - Transforming Scientific Data into XML, 8. Bioinformatic Sequence Markup Language (BSML), 9. BIOpolymer Markup Language (BIOML), 10. Gene Expression Markup Language (GEML), 11. GeneX Gene Expression Markup Language (GeneXML), 12. Genome Annotation Markup Elements (GAME), 13. XML for Multiple Sequence Alignments (MSAML), 14. Systems Biology Markup Language (SBML), 15. Protein Extensible Markup Language (PROXIML). Websites World Wide Web Consortium managing the specifications for XML: http://www.w3c.org Chemical Markup Language: http://www.xml-cml.org Further Reading Bosak J, Bray T (1999) XML and the second generation web. Scientific American, May 6 (http://www.sciam.com). Ezzell C (2001) Hooking up biologists. Scientific American, November 19. Murray-Rust P, Rzepa HS (2002) Scientific publications in XML -- towards a global knowledge base. Data Science 1:84-98. (http://journals.eecs.qub.ac.uk/codata/Journal/Contents/1_1/1_1pdf/DS115.Pdf) See Also Atomic coordinate files MIME Types /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-MSMail-priority: Normal References: <5.2.0.9.2.20030604104706.01f6bec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Sophia Siedlberg Subject: Re: Spam sent to list Date: Wed, 04 Jun 2003 17:42:43 +0100 To: rasmol@lists.umass.edu Hello Eric > We have tried in the past to block any attachments from being broadcast to > the list but this turns out to be problematic. The virus-blocking gates at > my campus may have stripped the attachment from yesterday's message. Did > anyone actually receive an attachment with the message spoofed from > yaya@bernstein-plus-sons.com with subject "Re: Submited (004756-3463)"? I did not recieve an attatchment, nor did any of the AV software I use pick it up. thankfully it seems the virus blocking gate took the attatchent off the email. All the best wishes Sophia Siedlberg Orlania Biosystems ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: mmCIF and XML Date: Wed, 04 Jun 2003 11:37:44 -0500 (CDT) To: rasmol@lists.umass.edu Hi, I just have a couple of issues with your XML entry that are often overlooked or ignored that don't make me a fan of XML. XML is an enhancement of HTML so, using a loose definition, HTML is also XML (strict definition requires certain minor changes such as closing tags). While XML is a 'worldwide standard' the contents don't have to be nor have to be Open. Your XML entry avoids saying that XML can hold binary data. On one hand this is good in that images and programs can be included. But on the other you need the 'key' to unlock the binary format that may require the certain software or operating system. Second that binary data include a virus or similar such as infected MS word file. Regards Bruce On Wed, 4 Jun 2003, Eric Martz wrote: > At 6/3/03, Dan Bolser wrote: > >Is the XML format an encoding of the mmCIF, > >or a new format? > > > mmCIF is a data format for atomic coordinates and related information, > expected to supercede the PDB format. XML is a more general way of > identifying data content (in any discipline) for information transferred > through the Internet. > mmCIF can be encoded in XML (http://pdb.rutgers.edu/mmcif/). Neither is in > wide use at this time, I believe, although the expectation is that both > will become increasingly important and predominant. > > Information on mmCIF is available from the PDB: > http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards > > Below is the XML entry I wrote for a forthcoming Dictionary of > Bioinformatics (Wiley). Henry Rzepa and Peter Murray-Rust helped a lot with > this XML entry. > > XML (eXtensible Markup Language) > > XML is a markup language that identifies data elements within a document. > It is widely considered the universal format for structured documents and > data on the Web. Its power is that the recipient of a document can > recognize the contained data elements following a worldwide standard, and > can therefore more easily utilize and display the data in any desired manner. > > XML annotates content, while, in contrast, HTML (HyperText Markup Language) > annotates primarily appearance. HTML has a fixed set of tags, while XML > (the X stands for eXtensible) is designed to accomodate an ever-growing set > of discipline-specific tags. XML is an emerging standard, whereas HTML is a > standard already in universal use for annotating information on the web. > > HTML specifies a static appearance for a document when displayed in a web > browser. HTML alone does not enable the recipient web browser to identify > the types of data elements contained in the document. For example, HTML can > specify that a particular phrase be displayed centered in a large red bold > font, but tells nothing about the kind of information in the phrase. In > contrast, XML identifies the type of information. For example, XML tags > could identify a certain portion of a document as the amino acid sequence > for a specified protein. Presently, the content of a document that is of > interest to a user must usually be selected by non-standard methods that > are often inadequately automated. Once the desired information is extracted > in computer-readable form, the format employed is often understood by only > a subset of the programs in the world that deal with that type of > information. XML provides a worldwide standard for content identification. > > XML itself is set of rules for writing discipline-specific implementations. > The specifications for XML are managed by the World-Wide Web consortium in the > form of W3C Recommendations. Each subject discipline must develop its own > a "Document Type Definition" (DTD) or "XML Schema" (see examples below). > Discipline-specific content within a document is identified by a > "namespace". A document can contain mixtures of types of content, that is, > multiple namespaces. Within each namespace, the allowed content-identifying > tags, and the nesting relationships of the tags, are specified by the > corresponding Schema or DTD. For example, in the Chemical Markup Language > (CML) Schema or DTD, one element is "cml:molecule". It can have child > elements such as "cml:atomArray" and "cml:bondArray". The cml:bondArray > element has "cml:atom" elements as its children. The XML Schema for a > particular discipline, such as CML, is enforced by a validation process. > Each Schema has a primary website, where the discipline-specific tags and > and rules for validation are defined. > > Examples of well defined XML languages for common generic use include: > 1. XHTML (a general document markup language derived from HTML), > 2. SVG (scalable vector graphics) for expressing diagrams and visual > information > 3. MathML (Mathematical markup language). > > Specific scientific, technical and medical (STM) namespaced applications > of XML include: > > 1. STMML (for description of scientific units and quantities), > 2. CML (Chemical markup language) for expressing molecular content, > 3. CellML for computer-based biological models, > 4. GAME (Genome annotation markup elements), > 5. MAGE-ML (MicroArray and Gene Expression Markup Language ), > 6. Molecular Dynamics [Markup] Language (MoDL), > 7. StarDOM - Transforming Scientific Data into XML, > 8. Bioinformatic Sequence Markup Language (BSML), > 9. BIOpolymer Markup Language (BIOML), > 10. Gene Expression Markup Language (GEML), > 11. GeneX Gene Expression Markup Language (GeneXML), > 12. Genome Annotation Markup Elements (GAME), > 13. XML for Multiple Sequence Alignments (MSAML), > 14. Systems Biology Markup Language (SBML), > 15. Protein Extensible Markup Language (PROXIML). > > Websites > World Wide Web Consortium managing the specifications for XML: > http://www.w3c.org > Chemical Markup Language: http://www.xml-cml.org > > Further Reading > Bosak J, Bray T (1999) XML and the second generation web. Scientific > American, May 6 (http://www.sciam.com). > Ezzell C (2001) Hooking up biologists. Scientific American, November 19. > Murray-Rust P, Rzepa HS (2002) Scientific publications in XML -- towards a > global knowledge base. Data Science 1:84-98. > (http://journals.eecs.qub.ac.uk/codata/Journal/Contents/1_1/1_1pdf/DS115.Pdf) > > See Also > Atomic coordinate files > MIME Types > > > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: mmCIF and XML Date: Wed, 04 Jun 2003 13:24:34 -0400 To: rasmol@lists.umass.edu at 11:37 AM EDT on (Wednesday) 4 June 2003 southey@ux1.cso.uiuc.edu said: > Hi, > > I just have a couple of issues with your XML entry that are often > overlooked or ignored that don't make me a fan of XML. > > XML is an enhancement of HTML so, using a loose definition, HTML is also > XML (strict definition requires certain minor changes such as closing tags). > > While XML is a 'worldwide standard' the contents don't have to > be nor have to be Open. > hi Bruce, I agree with your statements about XML. but I am not sure why you consider the first two issues as negative aspects of the language. can you clarify? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > Your XML entry avoids saying that XML can hold binary data. On one hand > this is good in that images and programs can be included. But on the other > you need the 'key' to unlock the binary format that may require the > certain software or operating system. Second that binary data include a > virus or similar such as infected MS word file. > > Regards > Bruce > > On Wed, 4 Jun 2003, Eric Martz wrote: > > > At 6/3/03, Dan Bolser wrote: > > >Is the XML format an encoding of the mmCIF, > > >or a new format? > > > > > > mmCIF is a data format for atomic coordinates and related information, > > expected to supercede the PDB format. XML is a more general way of > > identifying data content (in any discipline) for information transferred > > through the Internet. > > mmCIF can be encoded in XML (http://pdb.rutgers.edu/mmcif/). Neither is in > > wide use at this time, I believe, although the expectation is that both > > will become increasingly important and predominant. > > > > Information on mmCIF is available from the PDB: > > http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards > > > > Below is the XML entry I wrote for a forthcoming Dictionary of > > Bioinformatics (Wiley). Henry Rzepa and Peter Murray-Rust helped a lot with > > this XML entry. > > > > XML (eXtensible Markup Language) > > > > XML is a markup language that identifies data elements within a document. > > It is widely considered the universal format for structured documents and > > data on the Web. Its power is that the recipient of a document can > > recognize the contained data elements following a worldwide standard, and > > can therefore more easily utilize and display the data in any desired > manner. > > > > XML annotates content, while, in contrast, HTML (HyperText Markup Language) > > annotates primarily appearance. HTML has a fixed set of tags, while XML > > (the X stands for eXtensible) is designed to accomodate an ever-growing set > > of discipline-specific tags. XML is an emerging standard, whereas HTML is a > > standard already in universal use for annotating information on the web. > > > > HTML specifies a static appearance for a document when displayed in a web > > browser. HTML alone does not enable the recipient web browser to identify > > the types of data elements contained in the document. For example, HTML can > > specify that a particular phrase be displayed centered in a large red bold > > font, but tells nothing about the kind of information in the phrase. In > > contrast, XML identifies the type of information. For example, XML tags > > could identify a certain portion of a document as the amino acid sequence > > for a specified protein. Presently, the content of a document that is of > > interest to a user must usually be selected by non-standard methods that > > are often inadequately automated. Once the desired information is extracted > > in computer-readable form, the format employed is often understood by only > > a subset of the programs in the world that deal with that type of > > information. XML provides a worldwide standard for content identification. > > > > XML itself is set of rules for writing discipline-specific implementations. > > The specifications for XML are managed by the World-Wide Web consortium in > the > > form of W3C Recommendations. Each subject discipline must develop its own > > a "Document Type Definition" (DTD) or "XML Schema" (see examples below). > > Discipline-specific content within a document is identified by a > > "namespace". A document can contain mixtures of types of content, that is, > > multiple namespaces. Within each namespace, the allowed content-identifying > > tags, and the nesting relationships of the tags, are specified by the > > corresponding Schema or DTD. For example, in the Chemical Markup Language > > (CML) Schema or DTD, one element is "cml:molecule". It can have child > > elements such as "cml:atomArray" and "cml:bondArray". The cml:bondArray > > element has "cml:atom" elements as its children. The XML Schema for a > > particular discipline, such as CML, is enforced by a validation process. > > Each Schema has a primary website, where the discipline-specific tags and > > and rules for validation are defined. > > > > Examples of well defined XML languages for common generic use include: > > 1. XHTML (a general document markup language derived from HTML), > > 2. SVG (scalable vector graphics) for expressing diagrams and visual > > information > > 3. MathML (Mathematical markup language). > > > > Specific scientific, technical and medical (STM) namespaced applications > > of XML include: > > > > 1. STMML (for description of scientific units and quantities), > > 2. CML (Chemical markup language) for expressing molecular content, > > 3. CellML for computer-based biological models, > > 4. GAME (Genome annotation markup elements), > > 5. MAGE-ML (MicroArray and Gene Expression Markup Language ), > > 6. Molecular Dynamics [Markup] Language (MoDL), > > 7. StarDOM - Transforming Scientific Data into XML, > > 8. Bioinformatic Sequence Markup Language (BSML), > > 9. BIOpolymer Markup Language (BIOML), > > 10. Gene Expression Markup Language (GEML), > > 11. GeneX Gene Expression Markup Language (GeneXML), > > 12. Genome Annotation Markup Elements (GAME), > > 13. XML for Multiple Sequence Alignments (MSAML), > > 14. Systems Biology Markup Language (SBML), > > 15. Protein Extensible Markup Language (PROXIML). > > > > Websites > > World Wide Web Consortium managing the specifications for XML: > > http://www.w3c.org > > Chemical Markup Language: http://www.xml-cml.org > > > > Further Reading > > Bosak J, Bray T (1999) XML and the second generation web. Scientific > > American, May 6 (http://www.sciam.com). > > Ezzell C (2001) Hooking up biologists. Scientific American, November 19. > > Murray-Rust P, Rzepa HS (2002) Scientific publications in XML -- towards a > > global knowledge base. Data Science 1:84-98. > > > (http://journals.eecs.qub.ac.uk/codata/Journal/Contents/1_1/1_1pdf/DS115.Pdf) > > > > See Also > > Atomic coordinate files > > MIME Types > > > > > > > > > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > > Protein Explorer - 3D Visualization: http://proteinexplorer.org > > Workshops: http://www.umass.edu/molvis/workshop > > World Index of Molecular Visualization Resources: http://molvisindex.org > > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > > PDB Lite Macromolecule Finder: http://pdblite.org > > Molecular Visualization EMail List: > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > Eric Martz, Professor (Immunology), Dept Microbiology > > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > > http://www.umass.edu/molvis/martz > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: mmCIF and XML Date: Wed, 04 Jun 2003 13:23:32 -0500 (CDT) To: timothy driscoll Cc: rasmol@lists.umass.edu Hi, No! :-) :-) > > I just have a couple of issues with your XML entry that are often > > overlooked or ignored that don't make me a fan of XML. > > > > XML is an enhancement of HTML so, using a loose definition, HTML is also > > XML (strict definition requires certain minor changes such as closing tags). I'm just too lazy to find all those

and

to them :-) > > > > While XML is a 'worldwide standard' the contents don't have to > > be nor have to be Open. I can put a MS word document as binary in my XML document. MS Word format is not standard except by ignorance (because you think you need it because people send you files with that format) nor is it Open. MS word is not that big a deal especially with Open Office (who uses an Open XML format by default) but other applications, especially multimedia, may even require a specific program and operating system (By the way, I actually like MS Word and Excel as programs - hard to argue with over ten years of effort. Open office is also excellent not only for it's price - free! But not MS Windows except to play games - yes, Wine and WineX are getting better.) Regards Bruce > > hi Bruce, > > I agree with your statements about XML. but I am not sure why you consider > the first two issues as negative aspects of the language. can you clarify? > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > Your XML entry avoids saying that XML can hold binary data. On one hand > > this is good in that images and programs can be included. But on the other > > you need the 'key' to unlock the binary format that may require the > > certain software or operating system. Second that binary data include a > > virus or similar such as infected MS word file. > > > > Regards > > Bruce > > > > On Wed, 4 Jun 2003, Eric Martz wrote: > > > > > At 6/3/03, Dan Bolser wrote: > > > >Is the XML format an encoding of the mmCIF, > > > >or a new format? > > > > > > > > > mmCIF is a data format for atomic coordinates and related information, > > > expected to supercede the PDB format. XML is a more general way of > > > identifying data content (in any discipline) for information transferred > > > through the Internet. > > > mmCIF can be encoded in XML (http://pdb.rutgers.edu/mmcif/). Neither is in > > > wide use at this time, I believe, although the expectation is that both > > > will become increasingly important and predominant. > > > > > > Information on mmCIF is available from the PDB: > > > http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards > > > > > > Below is the XML entry I wrote for a forthcoming Dictionary of > > > Bioinformatics (Wiley). Henry Rzepa and Peter Murray-Rust helped a lot > with > > > this XML entry. > > > > > > XML (eXtensible Markup Language) > > > > > > XML is a markup language that identifies data elements within a document. > > > It is widely considered the universal format for structured documents and > > > data on the Web. Its power is that the recipient of a document can > > > recognize the contained data elements following a worldwide standard, and > > > can therefore more easily utilize and display the data in any desired > > manner. > > > > > > XML annotates content, while, in contrast, HTML (HyperText Markup > Language) > > > annotates primarily appearance. HTML has a fixed set of tags, while XML > > > (the X stands for eXtensible) is designed to accomodate an ever-growing > set > > > of discipline-specific tags. XML is an emerging standard, whereas HTML is > a > > > standard already in universal use for annotating information on the web. > > > > > > HTML specifies a static appearance for a document when displayed in a web > > > browser. HTML alone does not enable the recipient web browser to identify > > > the types of data elements contained in the document. For example, HTML > can > > > specify that a particular phrase be displayed centered in a large red bold > > > font, but tells nothing about the kind of information in the phrase. In > > > contrast, XML identifies the type of information. For example, XML tags > > > could identify a certain portion of a document as the amino acid sequence > > > for a specified protein. Presently, the content of a document that is of > > > interest to a user must usually be selected by non-standard methods that > > > are often inadequately automated. Once the desired information is > extracted > > > in computer-readable form, the format employed is often understood by only > > > a subset of the programs in the world that deal with that type of > > > information. XML provides a worldwide standard for content identification. > > > > > > XML itself is set of rules for writing discipline-specific > implementations. > > > The specifications for XML are managed by the World-Wide Web consortium in > > the > > > form of W3C Recommendations. Each subject discipline must develop its own > > > a "Document Type Definition" (DTD) or "XML Schema" (see examples below). > > > Discipline-specific content within a document is identified by a > > > "namespace". A document can contain mixtures of types of content, that is, > > > multiple namespaces. Within each namespace, the allowed > content-identifying > > > tags, and the nesting relationships of the tags, are specified by the > > > corresponding Schema or DTD. For example, in the Chemical Markup Language > > > (CML) Schema or DTD, one element is "cml:molecule". It can have child > > > elements such as "cml:atomArray" and "cml:bondArray". The cml:bondArray > > > element has "cml:atom" elements as its children. The XML Schema for a > > > particular discipline, such as CML, is enforced by a validation process. > > > Each Schema has a primary website, where the discipline-specific tags and > > > and rules for validation are defined. > > > > > > Examples of well defined XML languages for common generic use include: > > > 1. XHTML (a general document markup language derived from HTML), > > > 2. SVG (scalable vector graphics) for expressing diagrams and visual > > > information > > > 3. MathML (Mathematical markup language). > > > > > > Specific scientific, technical and medical (STM) namespaced applications > > > of XML include: > > > > > > 1. STMML (for description of scientific units and quantities), > > > 2. CML (Chemical markup language) for expressing molecular content, > > > 3. CellML for computer-based biological models, > > > 4. GAME (Genome annotation markup elements), > > > 5. MAGE-ML (MicroArray and Gene Expression Markup Language ), > > > 6. Molecular Dynamics [Markup] Language (MoDL), > > > 7. StarDOM - Transforming Scientific Data into XML, > > > 8. Bioinformatic Sequence Markup Language (BSML), > > > 9. BIOpolymer Markup Language (BIOML), > > > 10. Gene Expression Markup Language (GEML), > > > 11. GeneX Gene Expression Markup Language (GeneXML), > > > 12. Genome Annotation Markup Elements (GAME), > > > 13. XML for Multiple Sequence Alignments (MSAML), > > > 14. Systems Biology Markup Language (SBML), > > > 15. Protein Extensible Markup Language (PROXIML). > > > > > > Websites > > > World Wide Web Consortium managing the specifications for XML: > > > http://www.w3c.org > > > Chemical Markup Language: http://www.xml-cml.org > > > > > > Further Reading > > > Bosak J, Bray T (1999) XML and the second generation web. Scientific > > > American, May 6 (http://www.sciam.com). > > > Ezzell C (2001) Hooking up biologists. Scientific American, November 19. > > > Murray-Rust P, Rzepa HS (2002) Scientific publications in XML -- towards a > > > global knowledge base. Data Science 1:84-98. > > > > > > (http://journals.eecs.qub.ac.uk/codata/Journal/Contents/1_1/1_1pdf/DS115.Pdf) > > > > > > See Also > > > Atomic coordinate files > > > MIME Types > > > > > > > > > > > > > > > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > > > Protein Explorer - 3D Visualization: http://proteinexplorer.org > > > Workshops: http://www.umass.edu/molvis/workshop > > > World Index of Molecular Visualization Resources: http://molvisindex.org > > > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > > > PDB Lite Macromolecule Finder: http://pdblite.org > > > Molecular Visualization EMail List: > > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > > > Eric Martz, Professor (Immunology), Dept Microbiology > > > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > > > http://www.umass.edu/molvis/martz > > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <5.2.0.9.0.20030603175622.00af0748@selway.umt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: The PDB and Education Date: Wed, 04 Jun 2003 14:54:26 -0400 To: rasmol@lists.umass.edu Judy, Thanks, I'm okay to be on the list. The one thing I would like to see for education is someone to update Chime and keep it current for all browsers; this is still the most student-friendly PDB tool for students, in my opinion. Joan Judy Voet wrote: > Dear Rasmol Colleagues, > I'm on the Advisory Board for the Protein Data Bank and the sole > representative of the undergraduate education community. I'd like to > be of as much service to that community as I can and so would like to > set up an email discussion group concerned with how the PDB can best > serve educational users. I don't want to fill Rasmolers email boxes > unnecessarily, so if you are interested in being part of such a > discussion group please email me back directly > (jvoet1@swarthmore.edu) and I'll set up an email list for us to use. > Thanks for your potential interest. > Judy Voet > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: Spam sent to list Date: Wed, 04 Jun 2003 22:16:22 +0200 To: rasmol@lists.umass.edu It's good to remind people who do use Outlook Express that they can change the default values so they have some control over the opening of attachments. It is also good to remind people that there are several formats for presenting virus/worms and gateway virus-checkers can often miss compressed files, etc. which contain such. I think the most important caveat is never open an executable file without verifying from the ostensible source the authorship of such files. Only twice since installing a firewall virus checker with McAfee on the client machines have virus/worms gotten past these barriers and in both cases these were embedded into zipped programs. Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz Sent: Wednesday, June 04, 2003 5:24 PM From: owner-rasmol@lists.umass.edu Subject: Spam sent to list To: rasmol@lists.umass.edu This list currently has 617 subscribers. Junk mail sent to the list is rejected automatically unless sent by a subscriber. I get several messages each day from the listproc reporting such rejections. I approve all subscriptions manually, thereby avoiding obvious spam. It is possible that by spoofing the address of a subscriber as the sender, yesterday's junk/virus email got through. To my knowledge, it is the first. I am attempting to trace the true sender. All subscribers should have virus detection software installed and keep their virus definitions up to date. I will remove the subscription of any subscriber whose computer is suspected of sending spam to the list more than once (presumably as a result of being infected with a virus). We have tried in the past to block any attachments from being broadcast to the list but this turns out to be problematic. The virus-blocking gates at my campus may have stripped the attachment from yesterday's message. Did anyone actually receive an attachment with the message spoofed from yaya@bernstein-plus-sons.com with subject "Re: Submited (004756-3463)"? Of course you should never open any attachment that you don't trust. Opening a virus-infected attachment will infect your computer. Our campus strongly discourages using Outlook Express for email because, by default, it automatically opens attachments. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <5.2.0.9.0.20030603175622.00af0748@selway.umt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert F. Volp" Subject: Re: The PDB and Education Date: Thu, 05 Jun 2003 08:58:53 -0500 To: rasmol@lists.umass.edu I am interested: robert.volp@murraystate.edu Bob Volp Department of Chemistry Murray State University (270)762-6598 ----- Original Message ----- Sent: Tuesday, 03 Jun 2003 19:26 From: "Judy Voet" Subject: The PDB and Education To: > Dear Rasmol Colleagues, > I'm on the Advisory Board for the Protein Data Bank and the sole > representative of the undergraduate education community. I'd like to > be of as much service to that community as I can and so would like to > set up an email discussion group concerned with how the PDB can best > serve educational users. I don't want to fill Rasmolers email boxes > unnecessarily, so if you are interested in being part of such a > discussion group please email me back directly > (jvoet1@swarthmore.edu) and I'll set up an email list for us to use. > Thanks for your potential interest. > Judy Voet > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: new virus alert Date: Thu, 05 Jun 2003 17:33:26 -0400 To: LIST rasmol hi folks, to follow up on a recent thread, there is another email virus running around: http://securityresponse.symantec.com/avcenter/venc/data/w32.bugbear.b@mm.html it is relevant to RasMol users in particular because the contaminated enclosure from this virus may have the extension .scr (commonly used for RasMol scripts). as always, do not open any enclosures without prior verification! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en X-MDRemoteIP: 194.225.5.223 X-Return-Path: goliaei@ibb.ut.ac.ir X-MDaemon-Deliver-To: rasmol@lists.umass.edu References: <5.2.0.9.0.20030603175622.00af0748@selway.umt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Bahram Goliaei Subject: Re: The PDB and Education Date: Sat, 07 Jun 2003 09:36:51 +0430 To: rasmol@lists.umass.edu I would like to be on this email list server for the PDB and education. Thanks, Bahram Goliaei Judy Voet wrote: > Dear Rasmol Colleagues, > I'm on the Advisory Board for the Protein Data Bank and the sole > representative of the undergraduate education community. I'd like to > be of as much service to that community as I can and so would like to > set up an email discussion group concerned with how the PDB can best > serve educational users. I don't want to fill Rasmolers email boxes > unnecessarily, so if you are interested in being part of such a > discussion group please email me back directly > (jvoet1@swarthmore.edu) and I'll set up an email list for us to use. > Thanks for your potential interest. > Judy Voet > -- Bahram Goliaei, PhD Professor of Biophysics, Bioinformatics Center, Laboratory of Biophysics and Molecular Biology, Institute of Biochemistry and Biophysics, University of Tehran P.O.Box 13145-1384 Tehran, Iran Tel: (009821) 6498672 Fax: (009821) 6956985 Email: goliaei@ibb.ut.ac.ir ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Searching, viewing theoretical models Date: Tue, 10 Jun 2003 19:32:52 -0400 To: rasmol@lists.umass.edu Cc: Jaime.Prilusky@weizmann.ac.il Since RCSB moved theoretical models to a separate database, it is hard to find them (see tiny "click here" link near the top of SearchFields), and apparently impossible to search them except for single-term matches. In contrast, the alternative search interface OCA (http://bioinfo.weizmann.ac.il:8500/) not only searches theoretical models, but can do a single search over both experimental and theoretical models. (The Method option "ANY Experimental Method" in fact searches theoretical models as well. For example, search for "bilayer" in the text query field and there are both experimental and theoretical models among the hits.) Thus, you can search for theoretical models submitted in 2003. There are 19, including for example 1P9T, a coronavirus protease which is an anti-SARS drug target. Trying to view 1P9T in Protein Explorer by entering the PDB code at the front door, or clicking on a PE link at OCA, won't work if you leave the source of PDB files at the default, RCSB. In order to view theoretical models in Protein Explorer conveniently, set your preferred source of PDB files to http://bioinfo.weizmann.ac.il:8500/. Click on Options above the message box, then on Preferences, then on Change Server, and follow instructions. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: [pdb_education] cross-platform functionality Date: Wed, 11 Jun 2003 12:17:11 +0200 To: owner-pdb_education@swarthmore.edu Cc: rasmol@lists.umass.edu RE: Ioannis Michalopoulos' comment: "As far as I am concerned these tools do not run on Linux machines. What we really need is a plug-in that would run in all browsers and all operating systems. Is there anything like that?" Cross-platform functionality is possible. For those who might have missed the comments on Jmol - here is the web-address: http://jmol.sourceforge.net. Take a look at what other projects are going on at www.sourceforge.net. I sent an email today to Jonathan Schwartz (EVP Sun Software Development)requesting Sun's support for the developing Jmol project. We will see how this goes. Oftentimes corporate programmers end up with a sandwich in one hand while they jot down ideas on their lunch breaks... all it takes is getting the word out in the right places. Right? So, trot on over to the Computer Science Department at your university and see if there are any "javaheads" with a minute to spare... Just curious: Anyone with update info concerning the Jmol problem with macromolecule presentation? That part of the jmol site was down when I looked at it last. Lewis Edgel -----Original Message----- [mailto:owner-pdb_education@swarthmore.edu]On Behalf Of Ioannis Michalopoulos Sent: Wednesday, June 11, 2003 10:58 AM From: owner-pdb_education@swarthmore.edu Subject: Re: [pdb_education] pdb/education Welcome To: pdb_education@swarthmore.edu Cc: Nicola Gold On Tue, 10 Jun 2003, Judy Voet wrote: > 1. Should the PDB maintain or support open source visualization tools > like Chime and/or WebLab so as to assure the continuation of such > free resources? Are there problems associated with this? As far as I am concerned these tools do not run on Linux machines. What we really need is a plug-in that would run in all browsers and all operating systems. Is there anything like that? > 2. How can the PDB search engine become as user-friendly as possible? > What problems should be addressed? Are there any coments on PDB Lite > maintained by Eric Martz, versus SearchLite on the PDB site? I think that a PDB search engine should take into account that information is stored in various fields in a PDB header, just like what "PDB SearchFields" does: http://www.rcsb.org/pdb/cgi/queryForm.cgi > Any feedback? > What other topics should we be addressing? We can address another two issues: * Uniformity of data. In many entries, we have deviations from the conventional PDB format. * PDB Mirroring. It would be very helpful if PDB was made available in an unzipped format via FTP in one single directory (EBI provides this service but it isn't sufficient because they retain obsolete files in the same directory). It would also be ideal if obsolete files were maintained in another single directory, instead of being fragmented in several directories. > Best regards, > Judy Best Regards, Ioannis -- .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr Ioannis Michalopoulos Research Fellow in Bioinformatics School of Biochemistry and Molecular Biology Tel: +44 113 34 33072 University of Leeds Fax: +44 113 34 33167 Leeds LS2 9JT ioannis@bioinformatics.leeds.ac.uk UK http://www.bioinformatics.leeds.ac.uk/~ioannis/ .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Sarnow Subject: Re: [pdb_education] cross-platform functionality Date: Wed, 11 Jun 2003 15:58:15 +0200 To: rasmol@lists.umass.edu Lewis Edgel wrote: > RE: Ioannis Michalopoulos' comment: > > "As far as I am concerned these tools do not run on Linux machines. What we > really need is a plug-in that would run in all browsers and all operating > systems. Is there anything like that?" > > Cross-platform functionality is possible. For those who might have missed > the comments on Jmol - here is the web-address: http://jmol.sourceforge.net. > Take a look at what other projects are going on at www.sourceforge.net. > > I sent an email today to Jonathan Schwartz (EVP Sun Software > Development)requesting Sun's support for the developing Jmol project. We > will see how this goes. Oftentimes corporate programmers end up with a > sandwich in one hand while they jot down ideas on their lunch breaks... all > it takes is getting the word out in the right places. Right? So, trot on > over to the Computer Science Department at your university and see if there > are any "javaheads" with a minute to spare... > > Just curious: Anyone with update info concerning the Jmol problem with > macromolecule presentation? That part of the jmol site was down when I > looked at it last. > > Lewis Edgel Thanks for this hint. Jmol is a nice program which frees all of us from thinking about the right operating system. Karl Sarnow -- Dr. Karl Sarnow Teacher at Gymnasium Isernhagen German national co-ordinator of the European Schools Project e-Mail: karl@dadoka.h.ni.schule.de URL: http://www.shuttle.schule.de/h/dadoka ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- egonw@sci.kun.nl Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: RE: [pdb_education] cross-platform functionality Date: Wed, 11 Jun 2003 17:37:25 +0200 (CEST) To: rasmol@lists.umass.edu Cc: lewis.edgel@telia.com, owner-pdb_education@swarthmore.edu, Lewis, Speaking on behalf of the jmol development team ... thanks for referring people to http://jmol.sourceforge.net > Cross-platform functionality is possible. For those who might have > missed the comments on Jmol - here is the web-address: > http://jmol.sourceforge.net. Take a look at what other projects are > going on at www.sourceforge.net. We realize that Jmol still has performance and functionality shortcomings for those who need to work with proteins. But we have made excellent progress in the last six months, including a very robust RasMol script interpreter. And we have very good momentum. I think you will be pleasantly surprised at what we will release over the next 6 months. All of my efforts right now are oriented towards two things: - dramatically improving rendering performance for large molecules - building a zbuffered 3d rendering engine to supports isosurfaces and protein visualization shapes (cartoons, ribbons, etc.) > I sent an email today to Jonathan Schwartz (EVP Sun Software > Development)requesting Sun's support for the developing Jmol project. > We will see how this goes. Thank you very much. > Just curious: Anyone with update info concerning the Jmol problem with > macromolecule presentation? That part of the jmol site was down when I > looked at it last. Hmmm ... If you haven't been to the jmol site within the last 6 weeks then I encourage you to take another look. I am eager to answer any/all questions you (or anyone) may have about jmol's support for macromolecules. To elaborate a little more on what I said above: Graphics rendering performance in the jmol 6.1 release is at least 4-8 times faster than it was 6 months ago. The development version is *another* 2-4 times faster still. Fundamentally, I am now convinced that there is no reason for us to be significantly slower than Rasmol/Chime. I am building a software 3d engine especially for rendering molecules. Java3d will *not* be required. And it *will* run on browsers with 1.1 JVMs. Currently, I am still working on basic shapes (spheres & cylinders), so I have not moved on to ribbons, etc. But the core of the engine is there, and intersecting spheres (spacefill on) look great :) I'll be glad to answer any other questions. And any feedback/assistance/advice from the Rasmol/Chime community would be greatly appreciated. Miguel > > Lewis Edgel > > -----Original Message----- > From: owner-pdb_education@swarthmore.edu > [mailto:owner-pdb_education@swarthmore.edu]On Behalf Of Ioannis > Michalopoulos > Sent: Wednesday, June 11, 2003 10:58 AM > To: pdb_education@swarthmore.edu > Cc: Nicola Gold > Subject: Re: [pdb_education] pdb/education Welcome > > > On Tue, 10 Jun 2003, Judy Voet wrote: >> 1. Should the PDB maintain or support open source visualization tools >> like Chime and/or WebLab so as to assure the continuation of such >> free resources? Are there problems associated with this? > > As far as I am concerned these tools do not run on Linux machines. > What we really need is a plug-in that would run in all browsers and > all operating systems. Is there anything like that? > >> 2. How can the PDB search engine become as user-friendly as possible? >> What problems should be addressed? Are there any coments on PDB Lite >> maintained by Eric Martz, versus SearchLite on the PDB site? > > I think that a PDB search engine should take into account that > information is > stored in various fields in a PDB header, just like what "PDB > SearchFields" does: > > http://www.rcsb.org/pdb/cgi/queryForm.cgi > >> Any feedback? >> What other topics should we be addressing? > > We can address another two issues: > > * Uniformity of data. In many entries, we have deviations from the > conventional > PDB format. > > * PDB Mirroring. It would be very helpful if PDB was made available in > an unzipped format via FTP in one single directory (EBI provides this > service but > it isn't sufficient because they retain obsolete files in the same > directory). > It would also be ideal if obsolete files were maintained in another > single directory, instead of being fragmented in several directories. > >> Best regards, >> Judy > > Best Regards, > Ioannis > -- > .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. > /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ > X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ > \|||X > `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' > Dr Ioannis Michalopoulos Research Fellow in > Bioinformatics School of Biochemistry and Molecular Biology Tel: > +44 113 34 33072 University of Leeds > Fax: +44 113 34 33167 Leeds LS2 9JT > ioannis@bioinformatics.leeds.ac.uk UK > http://www.bioinformatics.leeds.ac.uk/~ioannis/ > .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. > /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ > X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ > \|||X > `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Craig Subject: Bioinformatics workshop at RIT Date: Thu, 12 Jun 2003 14:25:34 -0400 To: rasmol@lists.umass.edu A bioinformatics workshop will be held at the Rochester Institute of Technology in Rochester NY from July 10-12, 2003. This workshop is sponsored by NSF and intended to bring computer scientists and biologists together. We still have openings for biologists. Please see the attached brochure. Paul Paul A. Craig Associate Professor Dept. of Chemistry Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623-5603 Telephone: 585-475-6145 FAX: 585-475-7800 ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Craig Subject: Bioinformatics workshop at RIT Date: Fri, 13 Jun 2003 10:36:37 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_5wLB54W/3zgN+0jkjdr7+Q) A bioinformatics workshop will be held at the Rochester Institute of Technology in Rochester NY from July 10-12, 2003. This workshop is sponsored by NSF and intended to bring computer scientists and biologists together. We still have openings for biologists. Please see the description below. I apologize for sending the announcement as an attachment before. Paul Paul A. Craig Associate Professor Dept. of Chemistry Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623-5603 Telephone: 585-475-6145 FAX: 585-475-7800 Rochester Institute of Technology Bioinformatics Program Department of Biological Sciences 585.475.2532 www.bioinformatics.rit.edu grssbi@rit.edu bioinformatics workshop for educators v2.0 As educators we are challenged to integrate the diverse disciplines underlying modern Bioinformatics into our courses and curricula. This July we will bring together educators from around the country to participate in the second annual bioinformatics workshop for educators. This workshop will: . introduce computer scientists and biologists to each other's discipline . demonstrate methods for incorporating computer science into the biological sciences . demonstrate methods for incorporating the biological sciences into computer science . promote the formation of a network of collaborating educators Due to the generous sponsorship of the NSF there will be no charge for registration, food or lodging. However, each participant is responsible for his or her own travel expenses and arrangements. The workshop will be held on the RIT campus in Rochester, NY. Accommodations will be provided in the spacious, air conditioned, RIT dormitories. Workshop instructors include faculty from the RIT departments of Biological Sciences, Computer Science, Information Technology, Mathematics and Statistics and Computer Science at Canisius College. Space is limited so please call 585.475.2532 to reserve your place in this important workshop. when: 07/10/02-07/12/03 where: rochester institute of technology rochester, ny rsvp: 585.475.2532 bioinformatics workshop for educators v2.0 Rochester Institute of Technology Bioinformatics Program Department of Biological Sciences 585.475.2532 www.bioinformatics.rit.edu grssbi@rit.edu Day 1 Biology Track for CS CS Track for Biologists July 10, 2003 8:15-8:30 Welcome 8:30-9:30 The Central Dogma(s) Computing for Biologists 9:30-10:00 Computational Tools: Perl Programming (lab) 10:00-10:15 Morning Break 10:15-12:00 Computational Tools: Perl Programming (continued) 12:00-1:30 Lunch 1:30-3:45 Gene Identification (lab) 3:45-4:00 Afternoon Break 4:00-5:00 Development and Pathogenesis Sequence Alignments 6:00-8:00 Dinner Day 2 Biology Track for CS CS Track for Biologists Friday, July 11, 2003 8:30-10:00 DNA Sequencing and Fragment Reassembly (lab) 10:00-10:15 Morning Break 10:15-11:00 DNA Sequencing and Fragment Reassembly (continued) 11:00-12:00 Bioanalytical Tools:DNA Sequencing (lab tour) (Biology Track for CS) High Performance Computing for Bioinformatics (CS Track for Biologists) 12:00-1:30 Lunch 1:30-3:45 Gene Expression Analysis (lab) 3:45-4:00 Afternoon Break 4:00-5:00 Statistical Methods for Bioinformatics 6:00-8:00 Dinner with Discussion of Bioinformatics Education Day 3 Plenary Sessions 8:30-11:00 Building and Using Biological Databases (lab) 10:00-10:15 Morning Break 10:15-11:00 Building and Using Biological Databases (continued) 11:00-12:00 Proteomics 12:00-1:30 Lunch 1:30-3:45 Predicting and Visualizing Protein Structure (lab) 3:45-4:00 Afternoon Break 4:00-5:00 Comparative Genomics Participants should arrive on Wednesday 9 July 2003, the first day of the workshop is Thursday 10 July 2003. Labs indicated above are computer labs and will involve a mixture of lecture and hands-on exercises. ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: mac IE5 is the end Date: Tue, 17 Jun 2003 07:48:58 -0400 To: LIST rasmol thought you might like to know: > We'll always have Safari: Microsoft announced on Friday that they > no longer plan to develop Internet Explorer for the Mac platform. > Although the company will release an update that offers security > and performance tweaks, they will no longer roll out browsers > with new features. "Support for IE 5 is not ending, but we will > no longer be developing future versions of Internet Explorer," > Jessica Sommer, product manager for Microsoft's Mac Business Unit, > told MacCentral. > > Microsoft Drops Development of Internet Explorer for Mac > http://click.macworld.email-publisher.com/maabaUhaaYEmObWgnCgb/ regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_pUxGEbwTXHIL22Xui64pAw)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 13:22:47 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_pUxGEbwTXHIL22Xui64pAw) Funny, I was just thinking the other day that mac osX had the benifits of two worlds - linux open source and windows office (the only thing windows is good for) I wonder how long this situation will last before the tipical 'Windows is feeling insecure' dialogue appears, and they stop supporting mac altogether. timothy driscoll wrote: >thought you might like to know: > > > >>We'll always have Safari: Microsoft announced on Friday that they >>no longer plan to develop Internet Explorer for the Mac platform. >>Although the company will release an update that offers security >>and performance tweaks, they will no longer roll out browsers >>with new features. "Support for IE 5 is not ending, but we will >>no longer be developing future versions of Internet Explorer," >>Jessica Sommer, product manager for Microsoft's Mac Business Unit, >>told MacCentral. >> >>Microsoft Drops Development of Internet Explorer for Mac >>http://click.macworld.email-publisher.com/maabaUhaaYEmObWgnCgb/ >> >> > > >regards, > >:tim > > > --Boundary_(ID_pUxGEbwTXHIL22Xui64pAw) Funny, I was just thinking the other day that mac osX had the
benifits of two worlds - linux open source and windows office
(the only thing windows is good for) I wonder how long this
situation will last before the tipical 'Windows is feeling insecure'
dialogue appears, and they stop supporting mac altogether.

timothy driscoll wrote:
thought you might like to know:

  
We'll always have Safari: Microsoft announced on Friday that they
no longer plan to develop Internet Explorer for the Mac platform.
Although the company will release an update that offers security
and performance tweaks, they will no longer roll out browsers
with new features. "Support for IE 5 is not ending, but we will
no longer be developing future versions of Internet Explorer,"
Jessica Sommer, product manager for Microsoft's Mac Business Unit, 
told MacCentral.

Microsoft Drops Development of Internet Explorer for Mac
http://click.macworld.email-publisher.com/maabaUhaaYEmObWgnCgb/
    


regards,

:tim

--Boundary_(ID_pUxGEbwTXHIL22Xui64pAw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 08:48:33 -0400 To: rasmol@lists.umass.edu at 1:22 PM EDT on (Tuesday) 17 June 2003 Dan Bolser said: > Funny, I was just thinking the other day that mac osX had the > benifits of two worlds - linux open source and windows office > (the only thing windows is good for) I wonder how long this > situation will last before the tipical 'Windows is feeling insecure' > dialogue appears, and they stop supporting mac altogether. > is there an actual dialog box in offiice:mac that says "Windows is feeling insecure"? that would be amusing :-) according to the microsoft release, they are still actively developing office for mac. but I wonder, too - that may only last until apple finds a viable alternative to office. then, poof? ynk. (no, appleworks 6 is not viable.) microsoft, of course, will deny everything until the nanosecond before they pull the plug. remember when they discontinued support for old-style plug-ins and had everyone scrambling to activex? well, almost everyone ;-) personally, I think safari browses faster, does a better job with javascript and css support, and looks cooler than ie5mac - but that's just me. now if only chime would run in safari... regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > timothy driscoll wrote: > > >thought you might like to know: > > > > > > > >>We'll always have Safari: Microsoft announced on Friday that they > >>no longer plan to develop Internet Explorer for the Mac platform. > >>Although the company will release an update that offers security > >>and performance tweaks, they will no longer roll out browsers > >>with new features. "Support for IE 5 is not ending, but we will > >>no longer be developing future versions of Internet Explorer," > >>Jessica Sommer, product manager for Microsoft's Mac Business Unit, > >>told MacCentral. > >> > >>Microsoft Drops Development of Internet Explorer for Mac > >>http://click.macworld.email-publisher.com/maabaUhaaYEmObWgnCgb/ > >> > >> > > > > > >regards, > > > >:tim > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_wRYky9+zDnhZXlFKxdxa/Q)" ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 09:09:32 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_wRYky9+zDnhZXlFKxdxa/Q) I just downloaded Safari and it is amazingly fast. Chime does not work, nor does JavaScript 1.1 http://webphysics.davidson.edu/Applets/animator4/default.html Since Safari is open source, this should provide opportunities for further development. But I am not the person who can do this. Jmol also is missing the central carbons, and the animations do not play. Malcolm ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_wRYky9+zDnhZXlFKxdxa/Q) I just downloaded Safari and it is amazingly fast. Chime does not work, nor does JavaScript 1.1 http://webphysics.davidson.edu/Applets/animator4/default.html Since Safari is open source, this should provide opportunities for further development. But I am not the person who can do this. Jmol also is missing the central carbons, and the animations do not play. Malcolm Helvetica ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_wRYky9+zDnhZXlFKxdxa/Q)-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 08:13:08 -0500 (CDT) To: timothy driscoll Cc: rasmol@lists.umass.edu Hi, > > according to the microsoft release, they are still actively developing office > for mac. but I wonder, too - that may only last until apple finds a viable > alternative to office. then, poof? ynk. (no, appleworks 6 is not viable.) Try OpenOffice.org :-) There is are Linux, Mac, Windows and Solaris versions. It is rather powerful and free. > > microsoft, of course, will deny everything until the nanosecond before they > pull the plug. remember when they discontinued support for old-style plug-ins > and had everyone scrambling to activex? well, almost everyone ;-) > > personally, I think safari browses faster, does a better job with javascript > and css support, and looks cooler than ie5mac - but that's just me. now if > only chime would run in safari... > > regards, > > :tim Safari is based the engine of KDE's Konqueror browser and one of reasons the Mac team chose it was speed. Under Linux with the crossover plugin, Konqueror does run chime. It has been reported that Wine will build under Mac OS X so there might eventually be a way around this as the crossover plugin uses Wine. However, running Protein Explorer is a different story due executescript issue. Regards Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.3 X-Spam-Status: No, hits=-106.2 required=5.8 tests=AWL,BAYES_01,EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REFERENCES,REPLY_WITH_QUOTES,SIGNATURE_LONG_DENSE, USER_AGENT_KMAIL,USER_IN_WHITELIST autolearn=ham version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) References: <3EEF0817.3030203@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 16:31:58 +0000 To: rasmol@lists.umass.edu, Dan Bolser On Tuesday 17 June 2003 12:22 pm, Dan Bolser wrote: > Funny, I was just thinking the other day that mac osX had the > benifits of two worlds - linux open source and windows office You might think of crossover-officehttp://www.codeweavers.com/products/office/ , or lindows http://www.lindows.com/ they both are MUCH cheaper than MacOSX > (the only thing windows is good for) -- Boris Gorelik -= ( 2*b || !(2*b)) That's the question =- Tue, 17/Jun/2003, 17 Sivan 5763 ------------------------------------------------- ! Molecular Modelling Group ! ! Pharmacy School, Hadassa Faculty of medicine ! ! The Hebrew University of Jerusalem ! ! http://www.md.huji.ac.il/models/group.html ! ! !------------------------------------------------ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 09:42:46 -0400 To: rasmol@lists.umass.edu at 9:09 AM EDT on (Tuesday) 17 June 2003 A.Malcolm Campbell said: > I just downloaded Safari and it is amazingly fast. Chime does not work, > nor does JavaScript 1.1 > http://webphysics.davidson.edu/Applets/animator4/default.html > afaik, safari should support js 1.1. are you speaking from experience, or did you find some documentation? determining why js code breaks in safari is frustrating, since it does not provide a js error reporting method. in general, safari stacks up pretty well when it comes to js support: so I would be very surprised if it didn't support core js 1.1. you might try setting your javascript to v1.1 in your html; iow, use script language="javascript 1.1" instead of script language="javascript" > Since Safari is open source, this should provide opportunities for > further development. But I am not the person who can do this. > > Jmol also is missing the central carbons, and the animations do not play. > > Malcolm > does jmol require the java3d plug-in? (sorry; I don't use it and can't scare up a link right now.) for example, javamage (an applet) works omm (os 10.2.6, safari 1.0b2 v74): but mice, which requires the java3d plug-in, does not. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3EEF0817.3030203@mrc-dunn.cam.ac.uk> <200306171631.58355.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 17:01:37 +0100 (BST) To: bgbg@pob.huji.ac.il Cc: rasmol@lists.umass.edu Boris Gorelik said: > On Tuesday 17 June 2003 12:22 pm, Dan Bolser wrote: >> Funny, I was just thinking the other day that mac osX had the >> benifits of two worlds - linux open source and windows office > > You might think of crossover-officehttp://www.codeweavers.com/products/office/ , > or lindows http://www.lindows.com/ > they both are MUCH cheaper than MacOSX Cool, I have found codeweavers to be an excelent choice in the past - I always promised them I would actually buy the software one day! Now that they actually support office in full, maby it is finally time to put MS in the bin! It does make me laugh when MS detects my linux disk... "Windows is feeling paranoid, format this disk?" >> (the only thing windows is good for) Cheers, Dan. > -- > Boris Gorelik > -= ( 2*b || !(2*b)) That's the question =- > Tue, 17/Jun/2003, 17 Sivan 5763 > ------------------------------------------------- > ! Molecular Modelling Group ! > ! Pharmacy School, Hadassa Faculty of medicine ! > ! The Hebrew University of Jerusalem ! > ! http://www.md.huji.ac.il/models/group.html ! > ! > !------------------------------------------------ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-MSMail-priority: Normal References: <3EEF0817.3030203@mrc-dunn.cam.ac.uk> <200306171631.58355.bgbg@pob.huji.ac.il> <3131.213.107.104.19.1055865697.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Sophia Siedlberg Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 17:30:07 +0100 To: rasmol@lists.umass.edu Hi > "Windows is feeling paranoid, format this disk?" Well I am getting sick of windows quite frankly. The only real problems I have with getting hold of linux are the fact that downloading the distros via a dial up modem are impractical, and I have yet to find a CD of any distro that can be installed without wasting a lot of time fiddling and tweaking. I really need to get linux, because then I can port all my Borland Delphi source over to Kylix and just bin Windoze all together. As well as take advantage of the software discussed here :-) If anyone can suggest a good copy of Linux, and where to get it, This would be most helpful All the best Sophia Siedlberg Orlania Biosystems. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: rgb color converter Date: Tue, 17 Jun 2003 13:22:34 -0400 To: LIST rasmol greetings, most of you probably know that chime and html use hex rgb color codes, while rasmol and other programs use decimal. I have often been forced to convert lists of color codes by hand, which is tedious. to get around that, I have written a javascript utility that allows easy conversion between hex and decimal color codes: just type or paste your color codes into the entry box, select your output options, and hit the convert button. current options include: 1. single code or batch processing. 2. output to a new window. 3. add a custom prefix and suffix onto converted color codes. 4. use a custom separator between multiple codes. 5. force all codes in a batch into either hex or decimal format (by default, the converter looks at each color code individually and converts it into the opposite type.) for example, my entry might be directly from a rasmol script: select all color [200,200,200] select protein color [100,250,250] select dna color [210,50,210] select hetero color [255,255,255] select water color [50,50,210] using the converter, I can quickly turn this into a series of html tags: the instructions and explanations are fairly straightforward, and syntax rules are included on site. if you have any questions or want to suggest other features, please feel free to drop me a line. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: rgb color converter Date: Tue, 17 Jun 2003 21:04:44 +0200 To: rasmol@lists.umass.edu Go Timothy! That was a great idea! I noticed you reserve all rights:()I will want to use this occasionally when I teach JS to high-school students. I am sure some of the students will want to include the script in their creations. Is that OK? Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of timothy driscoll Sent: den 17 juni 2003 19:23 From: owner-rasmol@lists.umass.edu Subject: rgb color converter To: LIST rasmol greetings, most of you probably know that chime and html use hex rgb color codes, while rasmol and other programs use decimal. I have often been forced to convert lists of color codes by hand, which is tedious. to get around that, I have written a javascript utility that allows easy conversion between hex and decimal color codes: just type or paste your color codes into the entry box, select your output options, and hit the convert button. current options include: 1. single code or batch processing. 2. output to a new window. 3. add a custom prefix and suffix onto converted color codes. 4. use a custom separator between multiple codes. 5. force all codes in a batch into either hex or decimal format (by default, the converter looks at each color code individually and converts it into the opposite type.) for example, my entry might be directly from a rasmol script: select all color [200,200,200] select protein color [100,250,250] select dna color [210,50,210] select hetero color [255,255,255] select water color [50,50,210] using the converter, I can quickly turn this into a series of html tags: the instructions and explanations are fairly straightforward, and syntax rules are included on site. if you have any questions or want to suggest other features, please feel free to drop me a line. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerAdmin: mail-scanner-support@ucs.cam.ac.uk X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: References: <3EEF0817.3030203@mrc-dunn.cam.ac.uk> <200306171631.58355.bgbg@pob.huji.ac.il> <3131.213.107.104.19.1055865697.squirrel@www.mrc-dunn.cam.ac.uk> <001b01c334ed$cb575e60$698e883e@u9a0y7> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 20:31:25 +0100 (BST) To: rasmol@lists.umass.edu Cc: sophie@orlania.fsnet.co.uk Red Hat 9 has the best install of the RH series I have seen, and you can mail order the CD's (three of them) from the Red Hat website. In other respects RH9 is a step backwards. Sadly, if your hardware is slightly non standard, you will still have to tweek. Good luck. Sophia Siedlberg said: > Hi > > >> "Windows is feeling paranoid, format this disk?" > > Well I am getting sick of windows quite frankly. The only real problems I have > with getting hold of linux are the fact that downloading the distros via a dial up > modem are impractical, and I have yet to find a CD of any distro that can be > installed without wasting a lot of time fiddling and tweaking. > > I really need to get linux, because then I can port all my Borland Delphi source > over to Kylix and just bin Windoze all together. As well as take advantage of the > software discussed here :-) > > If anyone can suggest a good copy of Linux, and where to get it, This would be > most helpful > > All the best > > Sophia Siedlberg > > Orlania Biosystems. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer and executeScript() Date: Tue, 17 Jun 2003 15:19:26 -0400 To: rasmol@lists.umass.edu At 6/17/03, Bruce Southey wrote: >However, running Protein Explorer is a different story >due executescript issue. Actually, Bruce, since Protein Explorer was adapted to run in Internet Explorer (in 2002), it has browser-specific code that avoids executeScript() entirely when running in IE. It should be possible to adapt PE to work in any browser that is compatible with the major functions of Chime. In fact, Chime works far from perfectly in IE but so far, with months of extra effort, I have been able to work around the problems (see details at http://molvis.sdsc.edu/protexpl/ie.htm). I am not aware of any browsers that fully support Chime except for Netscape 4.x and IE 5.5SP2/6.0. I am unclear whether Netscape 6 is. I personally do not have time to adapt PE to other browsers because the very limited audience they have means this it is not a priority compared to other enhancements I can do. However, volunteers are free to do so. The entire source code of PE comes with every download and I'm happy to help someone get started or when they get stuck. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: rgb color converter Date: Tue, 17 Jun 2003 15:28:34 -0400 To: rasmol@lists.umass.edu at 9:04 PM EDT on (Tuesday) 17 June 2003 Lewis Edgel said: > Go Timothy! That was a great idea! I noticed you reserve all rights:()I will want to > use this occasionally when I teach JS to high-school students. I am sure > some of the students will want to include the script in their creations. Is > that OK? > > Lewis Edgel > oops - sorry. that notice is a holdover from my normal web page template. the rgb converter is completely free of any restriction on its use, distribution, or modification. if you want the full utility for local use, just drop me an email and I can provide it intact. sorry for the confusion! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of timothy driscoll > Sent: den 17 juni 2003 19:23 > To: LIST rasmol > Subject: rgb color converter > > > greetings, > > most of you probably know that chime and html use hex rgb color codes, while > rasmol and other programs use decimal. I have often been forced to convert > lists of color codes by hand, which is tedious. to get around that, I have > written a javascript utility that allows easy conversion between hex and > decimal color codes: > > > > > just type or paste your color codes into the entry box, select your output > options, and hit the convert button. current options include: > > 1. single code or batch processing. > 2. output to a new window. > 3. add a custom prefix and suffix onto converted color codes. > 4. use a custom separator between multiple codes. > 5. force all codes in a batch into either hex or decimal format (by default, > the converter looks at each color code individually and converts it into the > opposite type.) > > > for example, my entry might be directly from a rasmol script: > > select all > color [200,200,200] > select protein > color [100,250,250] > select dna > color [210,50,210] > select hetero > color [255,255,255] > select water > color [50,50,210] > > > using the converter, I can quickly turn this into a series of html tags: > > > > > > > > > the instructions and explanations are fairly straightforward, and syntax > rules > are included on site. if you have any questions or want to suggest other > features, please feel free to drop me a line. > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: <3EEF0817.3030203@mrc-dunn.cam.ac.uk> <200306171631.58355.bgbg@pob.huji.ac.il> <3131.213.107.104.19.1055865697.squirrel@www.mrc-dunn.cam.ac.uk> <001b01c334ed$cb575e60$698e883e@u9a0y7> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: mac IE5 is the end Date: Tue, 17 Jun 2003 18:40:41 -0300 To: rasmol@lists.umass.edu Hi, The best linux distros are Debian and Slackware because they are solid and mantain the GNU/Open Source spirit. If you want an easy installation distro use Mandrake, RedHat or SuSe. Regards, Sophia Siedlberg wrote: > Hi > > > >>"Windows is feeling paranoid, format this disk?" > > > Well I am getting sick of windows quite frankly. The only real problems I > have with getting hold of linux are the fact that downloading the distros > via a dial up modem are impractical, and I have yet to find a CD of any > distro that can be installed without wasting a lot of time fiddling and > tweaking. > > I really need to get linux, because then I can port all my Borland Delphi > source over to Kylix and just bin Windoze all together. As well as take > advantage of the software discussed here :-) > > If anyone can suggest a good copy of Linux, and where to get it, This would > be most helpful > > All the best > > Sophia Siedlberg > > Orlania Biosystems. > > > -- Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- dcr@kinemage.biochem.duke.edu, bryant@ncbi.nlm.nih.gov, hogue@mshri.on.ca, neshich@cbi.cnptia.embrapa.br ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Some molvis software citation stats Date: Tue, 17 Jun 2003 23:17:04 -0400 To: rasmol@lists.umass.edu, discuspv@USM.MAINE.EDU Cc: jsr@biochem.duke.edu, dcrjsr@kinemage.biochem.duke.edu, Dear MolVisualizers: At highwire.stanford.edu you can search full text of a subset of journals for the past few years only (since full text began to be on-line, ca. 2000). This enables one to find papers that mention/acknowledge visualization software. 5 papers cite RasTop. 21 papers not authored by me cite Protein Explorer (http://molvis.sdsc.edu/protexpl/pe_lit.htm#cits) There are 30-some papers not authored by the NCBI team that cite Cn3D. There are probably >50 that cite "deepview", "deep view", or "swisspdb". There appear to be >50 that cite PyMol. "Weblab" gets 179 hits (now "Accelrys Viewer" but that phrase gets zero hits). "kinemage*" gets 453 hits. And finally ... stand back ... there are >700 papers that mention RasMol! Congratulations to Roger Sayle, the openrasmol team, and David Richardson! Some names are confounded by synonyms making it difficult to get an accurate count. MAGE is a gene family. CHIME is a common word and acronym (e.g. Collaborative Home Infant Monitor Evaluation). CHIMERA and STING are biologial terms. DINO is a gene and shorthand for dinosaur. QMOL is a chemical term. VMD is a common acronym (e.g. vitelliform macular dystrophy). (The home pages for these and other software packages are at http://molvisindex.org in the freeware category.) -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: mac IE5 is the end Date: Wed, 18 Jun 2003 09:04:06 -0500 (CDT) To: rasmol@lists.umass.edu Hi, On Tue, 17 Jun 2003, Fernando Gabriel Ranea wrote: > Hi, > > The best linux distros are Debian and Slackware because they are solid > and mantain the GNU/Open Source spirit. The assertion that Debian and Slackware "maintain the GNU/Open Source spirit" and other distributions don't is very incorrect! Not to mention that Free Software Foundation/GNU don't have the same "spirit" as Open Source. However, this is not the forum for this. Red Hat, SuSE and Mandrake are widely recommended for new users to Linux for very good reasons, especially for ease of use and hardware support, whereas Debian is not. There are also other ways to examine Linux without installing such as SuSE Linux for i386 Live-Eval (a free download if you can burn it) or pure cd-based distributions (KNOPPIX is very popular one). Regards Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en-us, en References: <3EEF0817.3030203@mrc-dunn.cam.ac.uk> <200306171631.58355.bgbg@pob.huji.ac.il> <3131.213.107.104.19.1055865697.squirrel@www.mrc-dunn.cam.ac.uk> <001b01c334ed$cb575e60$698e883e@u9a0y7> ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Sarnow Subject: Re: mac IE5 is the end Date: Wed, 18 Jun 2003 16:46:13 +0200 To: rasmol@lists.umass.edu Sophia Siedlberg wrote: ... > If anyone can suggest a good copy of Linux, and where to get it, This would > be most helpful > > All the best > > Sophia Siedlberg > > Orlania Biosystems. > I had my first positive experiences with SuSE Linux. Just because of the YaST, which is an easy to follow adminstration tool. You can administer a whole network by using this GUI tool. It helped me a lot. Karl -- Dr. Karl Sarnow Teacher at Gymnasium Isernhagen German national co-ordinator of the European Schools Project e-Mail: karl@dadoka.h.ni.schule.de URL: http://www.shuttle.schule.de/h/dadoka ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Protein Explorer and executeScript() Date: Wed, 18 Jun 2003 11:18:59 -0500 (CDT) To: rasmol@lists.umass.edu Hi, For those interested, under Mozilla 1.2.1 with crossover plugin, using the current IMBIF hangs in s2c2.js at the command (about line 550): tg = top.fr_chime.document.invisible.document; This probably due to the different document object models involved between Netscape and IE. Although the downloadable interface examples work... Regards Bruce On Tue, 17 Jun 2003, Eric Martz wrote: > At 6/17/03, Bruce Southey wrote: > >However, running Protein Explorer is a different story > >due executescript issue. > > > Actually, Bruce, since Protein Explorer was adapted to run in Internet > Explorer (in 2002), it has browser-specific code that avoids > executeScript() entirely when running in IE. > > It should be possible to adapt PE to work in any browser that is compatible > with the major functions of Chime. In fact, Chime works far from perfectly > in IE but so far, with months of extra effort, I have been able to work > around the problems (see details at http://molvis.sdsc.edu/protexpl/ie.htm). > > I am not aware of any browsers that fully support Chime except for Netscape > 4.x and IE 5.5SP2/6.0. I am unclear whether Netscape 6 is. I personally do > not have time to adapt PE to other browsers because the very limited > audience they have means this it is not a priority compared to other > enhancements I can do. However, volunteers are free to do so. The entire > source code of PE comes with every download and I'm happy to help someone > get started or when they get stuck. > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: es-ar, es, en References: X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h5J43fj17706 ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: mac IE5 is the end Date: Wed, 18 Jun 2003 15:36:08 -0300 To: rasmol@lists.umass.edu Hi, First: When I said that "other distributions don't mantains the GNU/Open Source"? Debian and Slackare are the only Linux distro that not change de Kernel from kernel.org and they mantain a "pure" GNU spirit. Second: SuSe is a restrictive Linux distro and Yasta (the "visual install" for SuSe is not Open Source). Third: Debian and Slackware aren´t in NASDAQ Stock Market. Fourth: Linux is GNU/Linux and Open Source is not equal a "freeware". You can obtain money develop Open Source software Regards southey@ux1.cso.uiuc.edu wrote: > Hi, > > On Tue, 17 Jun 2003, Fernando Gabriel Ranea wrote: > > >>Hi, >> >>The best linux distros are Debian and Slackware because they are solid >>and mantain the GNU/Open Source spirit. > > > The assertion that Debian and Slackware "maintain the GNU/Open Source > spirit" and other distributions don't is very incorrect! Not to mention > that Free Software Foundation/GNU don't have the same "spirit" as Open > Source. However, this is not the forum for this. > > Red Hat, SuSE and Mandrake are widely recommended for new users to Linux > for very good reasons, especially for ease of use and hardware support, > whereas Debian is not. There are also other ways to examine Linux without > installing such as SuSE Linux for i386 Live-Eval (a free download if you > can burn it) or pure cd-based distributions (KNOPPIX is very popular one). > > Regards > Bruce > > ----------------------------------------------------------------rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------rasmol-- > > -- Fernando Gabriel Ranea fernandoranea@microbiologia.org.ar http://www.microbiologia.org.ar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: Protein Explorer and executeScript() Date: Wed, 18 Jun 2003 20:52:29 +0200 To: rasmol@lists.umass.edu Hi, in fact, the IMBIF method works well with Netscape 6.2, 7.x and Mozilla (since 0.9 release). I tried to make Protein Explorer be compatible with Mozilla, but, if IMBIF does work there are many differences between the ways Mozilla and communicator handle javascript. So there are many places where tests must be included. I succeed in making MolUSc work under Mozilla. MolUSc is a simple Protein Explorer like program, which uses the IMBIF method. An updated english translation will be released in the following month. A beta version has been succesfully tested by Bruce Southey under Linux with the crossover plug-in (thanks Bruce ;-)). I'll drop a message to the list when MolUSc is ready. Regards Paul ----- Original Message ----- Sent: Wednesday, June 18, 2003 6:18 PM From: Subject: Re: Protein Explorer and executeScript() To: > Hi, > > For those interested, under Mozilla 1.2.1 with crossover plugin, using the > current IMBIF hangs in s2c2.js at the command (about line 550): > > tg = top.fr_chime.document.invisible.document; > > This probably due to the different document object models involved > between Netscape and IE. > > Although the downloadable interface examples work... > > Regards > Bruce > > On Tue, 17 Jun 2003, Eric Martz wrote: > > > At 6/17/03, Bruce Southey wrote: > > >However, running Protein Explorer is a different story > > >due executescript issue. > > > > > > Actually, Bruce, since Protein Explorer was adapted to run in Internet > > Explorer (in 2002), it has browser-specific code that avoids > > executeScript() entirely when running in IE. > > > > It should be possible to adapt PE to work in any browser that is compatible > > with the major functions of Chime. In fact, Chime works far from perfectly > > in IE but so far, with months of extra effort, I have been able to work > > around the problems (see details at http://molvis.sdsc.edu/protexpl/ie.htm). > > > > I am not aware of any browsers that fully support Chime except for Netscape > > 4.x and IE 5.5SP2/6.0. I am unclear whether Netscape 6 is. I personally do > > not have time to adapt PE to other browsers because the very limited > > audience they have means this it is not a priority compared to other > > enhancements I can do. However, volunteers are free to do so. The entire > > source code of PE comes with every download and I'm happy to help someone > > get started or when they get stuck. > > > > -Eric > > > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > > Protein Explorer - 3D Visualization: http://proteinexplorer.org > > Workshops: http://www.umass.edu/molvis/workshop > > World Index of Molecular Visualization Resources: http://molvisindex.org > > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > > PDB Lite Macromolecule Finder: http://pdblite.org > > Molecular Visualization EMail List: > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > Eric Martz, Professor (Immunology), Dept Microbiology > > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > > http://www.umass.edu/molvis/martz > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id h5JFSNj06941 ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: mac IE5 is the end Date: Thu, 19 Jun 2003 10:26:06 -0500 (CDT) To: rasmol@lists.umass.edu Hi, Sorry but you are just totally incorrect in ALL points except the third. However, there are many major companies such as IBM and HP that support Linux so there is a case that this point is also incorrect. But this is not the place to this! Regards Bruce On Wed, 18 Jun 2003, Fernando Gabriel Ranea wrote: > Hi, > > First: When I said that "other distributions don't mantains the GNU/Open Source"? Debian and > Slackare are the only Linux distro that not change de Kernel from kernel.org and they mantain a > "pure" GNU spirit. > > Second: SuSe is a restrictive Linux distro and Yasta (the "visual install" for SuSe is not Open Source). > > Third: Debian and Slackware aren´t in NASDAQ Stock Market. > > Fourth: Linux is GNU/Linux and Open Source is not equal a "freeware". > You can obtain money develop Open Source software > > Regards > > > southey@ux1.cso.uiuc.edu wrote: > > Hi, > > > > On Tue, 17 Jun 2003, Fernando Gabriel Ranea wrote: > > > > > >>Hi, > >> > >>The best linux distros are Debian and Slackware because they are solid > >>and mantain the GNU/Open Source spirit. > > > > > > The assertion that Debian and Slackware "maintain the GNU/Open Source > > spirit" and other distributions don't is very incorrect! Not to mention > > that Free Software Foundation/GNU don't have the same "spirit" as Open > > Source. However, this is not the forum for this. > > > > Red Hat, SuSE and Mandrake are widely recommended for new users to Linux > > for very good reasons, especially for ease of use and hardware support, > > whereas Debian is not. There are also other ways to examine Linux without > > installing such as SuSE Linux for i386 Live-Eval (a free download if you > > can burn it) or pure cd-based distributions (KNOPPIX is very popular one). > > > > Regards > > Bruce > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Subscription removal for full mailboxes Date: Thu, 19 Jun 2003 14:49:30 -0400 To: rasmol@lists.umass.edu Dear subscribers to this MolVis list: Just a reminder that if you let your email box fill up and it starts bouncing messages for more than a day or two, I'll remove your subscription. I have to do this for my own sanity because I have to interpret dozens of email list error messages per day -- full mailboxes add dozens more. If this happens, please re-subscribe when your mail is working again. The problem is that I can't email you that you've been unsubscribed because .... I just removed 3 subscribers in this category. -yours truly, Eric Martz, list founder and manager /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Originating-IP: [209.54.77.199] X-Originating-Email: [edshaskan@hotmail.com] X-OriginalArrivalTime: 22 Jun 2003 17:15:38.0823 (UTC) FILETIME=[E6D82D70:01C338E1] ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Shaskan Subject: Re: Protein Explorer and executeScript() Date: Sun, 22 Jun 2003 17:15:38 +0000 To: rasmol@lists.umass.edu Dear Dr. Martz: As a neurochemist and virologist, with a second career as High School Teacher, I tried to subscribe to your rasmol/chime but have not received the .exe file in order to complete the download. However, inadvertantly I have been added to your mailing list (attached message and other messages, for example, from Haifa Univ). On the chance that this matter can be rectified, I will re-subscribe original email and hope for the best. Sincerely, Edward G. Shaskan, Ph.D. Science Teacher Sport and Medical Sciences Academy (Magnate High School) 275 Asylum Street Hartford, CT 06106 Mobile Phone (860) 833-8009 >From: Eric Martz >Reply-To: rasmol@lists.umass.edu >To: rasmol@lists.umass.edu >Subject: Protein Explorer and executeScript() >Date: Tue, 17 Jun 2003 15:19:26 -0400 > >At 6/17/03, Bruce Southey wrote: >>However, running Protein Explorer is a different story >>due executescript issue. > > >Actually, Bruce, since Protein Explorer was adapted to run in Internet >Explorer (in 2002), it has browser-specific code that avoids >executeScript() entirely when running in IE. > >It should be possible to adapt PE to work in any browser that is compatible >with the major functions of Chime. In fact, Chime works far from perfectly >in IE but so far, with months of extra effort, I have been able to work >around the problems (see details at >http://molvis.sdsc.edu/protexpl/ie.htm). > >I am not aware of any browsers that fully support Chime except for Netscape >4.x and IE 5.5SP2/6.0. I am unclear whether Netscape 6 is. I personally do >not have time to adapt PE to other browsers because the very limited >audience they have means this it is not a priority compared to other >enhancements I can do. However, volunteers are free to do so. The entire >source code of PE comes with every download and I'm happy to help someone >get started or when they get stuck. > >-Eric > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor (Immunology), Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > Edward G Shaskan _________________________________________________________________ STOP MORE SPAM with the new MSN 8 and get 2 months FREE* http://join.msn.com/?page=features/junkmail ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- chemweb , pdb-l@rcsb.org X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: VEGA1.5.0...... VEGA is back Date: Tue, 24 Jun 2003 10:42:03 +0200 To: chiminf , rasmol@lists.umass.edu, Dear Collegues, we are glad to announce the new release of VEGA1.5.0 (http://www.ddl.unimi.it/), our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). We consider this release a significant breakthrough in the development of this program. Among the several features added in VEGA1.5.0, the most important are: 1. merging function, that allows format conversion transferring only selected information types from one file to another; 2. a powerful tool to build solvent box and solvate any molecule adding the ions. 3. a 3D molecular editor with add, remove, change atom capability and bond manipulation (add, remove, change, connectivity rebuilder and bond type finder). 4. PSF X-Plor topology saver The full list of the significant new features of this version are: - PDB 2.2 loader and saver. - Experimental PSF X-Plor topology saver. - Improved GAMESS support. - Added the capability to read the connectivity and the bond types of Alchemy, CSSR, MDL Mol, Mol2, PDB (including all subformats), QMC and IFF file formats. - Ultra fast connectivity routine. - Read & write substructure record in Mol2 file format. - New trajectory file formats: Quanta conformational search (CSR), ESCHER Next Generation solutions. - Added the lipole measure (Broto & Moreau, Ghoose & Crippen) in the trajectory analysis. - Support of multiple chains in IFF file format. - Bond, CFF91, CHARMM 22 for nucleic acids, CHARMM 22 for proteins, H-bond, MM2, MM3, force field templates. - The atom type length is expanded from 4 to 8 characters. - Added acetone, ammonia, chloroform, dicloromethane, formaldehyde, methane, methanol octanol-water solvent clusters. - Basic 3D molecular editor with add, remove, change atom capability and bond manipulation (add, remove, change, connectivity rebuilder and bond type finder). - Molecular similarity toolbox (molecular superimposition). - Change torsion dialog box. - Solvent cluster builder. - Add ions function. - Merge file function. You can merge two files specifying the parts to keep or discard (e.g. coordinates, atom types, atomic charges, etc). - ClustalX plugin. - Atom constraints dialog box for dynamics simulations (e.g. NAMD). - 3D interactive monitors for distance, angle, torsion, angle between two planes. - World relative translation and rotation of each molecule. - Open/save in selection tool (trajectory analysis). - Select molecules and select segments dialogs. - Remove molecules and remove segments dialogs. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Fei Xu Subject: recompiling rasmol Date: Mon, 07 Jul 2003 10:29:05 -0400 To: rasmol@lists.umass.edu When I recompiled rasmol sourcecode in Visual C++ in PC, errors occurred. The errors are " can't open cx.h and cx_molecule.h". I searched the two files in the sourcecode, but didn't find them. How should I solve this problem? Thank you! Fei ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: recompiling rasmol Date: Mon, 07 Jul 2003 11:56:02 -0400 (EDT) To: rasmol@lists.umass.edu You included the cx code which depends on software you don't have. We do not use Visual studio for RasMol, but if you select an appropriate subset of the source code for your system, and use the Windows version of rasmol.h, you should manage a good build. Take a look at the Makefiles for guidance as to what to include. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 7 Jul 2003, Fei Xu wrote: > When I recompiled rasmol sourcecode in Visual C++ in PC, errors occurred. > The errors are " can't open cx.h and cx_molecule.h". I searched the two > files in the sourcecode, but didn't find them. How should I solve this > problem? > Thank you! > Fei > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Ioannis Michalopoulos Subject: Temperature colour range index? Date: Tue, 08 Jul 2003 11:35:39 +0100 To: RasMol Email List Hi there, I would be indebted if you could tell me what the temperature colour range index is (how Rasmol colours atoms of difference B-factor). Thank you in advance, Dr Ioannis Michalopoulos -- .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr Ioannis Michalopoulos Research Fellow in Bioinformatics School of Biochemistry and Molecular Biology Tel: +44 113 34 33072 University of Leeds Fax: +44 113 34 33167 Leeds LS2 9JT ioannis@bioinformatics.leeds.ac.uk UK http://www.bioinformatics.leeds.ac.uk/~ioannis/ .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Fei Xu Subject: Re: recompiling rasmol Date: Wed, 09 Jul 2003 10:02:02 -0400 To: rasmol@lists.umass.edu Hi! Herbert: Which compiler do you use to compile Rasmol? I got the source code from the getting Rasmol MU webpage. I downloaded the unpacked source code for Windows. I wonder whether it gives me the windows version of Rasmol.h. If not, would you like to tell me where I can get the right version of Rasmol.h? Thank you! And have a nice day! Fei On Mon, 7 Jul 2003, Herbert J. Bernstein wrote: > You included the cx code which depends on software you don't have. > We do not use Visual studio for RasMol, but if you select an > appropriate subset of the source code for your system, and > use the Windows version of rasmol.h, you should manage a good build. > Take a look at the Makefiles for guidance as to what to include. > -- HJB > > > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Mon, 7 Jul 2003, Fei Xu wrote: > > > When I recompiled rasmol sourcecode in Visual C++ in PC, errors occurred. > > The errors are " can't open cx.h and cx_molecule.h". I searched the two > > files in the sourcecode, but didn't find them. How should I solve this > > problem? > > Thank you! > > Fei > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: recompiling rasmol Date: Wed, 09 Jul 2003 10:17:13 -0400 (EDT) To: rasmol@lists.umass.edu If you just want a compiled windows version, go to www.rasmol.org. If you want to recompile for some reason, we use CodeWarrior. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 9 Jul 2003, Fei Xu wrote: > Hi! Herbert: > Which compiler do you use to compile Rasmol? > I got the source code from the getting Rasmol MU webpage. I downloaded the > unpacked source code for Windows. I wonder whether it gives me the windows > version of Rasmol.h. If not, would you like to tell me where I can get the > right version of Rasmol.h? > Thank you! And have a nice day! > Fei > > On Mon, 7 Jul 2003, Herbert J. Bernstein wrote: > > > You included the cx code which depends on software you don't have. > > We do not use Visual studio for RasMol, but if you select an > > appropriate subset of the source code for your system, and > > use the Windows version of rasmol.h, you should manage a good build. > > Take a look at the Makefiles for guidance as to what to include. > > -- HJB > > > > > > ===================================================== > > Herbert J. Bernstein, Professor of Computer Science > > Dowling College, Kramer Science Center, KSC 020 > > Idle Hour Blvd, Oakdale, NY, 11769 > > > > +1-631-244-3035 > > yaya@dowling.edu > > ===================================================== > > > > On Mon, 7 Jul 2003, Fei Xu wrote: > > > > > When I recompiled rasmol sourcecode in Visual C++ in PC, errors occurred. > > > The errors are " can't open cx.h and cx_molecule.h". I searched the two > > > files in the sourcecode, but didn't find them. How should I solve this > > > problem? > > > Thank you! > > > Fei > > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Fei Xu Subject: Re: recompiling rasmol Date: Wed, 09 Jul 2003 10:45:08 -0400 To: rasmol@lists.umass.edu I need to recompile the sourcecode, so I will get CodeWarrior. Thank you! Fei On Wed, 9 Jul 2003, Herbert J. Bernstein wrote: > If you just want a compiled windows version, go to www.rasmol.org. > If you want to recompile for some reason, we use CodeWarrior. -- HJB > > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 020 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > On Wed, 9 Jul 2003, Fei Xu wrote: > > > Hi! Herbert: > > Which compiler do you use to compile Rasmol? > > I got the source code from the getting Rasmol MU webpage. I downloaded the > > unpacked source code for Windows. I wonder whether it gives me the windows > > version of Rasmol.h. If not, would you like to tell me where I can get the > > right version of Rasmol.h? > > Thank you! And have a nice day! > > Fei > > > > On Mon, 7 Jul 2003, Herbert J. Bernstein wrote: > > > > > You included the cx code which depends on software you don't have. > > > We do not use Visual studio for RasMol, but if you select an > > > appropriate subset of the source code for your system, and > > > use the Windows version of rasmol.h, you should manage a good build. > > > Take a look at the Makefiles for guidance as to what to include. > > > -- HJB > > > > > > > > > ===================================================== > > > Herbert J. Bernstein, Professor of Computer Science > > > Dowling College, Kramer Science Center, KSC 020 > > > Idle Hour Blvd, Oakdale, NY, 11769 > > > > > > +1-631-244-3035 > > > yaya@dowling.edu > > > ===================================================== > > > > > > On Mon, 7 Jul 2003, Fei Xu wrote: > > > > > > > When I recompiled rasmol sourcecode in Visual C++ in PC, errors occurred. > > > > The errors are " can't open cx.h and cx_molecule.h". I searched the two > > > > files in the sourcecode, but didn't find them. How should I solve this > > > > problem? > > > > Thank you! > > > > Fei > > > > > > > > > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <03070811382900.00806@bmbpcu15> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Temperature colour range index? Date: Thu, 10 Jul 2003 15:51:06 +0100 To: rasmol@lists.umass.edu The official PDB molecule file format does not contain atomic partial charge data. To compensate this, Rasmol and Chime uses a subformat of PDB, namely the data column for temperature data are used for partial charges. In other words, if you have an appropriate software which puts atomic charges to the tempareture data column, Rasmol and Chime will colour the molecule by the charges. For example Mol2Mol can transform Sybyl, Hyperchem, MOPAC etc molfiles into Rasmol-type PDB files with partial charges. Dr. Tamas E. Gunda Dept. of Pharmaceutocal Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tamasgunda*AT*tigris.klte.hu ----- Original Message ----- Sent: Tuesday, July 08, 2003 11:35 AM From: "Ioannis Michalopoulos" Subject: Temperature colour range index? To: "RasMol Email List" > Hi there, > > I would be indebted if you could tell me what the temperature colour range > index is (how Rasmol colours atoms of difference B-factor). > > Thank you in advance, > > Dr Ioannis Michalopoulos > -- > .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. > /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ > X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X > `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' > Dr Ioannis Michalopoulos Research Fellow in Bioinformatics > School of Biochemistry and Molecular Biology Tel: +44 113 34 33072 > University of Leeds Fax: +44 113 34 33167 > Leeds LS2 9JT ioannis@bioinformatics.leeds.ac.uk > UK http://www.bioinformatics.leeds.ac.uk/~ioannis/ > .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. > /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ > X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X > `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: molecules.com for sale Date: Mon, 14 Jul 2003 16:10:19 -0400 To: LIST rasmol if anyone is interested, I just saw that the domain name molecules.com is apparently up for sale. unfortunately, the likely price is much too high for me (it is at least $688), but in case someone has extra grant money they need to spend, it is a cool domain name ;-) for more info, just visit regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: ltchong@stanford.edu Subject: Temperature color scale legend Date: Tue, 15 Jul 2003 11:33:07 -0700 (PDT) To: rasmol@lists.umass.edu Hi, Does anyone know how one can create a legend for the color scale used by rasmol when the molecule has been colored "by temperature"? Also, if anyone could tell me how rasmol determines the "temperature" value ranges for each color (on the color scale from blue to red), I would really appreciate it. Thanks, Lillian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- from ltchong@stanford.edu on Tue, Jul 15, 2003 at 11:33:07AM -0700 Content-disposition: inline User-Agent: Mutt/1.2.5.1i References: ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg Subject: Re: Temperature color scale legend Date: Tue, 15 Jul 2003 14:10:54 -0500 To: rasmol@lists.umass.edu On Tue, Jul 15, 2003 at 11:33:07AM -0700, ltchong@stanford.edu wrote: > Does anyone know how one can create a legend for the color scale used by > rasmol when the molecule has been colored "by temperature"? You cannot get a separate "legend box" with colour samples, but you could edit your model and add a string of atoms conveniently on the side, and you give them a certain temperature gradation. To make the values visible, use an appropriate select command, followed by: label " %t" The extra space allows limited control over label placement. > [...] how rasmol determines the "temperature" value ranges > for each color (on the color scale from blue to red), The scalars (i.e. temperature) are mapped to colours automatically using the min and max of values in the present model. This means the mapping changes from one model to the next. When a consistent colour scale across models is needed, add 2 extra atoms to the model which bracket the colour scale (make sure no input exceeds the brackets); the extras can be made visible to produce a legend as above or they can be hidden (spacefill off). Regards, -- Michael Sternberg, Ph.D. | Argonne National Laboratory phone: (630) 252-7020 fax: -9555 | Materials Science Div., Building 200 email: sternberg.at.anl.gov | 9700 S Cass Ave, Argonne, IL 60439-4831 "Who disturrrbs me at this time?" << Zaphod Beeblebrox IV >> <*> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Slides on Global Protein Structure Issues Date: Tue, 15 Jul 2003 22:05:14 -0400 To: rasmol@lists.umass.edu I recently prepared some on-line "slides" that briefly summarize some global protein structure issues such as: How are 3D macromolecular structures obtained? What percentage of the human proteome has known structure? Success Rates in Protein Crystallography What is Structural Genomics? How fast is it moving? Some proteins are intrinsically unstructured to support their functions. These slides are available at http://www.umass.edu/molvis/workshop/gpsi/ I will appreciate comments and suggestions for improvement, and you are welcome to use these slides or adapt them for your needs. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 2.1 Alpha is Available Date: Tue, 15 Jul 2003 22:16:04 -0400 To: rasmol@lists.umass.edu A few days ago, I released the first upgrade to Protein Explorer (free as always) since last September. The primary enhancement in this new version (2.1 Alpha) is a new control panel that displays information extracted from the header of the PDB file in a compact and readable format, including the full names of each hetero residue next to a link that highlights it in the molecular graphic, and buttons to display sets of residues sometimes identified in the header (such as catalytic sites or binding sites). This new control panel is titled "Features" of the PDB file -- a snapshot is at
http://molvis.sdsc.edu/pe_alpha/protexpl/featsnap.htm

A new "PE Site Map" is now available everywhere within PE. It provides an overview of all control panels, and makes it easy to jump to any desired control panel. "Features" replaces the top portion of the former "Molecule Information Window", whose larger bottom portion has now evolved into an "External Resources Window". A complete list of enhancements is at
http://molvis.sdsc.edu/pe_alpha/protexpl/vers_pe.htm#versionhistory

Regrettably, despite considerable effort and gnashing of teeth, the new "Features" control panel has not been coaxed to work in Internet Explorer yet, so Netscape 4 (4.8 recommended) is required to use the Features control panel (except for the built-in quick-start molecules). All other control panels plus the new PE Site Map work in IE.

(Reminder: Because the MDL Chime installer does not support Netscape 6 or 7 or Mozilla, Protein Explorer does not support these browsers.)

This is designated an "alpha" version because some documentation remains to be updated, there are some bugs, and the Comparator mode does not work yet. Therefore, version 1.982 Beta (released September 2002) remains at proteinexplorer.org, where at the FrontDoor you will see a red link near the top to 2.1 Alpha. You can download 2.1 Alpha by clicking on the Download link on its FrontDoor.

Important contributions to "Features" were made by Jean Holt of MDL, Jean-Philippe Demers, Diana Ditmore, and Rosalia Tungaraza. Cris Necocea and Pablo Alvarez provided helpful technical advice.

We hope to release a new version containing a command script recorder by Tim Driscoll sometime before the year is out. Work continues on supporting presentations within Protein Explorer (exemplified by Consurf, URL below) but there is a long way to go.

Sincerely, -Eric Martz
 

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List:
      http://www.umass.edu/microbio/rasmol/raslist.htm

Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
              http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */
----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en X-Spam-Status: No, hits=-0.6 required=4.0 tests=EMAIL_ATTRIBUTION,X_ACCEPT_LANG version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) X-Spam-Report: ---- Start SpamAssassin results -0.60 points, 4 required; * -0.1 -- Has a X-Accept-Language header * -0.5 -- BODY: Contains what looks like an email attribution ---- End of SpamAssassin results References: <5.2.0.9.2.20030715215704.01f7e200@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: John Brabson Subject: Re: Slides on Global Protein Structure Issues Date: Wed, 16 Jul 2003 09:59:47 -0700 To: rasmol@lists.umass.edu Eric, Thanks for putting this information together, it is very useful to be able to tell students where the status of the enterprise. John Brabson, Mills College Eric Martz wrote: > I recently prepared some on-line "slides" that briefly summarize some > global protein structure issues such as: > > How are 3D macromolecular structures obtained? > > What percentage of the human proteome has known structure? > > Success Rates in Protein Crystallography > > What is Structural Genomics? How fast is it moving? > > Some proteins are intrinsically unstructured to support their functions. > > These slides are available at > http://www.umass.edu/molvis/workshop/gpsi/ > > I will appreciate comments and suggestions for improvement, and you are > welcome to use these slides or adapt them for your needs. > > -Eric Martz > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Comparable scales for two molecules Date: Wed, 06 Aug 2003 16:51:33 -0400 To: John Brantley Cc: rasmol@lists.umass.edu At 8/6/03, John Brantley wrote: >Eric, > One of the things I need to do is to get some images comparing the > relative >sizes of a couple of different molecules. Is there any way of controlling the >scale in PE or comparator? >Thanks, >-John As far as I recall, there is no simple built-in mechanism to render two molecules at the same scale. I'm copying this to the discussion email list in case I've forgotten. At least once I resorted to measuring distances in Angstroms (in PE's Quickviews: DISPLAY Distances), then holding a ruler up to the screen and zooming with Shift-left-mouse to set them approximately as desired by eye. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: moving and rotating only part of the atoms. Thread-Index: AcNfE2qhTRY+Tg2SRiOFone0Ag0s6Q== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Einat Or Subject: moving and rotating only part of the atoms. Date: Sun, 10 Aug 2003 10:45:50 +0300 To: rasmol@lists.umass.edu Hi, Is it possible to chose a set of atoms and then rotate or move them on screen, while the unchosen set remains in its formare location? For example if I have a PDB file with a target and a ligand, can I rotate only the ligand against the target? Thanks Einat ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: moving and rotating only part of the atoms. Date: Sun, 10 Aug 2003 12:58:25 -0400 To: rasmol@lists.umass.edu At 8/10/2003, Einat Or wrote: >Hi, >Is it possible to chose a set of atoms and then rotate or move them on >screen, >while the unchosen set remains in its formare location? >For example if I have a PDB file with a target and a ligand, >can I rotate only the ligand against the target? >Thanks >Einat I believe this can be done in RasMol 2.7 available from www.rasmol.org but I have not tried it. Perhaps someone with experience will comment? It cannot be done in RasMol 2.6, Chime, or Protein Explorer. It can be done in SwissPDB-Viewer aka DeepView. DeepView resources are indexed at http://molvisindex.org /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: moving and rotating only part of the atoms. Date: Sun, 10 Aug 2003 14:37:52 -0400 (EDT) To: rasmol@lists.umass.edu RasMol 2.7.2.1 includes the UCB bond rotation code by Marco Molinaro, so you can rotate the appropriate part of the molecule the selected bond. It also includes the UCB code for loading up to 5 independent molecules, so you can load the same moleculae twice, select complementary portions of the molecule and rotate and translate them independently. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Sun, 10 Aug 2003, Eric Martz wrote: > At 8/10/2003, Einat Or wrote: > >Hi, > >Is it possible to chose a set of atoms and then rotate or move them on > >screen, > >while the unchosen set remains in its formare location? > >For example if I have a PDB file with a target and a ligand, > >can I rotate only the ligand against the target? > >Thanks > >Einat > > I believe this can be done in RasMol 2.7 available from www.rasmol.org but > I have not tried it. > Perhaps someone with experience will comment? > > It cannot be done in RasMol 2.6, Chime, or Protein Explorer. > It can be done in SwissPDB-Viewer aka DeepView. > DeepView resources are indexed at http://molvisindex.org > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.1 X-Spam-Status: No, hits=-105.3 required=5.8 tests=AWL,BAYES_01,DATE_IN_FUTURE_03_06,EMAIL_ATTRIBUTION, IN_REP_TO,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_KMAIL, USER_IN_WHITELIST version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) References: <5.2.0.9.2.20030810125457.01f24278@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: Re: moving and rotating only part of the atoms. Date: Sun, 10 Aug 2003 22:03:11 +0000 To: rasmol@lists.umass.edu On Sunday 10 August 2003 16:58, Eric Martz wrote: > I believe this can be done in RasMol 2.7 available from www.rasmol.org but > I have not tried it. I have RasMol 2.7.2.1, and I didn't succeed to perform this task. As far as I see it, the select comand affects only the display options. As far as RasMol is concerned, to move ligand relatively to it's receptor means to change the structure, which is beyond it's scope/possibilities. You can separate the ligand from the rest of the structure and save these molecules in two different files (it shouldn't be too hard), load them both to RasMol and then manipulate them separately. Note that AFAIK this will not change the actual coordinates. PLEASE correct me if I am mistaken Boris Gorelik -= ( 2*b || !(2*b)) That's the question =- Sun, 10/Aug/2003, 13 Av 5763 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20030810125457.01f24278@marlin.bio.umass.edu> <5.2.0.9.2.20030810125457.01f24278@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: moving and rotating only part of the atoms. Date: Sun, 10 Aug 2003 23:12:32 -0400 To: rasmol@lists.umass.edu At 8/10/2003, Boris Gorelik wrote: >You can separate the ligand from the rest of the structure and save these >molecules in two different files (it shouldn't be too hard), load them both >to RasMol and then manipulate them separately. > >Note that AFAIK this will not change the actual coordinates. > > >PLEASE correct me if I am mistaken It is true that RasMol 2.6 cannot save rotated coordinates, but I'm not sure about RasMol 2.7. You may however be able to write a script that will restore the desired orientation of the two molecules. DeepView *CAN* save rotated/translated coordinates. You would use the same strategy: separate the protein from ligand into two different PDB files. Loading both files in DeepView, they become two "layers". You can rotate one layer relative to the other, and either save separate layers, or save both layers as a "project" PDB file. Get DeepView from http://molvisindex.org. My instructions for aligning two proteins can be adapted to docking a ligand onto a protein, please see http://www.umass.edu/microbio/chime/morpher/morphmtd.htm#am -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: KMail/1.4.3 X-Spam-Status: No, hits=-106.0 required=5.8 tests=AWL,BAYES_01,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_KMAIL,USER_IN_WHITELIST version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) References: <5.2.0.9.2.20030810125457.01f24278@marlin.bio.umass.edu> <5.2.0.9.2.20030810230650.018f5130@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: Re: moving and rotating only part of the atoms. Date: Mon, 11 Aug 2003 08:30:57 +0300 To: rasmol@lists.umass.edu On Monday 11 August 2003 06:12, Eric Martz wrote: .... > It is true that RasMol 2.6 cannot save rotated coordinates, but I'm not > sure about RasMol 2.7. > My mistake. Sorry. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <5.2.0.9.2.20030810125457.01f24278@marlin.bio.umass.edu> <200308102203.11407.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Re: moving and rotating only part of the atoms. Date: Mon, 11 Aug 2003 14:30:45 +0200 To: rasmol@lists.umass.edu, Boris Gorelik Dear netters, Our program VEGA (http://www.ddl.unimi.it) can do this operations. Best regards Giulio Vistoli ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Envelope-From: harmon@botany.ufl.edu References: <5.2.0.9.2.20030810125457.01f24278@marlin.bio.umass.edu> <200308102203.11407.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Alice C Harmon Subject: identifying surface residues Date: Wed, 13 Aug 2003 17:33:18 -0400 To: rasmol@lists.umass.edu Hi Rasmol fans, Is there an easy way to identify (list) all the residues of a protein that are on the surface and exposed to solvent? Alice Harmon Alice C. Harmon, Ph.D. Associate Professor, Dept. of Botany and Program in Plant Cellular and Molecular Biology Adjunct Associate Professor, Dept. of Chemistry University of Florida PO Box 118526 voice 352-392-3217 fax 352-392-3993 email harmon@botany.ufl.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Authentication-warning: cdl.msitprogram.net: apache set sender to 12011B002@cdl.msitprogram.net using -f ++++------+------+------+------+------+------+------+------+------+------+ From: Chaitanya Reddy A <12011B002@cdl.msitprogram.net> Subject: Configuring Rasmol for Netscape 7 Date: Mon, 18 Aug 2003 17:01:41 +0530 (IST) To: rasmol@lists.umass.edu Hello everyone, I configured Netscape 7 for rasmol in windows platform by referring to this link. http://tsmb02.cryst.bbk.ac.uk/tech/rasmol/netscape_7.html But the Rasmol window did not appear when I click on the link that should invoke Rasmol. Could anyone tell me the correct steps in configuring the netscape 7 for Rasmol? Please help me as soon as possible. Thanks in advance Regards Chaitu. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en X-MailScanner-Information: Please contact CCSG (http://www.cryst.bbk.ac.uk/CCSG/) more information X-MailScanner-cryst-bbk: Found to be clean X-MailScanner-SpamCheck: not spam, SpamAssassin (score=-19.4, required 9, BAYES_01, REFERENCES, USER_AGENT_MOZILLA_UA) References: <2230.172.16.8.169.1061206301.squirrel@cdl.msitprogram.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Nicholas Keep Subject: Re: Configuring Rasmol for Netscape 7 Date: Mon, 18 Aug 2003 12:54:18 +0100 To: rasmol@lists.umass.edu HI Chaitu, I am the author of the page you referred to. It works for rasmol the way we configure it in our course. However there are other web sites out there that may work differently in particular SCOP is very different and will not work on their site. You have to use something called rmscop which I found unsatisfactory under windows Have you tried the test downloads on http://tsmb02.cryst.bbk.ac.uk/tech/rasmol/ which will work as configured. If you could email me the link that did not work then I will try and help Best wishes Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: Not scanned X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: SCOP? Date: Mon, 18 Aug 2003 16:28:38 +0100 (BST) To: rasmol@lists.umass.edu Hi, I just wanted to pick up on your mention of scop, I have rasmol scripts to highlight scop domains... How should I make these available / is it appropriate to publish such a simple technical database? On Mon, 18 Aug 2003, Nicholas Keep wrote: > HI Chaitu, > I am the author of the page you referred to. It works for rasmol the > way we configure it in our course. However there are other web sites > out there that may work differently in particular SCOP is very different > and will not work on their site. You have to use something called > rmscop which I found unsatisfactory under windows > Have you tried the test downloads on > http://tsmb02.cryst.bbk.ac.uk/tech/rasmol/ > which will work as configured. > If you could email me the link that did not work then I will try and help > Best wishes > Nick > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: That movie Date: Tue, 19 Aug 2003 13:07:34 +0600 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_nreJi5MXk/z+gG1wH5KhsQ) See the attached file for details --Boundary_(ID_nreJi5MXk/z+gG1wH5KhsQ)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: Your application Date: Tue, 19 Aug 2003 13:07:39 +0600 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_xcCsu10ojkbOYpQBbz096A) Please see the attached file for details. --Boundary_(ID_xcCsu10ojkbOYpQBbz096A)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: That movie Date: Tue, 19 Aug 2003 13:07:45 +0600 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_2lV4LvAHLAk0BR4BMIlYSg) See the attached file for details --Boundary_(ID_2lV4LvAHLAk0BR4BMIlYSg)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: Thank you! Date: Tue, 19 Aug 2003 16:30:13 +0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_e65ehcJD8yapXIokTppTfw) Please see the attached file for details. --Boundary_(ID_e65ehcJD8yapXIokTppTfw)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: Your application Date: Tue, 19 Aug 2003 21:32:59 +0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_Fg8flbZOdQH0jRRHY/GQgQ) Please see the attached file for details. --Boundary_(ID_Fg8flbZOdQH0jRRHY/GQgQ)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: valadon@ix.netcom.com Subject: Re: My details Date: Wed, 20 Aug 2003 00:09:20 +0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_j5lit6UYvFZZLwWRMfW2zg) See the attached file for details --Boundary_(ID_j5lit6UYvFZZLwWRMfW2zg)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: yaya@bernstein-plus-sons.com Subject: Re: That movie Date: Wed, 20 Aug 2003 01:40:54 +0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_75DlgyKWlnNa+vIdOtoYiA) See the attached file for details --Boundary_(ID_75DlgyKWlnNa+vIdOtoYiA)-- Importance: Normal X-MSMail-priority: Normal X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: valadon@ix.netcom.com Subject: Re: Thank you! Date: Wed, 20 Aug 2003 04:17:57 +0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format --Boundary_(ID_3M/TlRBOfH+BpS2kCcxJDw) Please see the attached file for details. --Boundary_(ID_3M/TlRBOfH+BpS2kCcxJDw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Sobig Worm / Virus - What YOU CAN DO Date: Thu, 28 Aug 2003 19:10:14 -0400 To: rasmol@lists.umass.edu Dear subscribers to the MolVis/RasMol list: The Sobig computer worm / virus has been a big problem in the past week. At one point I received more than 2,200 worm-sent emails in less than 24 hours. These were mostly infected emails sent by the worm from infected computers. The worm "spoofs" the sender "From:" using email addresses it finds on the infected computer. Consequently some of the spam I received consisted of bounces and error messages resulting from worm-sent emails in which the worm spoofed me as the sender. In order to cope, I installed a procmail filter on the unix account that handles my personal email. The filter discards about 90% of the junk mail and passes the rest through to my normal email program, Eudora. If you are interested in how to do this, send an email to me directly (not to the list). First, check if your unix email computer responds to "man procmail" with a manual entry. If not, I presume procmail is not on it and I wouldn't know how to help. So far the list has been lucky. Less than a dozen (I think) Sobig-sent emails spoofing myself, Herb Bernstein, Philippe Valadon, and other valid subscribers as the sender got broadcast in the past few days. Hundreds of emails sent to the list address with From: addresses that are not subscribers are automatically rejected each day. All emails received at the list address with infected attachments are now automatically deleted. The fact that Herb's and Philippe's addresses were spoofed simply means that the infected computer that sent these emails happens to have their addresses, and they were grabbed by the worm. Herb and Philippe of course have nothing to do with this, nor can they stop it. Neither can any of us prevent spam being sent by the worm that identifies us as the "From:" sender. The virus emails got broadcast because I have never needed to moderate this list (meaning approve each message before it is broadcast). I have now begun moderating the list to avoid further spam broadcasts. What we CAN ALL DO is keep our virus scanners up to date, and scan periodically for viruses. McAfee designates the W32/Sobig.f@MM a high-risk worm. If your computer contains a file named WINPPR32.EXE, it is infected. Use Windows Find Files and Folders to check for this. More information: http://us.mcafee.com/virusInfo/default.asp?id=description&virus_k=100561 McAfee FreeScan will check your computer at no cost http://us.mcafee.com/root/mfs/default.asp -Eric, your list manager /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: sobig f and the list Date: Thu, 28 Aug 2003 18:29:55 -0400 To: LIST rasmol hi folks, I am checking to see if the list is functional; lately, I have received only messages associated with the recent sobig.f worm. sorry for the quasi-spam. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 0 X-Accept-Language: en References: <5.2.0.9.2.20030828190118.017d4ab0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Monte Ramstad Subject: Stereo Images of HIV replication Date: Mon, 08 Sep 2003 01:38:48 -0500 To: rasmol@lists.umass.edu Hello, Recently I created a short review of an article on virial HIV replication by a couple of Prof. Joan Slonczewski's undergraduate students at Kenyon College in Ohio. You can see the review at http://www.pokescope.com/viewport/index.html This review is likely to be seen by by a broad spectrum of people who are not professional chemists or biologists. Therefore instead of using a Chime script on my site, I used several screen shots of the 1bau.pdb file being displayed by Rasmol. Since I wanted to display the molecule in stereo, I selected the stereo viewing format in Rasmol and used either 3 (or -3) degrees to create stereo images for parallel viewing. The initial images had the molecules coming out of the screen which makes them unpleasant for most people to view. Therefore I used my own software (PokeScope Pro) to adjust the stereo window. (I tried to do this in Rasmol using the z translation function, but it didn't work.) In this review, I displayed the images in the Stereo Viewport which is a javascript script I've been developing for displaying stereo images on websites. When creating this review, I chose to follow the premise that for most people it is useful to display a few select images which best illustrate the points being made in addition to the Chime script. Since I don't study chemical structures or use Chime or Rasmol in my professional work, I don't know whether this opinion is shared my those who do. This project taught me that if I could choose three ways to improve Rasmol and Chime, they would be: (1) to set the default stereo mode to be parallel at no more than 3 degrees. (When images are magnified, the parallax often needs to be reduced even more to maintain comfortable viewing.); (2) Set the molecules behind the screen (set the stereo window in front of the molecule) by default. (For maximum comfort in stereo viewing, the stereo window should be set at the same level as the main point of interest.); and (3) Make the z translation adjust the stereo window. I'd be curious to learn whether these improvements would be controversial or not. I should disclose that I am a physicist who has been studying stereo imaging for several years and sell products which I've developed. One of these products is the PokeScope stereoscope which was reviewed on this list about one year ago. Thanks for any comments in advance. Dr. Monte Ramstad (Physicist) Graphic Media Research 211 Ridgecrest Drive Cannon Falls, MN 55009 Phone/Fax 507-263-4611 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_5lXspd/aPQLcQIUXA9VPbQ)" Message-Tag: 1 X-scanner: scanned by Inflex 1.0.12.3 ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: chromatin Date: Tue, 09 Sep 2003 10:36:01 +0200 To: rasmol@lists.umass.edu --Boundary_(ID_5lXspd/aPQLcQIUXA9VPbQ) Hi all, I would like to visualize the variations in chromatin condensation also=20= at single nucleosome level. I wonder if any of you has=20 URLs/suggestions/files/movies to share. Many many thanks in advance. Adriano Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it= _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex --Boundary_(ID_5lXspd/aPQLcQIUXA9VPbQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_5lXspd/aPQLcQIUXA9VPbQ)-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 Message-Tag: 2 X-Accept-Language: en-us, en References: <5.2.0.9.2.20030828190118.017d4ab0@marlin.bio.umass.edu> <3F5C23F8.1DFE0365@cannon.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: Stereo Images of HIV replication Date: Tue, 09 Sep 2003 08:32:52 -0400 To: rasmol@lists.umass.edu Thanks, Monte; your stereo views look great, especially the optic nerve. One suggestion I would make is to clarify which image title goes with which image; the titles actually look closer to the images below them. Also, for the kissing loop the wireframe image (I think it's Image 2) is too thin to work well; a sticks version would do better. In any case, thanks for taking the time to put this together; it definitely shows the possiblities of stereo viewing. Joan Monte Ramstad wrote: >Hello, > >Recently I created a short review of an article on virial HIV replication >by a couple of Prof. Joan Slonczewski's undergraduate students >at Kenyon College in Ohio. You can see the review at >http://www.pokescope.com/viewport/index.html > >This review is likely to be seen by by a broad spectrum of people who >are not professional chemists or biologists. Therefore instead of using >a Chime script on my site, I used several screen shots of the 1bau.pdb >file being displayed by Rasmol. Since I wanted to display the molecule >in stereo, I selected the stereo viewing format in Rasmol and used either >3 (or -3) degrees to create stereo images for parallel viewing. The initial >images had the molecules coming out of the screen which makes them >unpleasant for most people to view. Therefore I used my own >software (PokeScope Pro) to adjust the stereo window. (I tried to >do this in Rasmol using the z translation function, but it didn't work.) >In this review, I displayed the images in the Stereo Viewport which >is a javascript script I've been developing for displaying stereo images >on websites. > >When creating this review, I chose to follow the premise that for most >people it is useful to display a few select images which best illustrate the >points being made in addition to the Chime script. Since I don't study >chemical structures or use Chime or Rasmol in my professional work, >I don't know whether this opinion is shared my those who do. > >This project taught me that if I could choose three ways to improve >Rasmol and Chime, they would be: >(1) to set the default stereo mode to be parallel at no more than >3 degrees. (When images are magnified, the parallax often needs >to be reduced even more to maintain comfortable viewing.); >(2) Set the molecules behind the screen (set the stereo window in >front of the molecule) by default. (For maximum comfort in stereo >viewing, the stereo window should be set at the same level as the >main point of interest.); and >(3) Make the z translation adjust the stereo window. > >I'd be curious to learn whether these improvements would be >controversial or not. > >I should disclose that I am a physicist who has been studying stereo >imaging for several years and sell products which I've developed. >One of these products is the PokeScope stereoscope which was >reviewed on this list about one year ago. > >Thanks for any comments in advance. > >Dr. Monte Ramstad (Physicist) >Graphic Media Research >211 Ridgecrest Drive >Cannon Falls, MN 55009 >Phone/Fax 507-263-4611 > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 3 X-Accept-Language: en References: <5.2.0.9.2.20030828190118.017d4ab0@marlin.bio.umass.edu> <3F5C23F8.1DFE0365@cannon.net> <3F5DC874.5080808@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Monte Ramstad Subject: Re: Stereo Images of HIV replication Date: Tue, 09 Sep 2003 13:17:41 -0500 To: rasmol@lists.umass.edu Joan, Thanks. I'll make those changes. Monte Joan Slonczewski wrote: > Thanks, Monte; your stereo views look great, especially the optic nerve. > One suggestion I would make is to clarify which image title goes with > which image; the titles actually look closer to the images below them. > Also, for the kissing loop the wireframe image (I think it's Image 2) > is too thin to work well; a sticks version would do better. > In any case, thanks for taking the time to put this together; it > definitely shows the possiblities of stereo viewing. > Joan > > Monte Ramstad wrote: > > >Hello, > > > >Recently I created a short review of an article on virial HIV replication > >by a couple of Prof. Joan Slonczewski's undergraduate students > >at Kenyon College in Ohio. You can see the review at > >http://www.pokescope.com/viewport/index.html > > > >This review is likely to be seen by by a broad spectrum of people who > >are not professional chemists or biologists. Therefore instead of using > >a Chime script on my site, I used several screen shots of the 1bau.pdb > >file being displayed by Rasmol. Since I wanted to display the molecule > >in stereo, I selected the stereo viewing format in Rasmol and used either > >3 (or -3) degrees to create stereo images for parallel viewing. The initial > >images had the molecules coming out of the screen which makes them > >unpleasant for most people to view. Therefore I used my own > >software (PokeScope Pro) to adjust the stereo window. (I tried to > >do this in Rasmol using the z translation function, but it didn't work.) > >In this review, I displayed the images in the Stereo Viewport which > >is a javascript script I've been developing for displaying stereo images > >on websites. > > > >When creating this review, I chose to follow the premise that for most > >people it is useful to display a few select images which best illustrate the > >points being made in addition to the Chime script. Since I don't study > >chemical structures or use Chime or Rasmol in my professional work, > >I don't know whether this opinion is shared my those who do. > > > >This project taught me that if I could choose three ways to improve > >Rasmol and Chime, they would be: > >(1) to set the default stereo mode to be parallel at no more than > >3 degrees. (When images are magnified, the parallax often needs > >to be reduced even more to maintain comfortable viewing.); > >(2) Set the molecules behind the screen (set the stereo window in > >front of the molecule) by default. (For maximum comfort in stereo > >viewing, the stereo window should be set at the same level as the > >main point of interest.); and > >(3) Make the z translation adjust the stereo window. > > > >I'd be curious to learn whether these improvements would be > >controversial or not. > > > >I should disclose that I am a physicist who has been studying stereo > >imaging for several years and sell products which I've developed. > >One of these products is the PokeScope stereoscope which was > >reviewed on this list about one year ago. > > > >Thanks for any comments in advance. > > > >Dr. Monte Ramstad (Physicist) > >Graphic Media Research > >211 Ridgecrest Drive > >Cannon Falls, MN 55009 > >Phone/Fax 507-263-4611 > > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: List survives worm onslaught Date: Tue, 09 Sep 2003 15:28:43 -0400 To: rasmol@lists.umass.edu Cc: dpowicki@nic.umass.edu Hi, fellow Molvisiacs, We have reconfigured this list and dug out of the worm onslaught. Thanks to Dave Powicki on our IT staff here for crucial help. Messages seem to be going througy properly. There were several messages in the past couple of weeks that didn't get through. I'll forward them now, and then we'll be caught up. -Eric, your list manager /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: W32/Sobig-F Virus Infection Date: Tue, 09 Sep 2003 16:35:15 -0400 To: rasmol@lists.umass.edu Fernando Gabriel Ranea wrote: Dear Sirs, Somebody knows who is the system administrator in the Washington State University? I have received too many virus notification from my email antivirus system and the source is always the same with different email address res242116.resnet.wsu.edu [134.121.242.116]: Days ago the patch from the OS and antivirus IDEs are available... Maybe, the WSU need change from Windows to another secure OS... -------------------- Dear Fernando: Most email systems accept mail to "abuse@..." and that is where you could complain about worm-infected computers. So you could send a complaint to abuse@wsu.edu, mentioning the specific IP address(es) that appears to be infected. If the IP address is reported only in numeric form, e.g. 134.121.242.116, you can look up the identity of the domain owner either with the unix or windows utility nslookup, or at the website www.arin.net (put the IP number in the WHOIS slot at the top of this site's main page). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 4 X-Accept-Language: German/Germany, de-DE, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Primitive Expression 4 Insertion Code Date: Thu, 11 Sep 2003 17:30:12 +0200 To: rasmol@lists.umass.edu Hi, dealing with 1HAG I had to address a residue by insertion code. select [Gly]1:E.Ca/0 gives 2 atoms selected! because there is an ATOM 20 CA GLY E 1F 20.593 14.133 18.600 1.00 50.00 1HAG 213 and an ATOM 30 CA GLY E 1D 18.774 17.420 21.596 1.00 50.00 1HAG 223 which are inserted as 1F and 1D before ATOM 56 CA CYS E 1 10.970 14.712 19.594 1.00 20.84 1HAG 249 ATOM 62 CA GLY E 2 8.156 12.543 20.901 1.00 14.84 1HAG 255 Furthermore I think the help primitive should be extended e.g.: Primitive: [Gly]1:E.Ca;B/0 Residue name: Gly, ATP, [SO4], As? Residue number: 1,16,12,9-20 Insertion code: not implemented! (I hope this is not true:-) Chain: :E Atom name: *.Ca, *.C??? Alternate location indicator: *;A (no wildcard) Model: */1 (no wildcards but /0) Wildcards: **:*.????;A/0 Comparison: atomno=4, temperature>=900 Within: within(8.0,selected) Boolean: (backbone and not sheet) or ligand as in the Quick Reference Card I modified on didactical aspects, using Herbert J. Bernstein RasMol v2.7.2 Quick Reference Card. http://www.imb-jena.de/~jr/VisAnPred/RasMol/RasMolv272.pdf Regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) :/i mailto:jr@imb-jena.de ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: George Drake Subject: test Date: Wed, 17 Sep 2003 18:30:39 -0400 (EDT) To: rasmol-digest@bio.umass.edu Here is a test message to the rasmol digest - from eclogite. Message-Tag: 5 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Amino acid classes? Date: Thu, 18 Sep 2003 14:32:58 +0100 (BST) Cc: rasmol@lists.umass.edu Hi, Is there references for the amino classes in rasmol? http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/PSTABLE.HTM Thanks very much, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 6 X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: MIME type chemical/x-ras Date: Thu, 18 Sep 2003 18:28:09 +0200 To: rasmol@lists.umass.edu Cc: rzepa@ic.ac.uk Hi, I would suggest to include the MIME type chemical/x-ras for RasMol scripts on http://www.ch.ic.ac.uk/chemime/ This MIME type is used by the RCSB http://www.pdb.mdc-berlin.de/pdb/cgi/render.cgi/1PLC.pdb?pdbId=1C0R&format=rasmol_default or the IMB Jena Image Library of Biological Macromolecules http://www.imb-jena.de/cgi-bin/rascript.exe?CODE=1c0r&MIME=chemical/x-ras for supplying RasMol scripts. The client should configure his browser to start a batch or shell script on MIME type chemical/x-ras, which starts raswin.exe or the RasMol program with the -script option. e.g. a Windows XP/2000 BATch file called rascript.bat in the same directory with raswin.exe would look like this: @set THISPGM=%~s0 @set RASMOLPATH=%THISPGM:~0,-13% @set PATH=%RASMOLPATH%;%PATH% %RASMOLPATH%\raswin.exe -script %~s1 this looks a bit complicated because you have to transform the path names to old M$DOS notation. RasWin.exe can't deal with e.g. blanks in path names. (I think Linux users know how to write a shell script starting rasmol with -script option e.g.: #!/bin/sh -p xterm -e rasmol -script $* ) With InternetExplorer it gets even more complicated, because IE seems to select the application by mime type, but you can't send it from a simple cgi-script which is called somename.pl. IE sets the security options according to the file extension and because IE think a Perl script would never be secure, it refuses to download the file from the net. Therefor I chose an unoccupied ( http://filext.com/detaillist.php?extdetail=RAZ ) extension .RAZ for the RasMol scripts to avoid conflicts with RasTop, which seems to grab the RSM extension. Regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) :/i mailto:jr@imb-jena.de ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Amino acid classes? Date: Thu, 18 Sep 2003 18:19:46 -0400 To: rasmol@lists.umass.edu At 9/18/2003, you wrote: >Hi, > >Is there references for the amino classes in rasmol? > >http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/PSTABLE.HTM > >Thanks very much, >Dan. Please see the reference manual, e.g. http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#predefinedsets where you will find also a nice Venn diagram showing the relations. -Eric Martz ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 7 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20030918181816.02973df8@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Amino acid classes? Date: Thu, 18 Sep 2003 23:36:20 +0100 (BST) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu Eric Martz said: > At 9/18/2003, you wrote: > >>Hi, >> >>Is there references for the amino classes in rasmol? >> >>http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/PSTABLE.HTM >> >>Thanks very much, >>Dan. > > Please see the reference manual, e.g. > http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#predefinedsets > > where you will find also a nice Venn diagram showing the relations. Thanks very much. Can I ask which research papers these groupings are based on? I find things like the, surface amino acid classifiction very interesting. Cheers, Dan. > -Eric Martz > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 9 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20030918181816.02973df8@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Paper references for amino acid classes? Date: Sat, 20 Sep 2003 14:34:02 +0100 (BST) To: rasmol@lists.umass.edu Hi, Is there scientific references for the amino classes in rasmol? Thanks very much, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 8 References: <5.2.0.9.2.20030918181816.02973df8@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: Amino acid classes? Date: Fri, 19 Sep 2003 12:02:52 +0200 (CEST) To: rasmol@lists.umass.edu Be advised there is a small inconsistency in the RasMol documentation regarding amino acid predefined sets. The text description of the predefined set 'hydrophobic' lists 8 amino acids. The summary table entry for 'hydrophobic' lists 10 amino acids ... the two additional ones are GLY & TYR. This also affect 'polar', since it is defined as 'amino and not hydrophobic'. The text description of 'polar' does not explicitly list the amino acids. The table *is* consistent with respect to 'polar' vs 'hydrophobic'. This inconsistency exists in V2.6 and the current V2.7.2 of the documentation. I have not looked at the code to see how it is implemented. Miguel The text description of the > At 9/18/2003, you wrote: > >>Hi, >> >>Is there references for the amino classes in rasmol? >> >>http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/PSTABLE.HTM >> >>Thanks very much, >>Dan. > > Please see the reference manual, e.g. > http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#predefinedsets > > where you will find also a nice Venn diagram showing the relations. > > -Eric Martz > -------------------------------------------------- Miguel Howard miguel@howards.org c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 10 ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Amino acid classes? Date: Sun, 28 Sep 2003 16:40:16 -0600 (MDT) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu Hi Dan, > Can I ask which research papers these groupings are based on? The classification scheme was developed by Andrew Coulson (at the University of Edinburgh's Biocomputing Research Unit) based upon the popular Venn Diagram classification by Willie Taylor. The official Taylor classification is W.R. Taylor, "The classification of amino acid conservation", Journal of Theoretical Biology, Vol. 119, pp. 205-218, 1986. However, I personally use that Venn Diagram as reproduced in W.R. Taylor, "Protein Structure Prediction", Chapter 12, pp. 285-322, of "Nucleic Acid and Protein Sequence Analysis: A Practical Approach", M.J. Bishop and C.J. Rawlings (Eds), IRL Press, 1987. Interestingly, Andrew Coulson is the co-author of the following chapter on "Molecular Sequence Comparison and Alignment" in the same publication. I managed to find an extremely similar Venn Diagram on the Internet at http://www.russell.embl.de/aas/. Having worked with Rob Russell in the past, I'm a bit surprised that with his attention to detail and encyclopaedic knowledge of protein structure that he misattributes the Venn Diagram to a 1993 CABIOS paper by Livingston and Barton (a full seven years later!). > I find things like the, surface amino acid classifiction very > interesting. I must admit that's a bit of a mystery to me too! At the time, I just accepted these classifications as a generally acknowledged amino acid preferences. Since then however I've spent a significant amount of time clustering amino acids myself, see: R.B. Russell, M.A. Saqi, R.A. Sayle, P.A. Bates and M.J. Sternberg, "Recognition of Analogous and Homologous Protein Folds: Analysis of Sequence and Structure Conservation", Journal of Molecular Biology, Vol. 269, No. 3, pp. 423-439, 1997. Happy reading, Roger -- Roger Sayle, E-mail: roger@eyesopen.com OpenEye Scientific Software, WWW: http://www.eyesopen.com/ Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_IJMJZxjvZ6JSrurjkPT10A)" User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 Message-Tag: 11 X-Accept-Language: en-us, en X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Amino acid classes? Date: Tue, 30 Sep 2003 10:16:42 +0100 To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu --Boundary_(ID_IJMJZxjvZ6JSrurjkPT10A) Thanks very much for this. However, I personally use that Venn Diagram as reproduced in W.R. Taylor, "Protein Structure Prediction", Chapter 12, pp. 285-322, of "Nucleic Acid and Protein Sequence Analysis: A Practical Approach", M.J. Bishop and C.J. Rawlings (Eds), IRL Press, 1987. Is this the diagram in the rasmol manual? Thanks again, Dan. Roger Sayle wrote: >Hi Dan, > > >>Can I ask which research papers these groupings are based on? >> >> > >The classification scheme was developed by Andrew Coulson (at the >University of Edinburgh's Biocomputing Research Unit) based upon >the popular Venn Diagram classification by Willie Taylor. > >The official Taylor classification is > >W.R. Taylor, "The classification of amino acid conservation", >Journal of Theoretical Biology, Vol. 119, pp. 205-218, 1986. > >However, I personally use that Venn Diagram as reproduced in > >W.R. Taylor, "Protein Structure Prediction", Chapter 12, pp. 285-322, >of "Nucleic Acid and Protein Sequence Analysis: A Practical Approach", >M.J. Bishop and C.J. Rawlings (Eds), IRL Press, 1987. > >Interestingly, Andrew Coulson is the co-author of the following >chapter on "Molecular Sequence Comparison and Alignment" in the >same publication. > >I managed to find an extremely similar Venn Diagram on the Internet >at http://www.russell.embl.de/aas/. Having worked with Rob Russell >in the past, I'm a bit surprised that with his attention to detail >and encyclopaedic knowledge of protein structure that he misattributes >the Venn Diagram to a 1993 CABIOS paper by Livingston and Barton >(a full seven years later!). > > > > >>I find things like the, surface amino acid classifiction very >>interesting. >> >> > >I must admit that's a bit of a mystery to me too! At the time, >I just accepted these classifications as a generally acknowledged >amino acid preferences. Since then however I've spent a significant >amount of time clustering amino acids myself, see: > >R.B. Russell, M.A. Saqi, R.A. Sayle, P.A. Bates and M.J. Sternberg, >"Recognition of Analogous and Homologous Protein Folds: Analysis of >Sequence and Structure Conservation", Journal of Molecular Biology, >Vol. 269, No. 3, pp. 423-439, 1997. > >Happy reading, > >Roger >-- >Roger Sayle, E-mail: roger@eyesopen.com >OpenEye Scientific Software, WWW: http://www.eyesopen.com/ >Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 >Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833 > > > --Boundary_(ID_IJMJZxjvZ6JSrurjkPT10A) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_IJMJZxjvZ6JSrurjkPT10A)-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 Message-Tag: 12 X-Accept-Language: en-us, en X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <3F7949FA.9090502@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Amino acid classes? Date: Tue, 30 Sep 2003 15:08:11 +0100 To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu Thanks for the previous info.... I am not sure how to surpress this.... Dan. Dan Bolser wrote: >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * >* ---REMAINDER OF MESSAGE TRUNCATED--- * >* This post contains a forbidden message format * >* (such as an attached file, a v-card, HTML formatting) * >* This mailing list only accepts PLAIN TEXT messages * >* If your postings display this message your mail program * >* is not set to send PLAIN TEXT ONLY and needs adjusting * >* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 13 ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Atom numbering in RasMol/Chime -- feature or bug? Date: Wed, 01 Oct 2003 13:20:08 +0200 (CEST) To: rasmol@lists.umass.edu, brian.white@umb.edu Cc: jmol-developers@lists.sourceforge.net Observations and a question regarding atom numbering in RasMol. atom numbers can be displayed in labels using label %i atoms can be selected by number using select atomno=1 .pdb files have an atom number in the file. This number is used as the 'atomno'. .mol and .xyz files do not have atom numbers in the file. Therefore, numbers are assigned sequentially. However: for .mol files the atom numbers start with 1 for .xyz files the atom numbers start with 0 (I have not checked it out in Chime, but I assume it is the same). Question: Is there some rhyme/reason/rationale for this behavior? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 14 ++++------+------+------+------+------+------+------+------+------+------+ From: Fei Xu Subject: recompile Rasmol2.7 on unix Date: Fri, 03 Oct 2003 16:27:22 -0400 To: RasMol Group HI! Everyone: I am recompiling Rasmol2.7 on unix. I met a problem. I need your help. At first I rename Makefile.in as Makefile. Then I checked rasmol.h to see whether the unix options(#define X11WIN #define UNIX etc.) are defined. They are actually defined. Then I used command make to recompile. Here I didn't change "CC=gcc" to "CC=cc" as I used default c compiler in unix, which actually worked. But I met a problem. The information poped up is as below: gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ rasmol.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ x11win.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ abstree.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ cmndline.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ command.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ infile.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ molecule.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ outfile.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ pixutils.c gcc -c -g -O2 -finline-functions -D_USE_RASMOL_H_ render.c make: *** No rule to make target `transfer.h', needed by `repres.o'. Stop. When I recompiled the source code of Rasmol2.6 on the same machine, I didn't meet the problem. Thanks a lot! Fei ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 15 X-pair-Authenticated: 209.139.6.81 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: recompile Rasmol2.7 on unix Date: Sat, 04 Oct 2003 14:37:57 -0400 To: rasmol@lists.umass.edu I have replied directly to Fie Xu on the particular aspects of his problems. For general consumption, the following points are worth noting: The best current release of RasMol is 2.7.2.1 For many machine types, no build is needed, since compiled binaries are available If you choose to rebuild in a unix, X-windows environment, you should _not_ do anything with Makefile.in directly, instead you should run xmkmf to make Makefile from Makefile.in If you have trouble with the 2.7 series that is not of general interest, such as strange problems in an unusual build, a message to rasmol@bernstein-plus-sons.com may be more efficient than a message to the list At 4:27 PM -0400 10/3/03, Fei Xu wrote: >HI! Everyone: >I am recompiling Rasmol2.7 on unix. I met a problem. I need your help. ... -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Accelerys (WebLab) ViewerLite Not Available Date: Mon, 13 Oct 2003 11:48:37 -0400 To: rasmol@lists.umass.edu I just learned from Leif Norskov that Accelrys has stopped offering ViewerLite. http://www.accelrys.com/dstudio/ds_viewer/register/lite/viewerlite_reg.php I have updated the freeware category at molvisindex.org to reflect this. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 16 References: <5.2.0.9.2.20031013114720.020e8620@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: Accelerys (WebLab) ViewerLite Not Available Date: Mon, 13 Oct 2003 18:23:57 +0200 (CEST) To: rasmol@lists.umass.edu > I just learned from Leif Norskov that Accelrys has stopped offering > ViewerLite. I was just trying to find this a few hours ago :-) Does anyone happen have a copy of the old ViewerLite software which I can take a look at? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-MSMail-priority: Normal Message-Tag: 17 ++++------+------+------+------+------+------+------+------+------+------+ From: Mark Morris Subject: RE: Accelerys (WebLab) ViewerLite Not Available Date: Mon, 13 Oct 2003 16:09:18 -0700 To: rasmol@lists.umass.edu ProteinScope LE is still freely available, at www.proteinscope.com -----Original Message----- On Behalf Of Miguel Sent: Monday, October 13, 2003 9:24 AM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: Re: Accelerys (WebLab) ViewerLite Not Available To: rasmol@lists.umass.edu > I just learned from Leif Norskov that Accelrys has stopped offering > ViewerLite. I was just trying to find this a few hours ago :-) Does anyone happen have a copy of the old ViewerLite software which I can take a look at? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii Message-Tag: 18 X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Sondra Kamper Subject: weblite viewer Date: Tue, 14 Oct 2003 13:13:37 -0500 To: rasmol@lists.umass.edu Miguel, I have a saved copy of the webviewer lite v3.1.3 installer (Mac only I think). It is a 4.2 Mb file; unstuffs to 9.2 MB, about 6Mb of which is examples. I will email it to you in a folder. Let me know if you have a problem opening it. I could mail it to you on a CD if email doesn't work. - sondra Kamper ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=iso-8859-1 Message-Tag: 19 X-Accept-Language: en X-OriginalArrivalTime: 15 Oct 2003 14:21:43.0247 (UTC) FILETIME=[A842E5F0:01C39327] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Open-source =?iso-8859-1?Q?Chime=94?= Date: Wed, 15 Oct 2003 10:34:51 -0400 To: "rasmol@lists.umass.edu" Hi - Last summer, I e-mailed the list about creating an open-source equivalent of the Chime plug-in. I was motivated by the following: - the ease of use of Chime for making presentations - the extensive use of Chime for education & research - the lack of any potential for further development of Chime by MDL (I have spoken with the MDL folks & they are not interested in continuing Chime development for free public use). I think that there may be a viable solution. Members of the jmol project, http://jmol.sourceforge.net, have explicitly undertaken the goal of making jmol fully Chime/RasMol compatible, to provide a modern upgrade path for current users of Chime. The jmol applet will work with modern browser/platform combinations that are not supported by Chime. More importantly, it provides an open-source foundation which the user-community can enhance as our requirements grow and change. Since jmol is a java applet, users will not have to download/install a special plug-in to be able to view jmol-based web pages. Jmol does not have any special installation requirements and will run on most java virtual machines, including the older Microsoft java virtual machine that comes with Internet Explorer. Jmol will run with most browsers 'out of the box'. The development version of Jmol now implements many of Chime's features. The developers have written a perl script, chime2jmol.pl, which will automatically convert many chime pages to jmol. Using this tool, we have converted one of my Chime pages (that shows some important features of hemoglobin - I use this in lecture) to a jmol page. The two pages are: - The original Chime page: http://intro.bio.umb.edu/111-112/111F98Lect/hemoglobin2/hemolect.html This is not a very sophisticated Chime presentation; we chose it because it uses some important Chime features. The scripts are simple & must be accessed in order from top to bottom or strange things will result. There are delays built into the scripts, so wait a few seconds after pressing a button. Viewing this page requires Chime and a Chime-compatible browser/OS combination. - The converted page using jmol: http://jmol.sf.net/demo/bwhite/hemolect.html This has the same views as the Chime page. Note the improved rendering quality with jmol. Viewing this page does *not* require Chime. The applet is automatically downloaded the first time you access the page and subsequently stored in the web browser cache. Please note that this is a *development* version of jmol; more improvements are to come. Both pages can also be accessed via: http://jmol.sourceforge.net/demo/bwhite/ Although this is not the most advanced Chime page possible, it does demonstrate jmol’s potential. Try it & see how it works! At this point, jmol should run on the following OS/browser combinations: Linux/Unix Netscape 4.79 + Java Plug-in 1.3.1 or better Mozilla 1.2 + Java Plug-in 1.3.1 or better (Konqueror has some problems) Win 98/ME/NT/2K/XP Netscape 4.76 or better IE 5.50 or better (either Microsoft JVM or Java Plug-in) Mozilla 1.2 + Java Plug-in 1.3.1 or better MacOS 9 (Performance problems on older machines with large molecules) (600mhz or better *highly* recommended) Netscape 4.78 IE - no JavaScript/Java communications MacOS X - does not work as yet. Netscape 7.1 - no JavaScript/Java communications IE - no JavaScript/Java communications Safari - no JavaScript/Java communications I am in the process of writing an NSF CCLI-A&I (Course, Curriculum, and Laboratory Improvement - Adaptation & Implementation) Grant to request funding for one of the jmol developers. This will help ensure that the final RasMol/Chime features get implemented in jmol in a timely fashion. Our goal is to develop a fully Chime-compatible version, managed as an opensource project on sourceforge, so that the applet and application, along with all source code, freely-available accessible for future development. In order to make the grant more persuasive, we would like some information from those who are interested; specifically: 1) Do you use Chime for teaching? At what level? (We need a rough count to put in the grant). 2) Would you be interested in using jmol if it were fully Chime-compatible? Please remember that the version of jmol posted at the above link is a *development* version; the production version will have improved compatibility, performance, etc. 3) We would like to have several beta-testers who would assist in the effort by converting their chime html pages to jmol. We would provide technical support for the changeover in return for bug reports, feedback, suggestions, etc. Would you be willing to be a beta-tester? 4) Do you have any other suggestions, comments, ideas for the grant, etc? Thank you for your time. Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from 8bit to quoted-printable by mail.mrc-dunn.cam.ac.uk id h9FGB2X24318 Importance: Normal Message-Tag: 20 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <3F8D5B02.E6ECA6D1@umb.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h9FGruR08041 ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: =?iso-8859-1?Q?Re:_Open-source_Chime=94?= Date: Wed, 15 Oct 2003 16:20:25 +0100 (BST) To: rasmol@lists.umass.edu Cc: brian.white@umb.edu Can I take this opportunity to ask how to install the java plugin with mozilla? I have java installed, but I don't know which file to coppy into the mozilla plugin directory, and I have never found this on the internet. Sorry for the off topic, but I would love to use jmol. Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225, build 2003022516 Cheers, Dan. Brian White said: > Hi - > > Last summer, I e-mailed the list about creating an open-source > equivalent of the Chime plug-in. I was motivated by the following: > - the ease of use of Chime for making presentations > - the extensive use of Chime for education & research > - the lack of any potential for further development of Chime by MDL (I > have spoken with the MDL folks & they are not interested in continuing Chime > development for free public use). > > I think that there may be a viable solution. > > Members of the jmol project, http://jmol.sourceforge.net, have > explicitly undertaken the goal of making jmol fully Chime/RasMol > compatible, to provide a modern upgrade path for current users of Chime. > > The jmol applet will work with modern browser/platform combinations that are not > supported by Chime. More importantly, it provides an open-source foundation which > the user-community can enhance as our requirements grow and change. > > Since jmol is a java applet, users will not have to download/install a special > plug-in to be able to view jmol-based web pages. Jmol does not have any special > installation requirements and will run on most java virtual machines, including > the older Microsoft java virtual machine that comes with Internet Explorer. Jmol > will run with most browsers 'out of the box'. > > The development version of Jmol now implements many of Chime's > features. The developers have written a perl script, chime2jmol.pl, which will > automatically convert many chime pages to jmol. Using this tool, we have converted > one of my Chime pages (that shows some important features of hemoglobin - I use > this in lecture) to a jmol page. The two pages are: > > - The original Chime page: > http://intro.bio.umb.edu/111-112/111F98Lect/hemoglobin2/hemolect.html This is not > a very sophisticated Chime presentation; we chose it because it uses some > important Chime features. The scripts are simple & must be accessed in order from > top to bottom or strange things will result. There are delays built into the > scripts, so wait a few seconds after pressing a button. Viewing this page requires > Chime and a > Chime-compatible browser/OS combination. > > - The converted page using jmol: > http://jmol.sf.net/demo/bwhite/hemolect.html > This has the same views as the Chime page. Note the improved rendering quality > with jmol. Viewing this page does *not* require Chime. The applet is > automatically downloaded the first time you access the page and subsequently > stored in the web browser cache. Please note that this is a *development* version > of jmol; more improvements are to come. > > Both pages can also be accessed via: > http://jmol.sourceforge.net/demo/bwhite/ > > Although this is not the most advanced Chime page possible, it does demonstrate > jmol’s potential. Try it & see how it works! > > At this point, jmol should run on the following OS/browser combinations: > > Linux/Unix > Netscape 4.79 + Java Plug-in 1.3.1 or better > Mozilla 1.2 + Java Plug-in 1.3.1 or better > (Konqueror has some problems) > > Win 98/ME/NT/2K/XP > Netscape 4.76 or better > IE 5.50 or better (either Microsoft JVM or Java Plug-in) > Mozilla 1.2 + Java Plug-in 1.3.1 or better > > MacOS 9 > (Performance problems on older machines with large molecules) > (600mhz or better *highly* recommended) > Netscape 4.78 > IE - no JavaScript/Java communications > > MacOS X - does not work as yet. > Netscape 7.1 - no JavaScript/Java communications > IE - no JavaScript/Java communications > Safari - no JavaScript/Java communications > > I am in the process of writing an NSF CCLI-A&I (Course, Curriculum, and Laboratory > Improvement - Adaptation & Implementation) Grant to request funding for one of the > jmol developers. This will help ensure that the final RasMol/Chime features get > implemented in jmol in a timely fashion. Our goal is to develop a fully > Chime-compatible version, managed as an opensource project on sourceforge, so that > the applet and application, along with all source code, freely-available > accessible for future development. > > In order to make the grant more persuasive, we would like some > information from those who are interested; specifically: > > 1) Do you use Chime for teaching? At what level? (We need a rough count to put > in the grant). > > 2) Would you be interested in using jmol if it were fully > Chime-compatible? Please remember that the version of jmol posted at the above > link is a *development* version; the production version will have improved > compatibility, performance, etc. > > 3) We would like to have several beta-testers who would assist in the effort by > converting their chime html pages to jmol. We would provide technical support for > the changeover in return for bug reports, > feedback, suggestions, etc. Would you be willing to be a beta-tester? > > 4) Do you have any other suggestions, comments, ideas for the grant, etc? > > Thank you for your time. > > Brian > > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > > ----------------------------------------------------------------rasmol-+ > > To change your address, unsubscribe, view previous messages/history, receive > messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------rasmol-- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal Message-Tag: 21 References: <3F8C3CD1.5E78DA70@austin.rr.com> ++++------+------+------+------+------+------+------+------+------+------+ From: "Roger A. Johnson" Subject: Re: weblite viewer Date: Wed, 15 Oct 2003 12:22:54 -0400 To: rasmol@lists.umass.edu Miguel and others, I have weblab viewer "ViewerLite42.exe" (5MB) for a PC and the corresponding active X files, "ViewerActiveX42.exe" (3MB), that allows one to include molecular rotation and other features in a PowerPoint presentation. Because of size restructions on my server these are best sent by CD or Zip disks. If these would be of use to you please let me know. Roger Johnson ----- Original Message ----- Sent: Tuesday, October 14, 2003 2:13 PM From: "Sondra Kamper" Subject: weblite viewer To: > Miguel, > I have a saved copy of the webviewer lite v3.1.3 > installer (Mac only I think). It is a 4.2 Mb file; > unstuffs to 9.2 MB, about 6Mb of which is > examples. I will email it to you in a folder. Let > me know if you have a problem opening it. I could > mail it to you on a CD if email doesn't work. > - sondra Kamper > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline Message-Tag: 22 ++++------+------+------+------+------+------+------+------+------+------+ From: George Helmkamp Subject: Re: Open-source Chime* Date: Wed, 15 Oct 2003 11:49:16 -0500 To: rasmol@lists.umass.edu Brian White, I am so pleased that you are developing a Chime substitute that will work on newer versions of Netscape and Internet Explorer. I have been using Chime modules in my lectures and especially our accompanying website for the past 5-6 years, teaching medical students (175-180) aspects of protein structure/function and membrane lipid structure/function. See http://www.kumc.edu/biochemistry/bioc800/start.html, using Index to get to the Proteins 1 or Membranes 1 lectures. I would be able to be a beta-tester of your new software. regards, George Helmkamp * * * * * * * * * * * * * * * * * * * * * * * * * George M. Helmkamp, Jr., Ph.D. Department of Biochemistry and Molecular Biology University of Kansas Medical Center 3901 Rainbow Boulevard Kansas City, Kansas 66160-7421 (USA) TEL: {001} 913.588.6958 FAX: {001} 913.588.7440 EMAIL: ghelmkam@kumc.edu * * * * * * * * * * * * * * * * * * * * * * * * * >>> brian.white@umb.edu Wed, 15 Oct 2003 >>> Hi - Last summer, I e-mailed the list about creating an open-source equivalent of the Chime plug-in. I was motivated by the following: - the ease of use of Chime for making presentations - the extensive use of Chime for education & research - the lack of any potential for further development of Chime by MDL (I have spoken with the MDL folks & they are not interested in continuing Chime development for free public use). I think that there may be a viable solution. Members of the jmol project, http://jmol.sourceforge.net, have explicitly undertaken the goal of making jmol fully Chime/RasMol compatible, to provide a modern upgrade path for current users of Chime. The jmol applet will work with modern browser/platform combinations that are not supported by Chime. More importantly, it provides an open-source foundation which the user-community can enhance as our requirements grow and change. Since jmol is a java applet, users will not have to download/install a special plug-in to be able to view jmol-based web pages. Jmol does not have any special installation requirements and will run on most java virtual machines, including the older Microsoft java virtual machine that comes with Internet Explorer. Jmol will run with most browsers 'out of the box'. The development version of Jmol now implements many of Chime's features. The developers have written a perl script, chime2jmol.pl, which will automatically convert many chime pages to jmol. Using this tool, we have converted one of my Chime pages (that shows some important features of hemoglobin - I use this in lecture) to a jmol page. The two pages are: - The original Chime page: http://intro.bio.umb.edu/111-112/111F98Lect/hemoglobin2/hemolect.html This is not a very sophisticated Chime presentation; we chose it because it uses some important Chime features. The scripts are simple & must be accessed in order from top to bottom or strange things will result. There are delays built into the scripts, so wait a few seconds after pressing a button. Viewing this page requires Chime and a Chime-compatible browser/OS combination. - The converted page using jmol: http://jmol.sf.net/demo/bwhite/hemolect.html This has the same views as the Chime page. Note the improved rendering quality with jmol. Viewing this page does *not* require Chime. The applet is automatically downloaded the first time you access the page and subsequently stored in the web browser cache. Please note that this is a *development* version of jmol; more improvements are to come. Both pages can also be accessed via: http://jmol.sourceforge.net/demo/bwhite/ Although this is not the most advanced Chime page possible, it does demonstrate jmol's potential. Try it & see how it works! At this point, jmol should run on the following OS/browser combinations: Linux/Unix Netscape 4.79 + Java Plug-in 1.3.1 or better Mozilla 1.2 + Java Plug-in 1.3.1 or better (Konqueror has some problems) Win 98/ME/NT/2K/XP Netscape 4.76 or better IE 5.50 or better (either Microsoft JVM or Java Plug-in) Mozilla 1.2 + Java Plug-in 1.3.1 or better MacOS 9 (Performance problems on older machines with large molecules) (600mhz or better *highly* recommended) Netscape 4.78 IE - no JavaScript/Java communications MacOS X - does not work as yet. Netscape 7.1 - no JavaScript/Java communications IE - no JavaScript/Java communications Safari - no JavaScript/Java communications I am in the process of writing an NSF CCLI-A&I (Course, Curriculum, and Laboratory Improvement - Adaptation & Implementation) Grant to request funding for one of the jmol developers. This will help ensure that the final RasMol/Chime features get implemented in jmol in a timely fashion. Our goal is to develop a fully Chime-compatible version, managed as an opensource project on sourceforge, so that the applet and application, along with all source code, freely-available accessible for future development. In order to make the grant more persuasive, we would like some information from those who are interested; specifically: 1) Do you use Chime for teaching? At what level? (We need a rough count to put in the grant). 2) Would you be interested in using jmol if it were fully Chime-compatible? Please remember that the version of jmol posted at the above link is a *development* version; the production version will have improved compatibility, performance, etc. 3) We would like to have several beta-testers who would assist in the effort by converting their chime html pages to jmol. We would provide technical support for the changeover in return for bug reports, feedback, suggestions, etc. Would you be willing to be a beta-tester? 4) Do you have any other suggestions, comments, ideas for the grant, etc? Thank you for your time. Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 23 References: <3F8D5B02.E6ECA6D1@umb.edu> <57747.193.60.81.207.1066231225.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Mehl Subject: Re: =?iso-8859-1?Q?Re:_Open-source_Chime=94?= Date: Wed, 15 Oct 2003 13:30:28 -0400 To: rasmol@lists.umass.edu Our next letter is from Dan Bolser , who writes: > Can I take this opportunity to ask how to install the java plugin > with mozilla? > > I have java installed, but I don't know which file to copy into > the mozilla plugin directory, and I have never found this on the > internet. > > Sorry for the off topic, but I would love to use jmol. > > Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225, > build 2003022516 > For Blackdown Java (http://www.blackdown.org/) you need to do a __symbolic__ link into your mozilla plugins directory: ln -s /java_directory/jre/plugin/i386/mozilla/javaplugin_oji.so ~/.mozilla/plugins where "/java_directory" is the path to your java installation. Look at the Mozilla instructions in the Blackdown INSTALL file. Note that there are "gcc2.95" and "gcc3.2" versions of Blackdown Linux. Obviously, you pick the one that matches your gcc compiler. One other "gotcha": I couldn't get Mozilla Firebird 0.7 to run with the gcc2.95 version of Java. Of course, I couldn't get it to run with the 3.2 version, either, because we're still running gcc 2.95. The solution is to back up to Firebird 0.6. I'd suspect a similar thing can happen with the full-bloat Mozilla browser. FWIW, there's another use of the jmol plugin on the pages below. E.g., go to http://cst-www.nrl.navy.mil/lattice/struk/a4.html and click on "visualize the structure". (If you don't see it, you may have to turn your pop-ups back on.) -- M. J. Mehl (mehl@dave.nrl.navy.mil), Center for Computational Materials Science Naval Research Laboratory For a Computational Physicist's View of Interesting Crystal Structures, see http://cst-www.nrl.navy.mil/lattice/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 24 ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Accelerys (WebLab) ViewerLite Not Available Date: Wed, 15 Oct 2003 13:52:19 -0400 To: rasmol@lists.umass.edu hi all, I have Accelrys ViewerLite 5.0 for Windows (the last release of this software, IIRC). anyone who wants it can download the 5.64 mb installer from (for curious folk, myself included, the ViewerLite agreement specifically allows redistribution.) regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 6:23 PM EDT on Monday, October 13, 2003 Miguel said: > > I just learned from Leif Norskov that Accelrys has stopped offering > > ViewerLite. > > I was just trying to find this a few hours ago :-) > > Does anyone happen have a copy of the old ViewerLite software which I can > take a look at? > > Miguel > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 25 References: <3F8D5B02.E6ECA6D1@umb.edu> <57747.193.60.81.207.1066231225.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: =?iso-8859-1?Q?Re:_Open-source_Chime=94?= Date: Wed, 15 Oct 2003 20:31:46 +0200 (CEST) To: dmb@mrc-dunn.cam.ac.uk Cc: rasmol@lists.umass.edu > Can I take this opportunity to ask how to install the java plugin > with mozilla? Dan, Not sure which version of Linux you are running, nor how java was installed. But ... You need to put the file javaplugin.so into /usr/lib/mozilla/plugins To help you find where the file is you might try: locate javaplugin.so Either copy the file or make a symbolic link to it. Alternatively, I *think* that if you just install the latest Sun Java rpm it will automatically take care of this for you. (You can reply to me directly ... no reason to cc: the entire rasmol list). Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_Fxnr+cD4EXF+3qt9olYC8w)" Message-Tag: 27 X-CTI-Corpmail-MailScanner-Information: Please contact the ISP for more information X-CTI-Corpmail-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: =?ISO-8859-1?Q?Re:_Open-source_Chime=94?= Date: Wed, 15 Oct 2003 15:59:34 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_Fxnr+cD4EXF+3qt9olYC8w) Brian, You might consider this for your CCLI. You could add this for your dissemination component. Sarah Elgin (Washington Univ in St. Louis) and I are co-Editors-in-Chief of Cell Biology Education (CBE; www.cellbioed.org). CBE is interested in articles that addresses any areas of life science education - NOT JUST CELL BIOLOGY. CBE's primary audience is undergraduate materials, but we are keen to publish K-12 school material as well. Our mission is to bring together life science researchers who teach some courses and/or train students in the lab, biology teachers at all levels, and educators (e.g. those in education departments) to a common journal. As you may know, there is good literature in the education journals but too often it is only read by educators and not those who actually teach biology courses. Furthermore, we feel the scholarly work of people like you and me deserves a higher profile form of recognition. Since CBE is published by a premier biomedical professional society (American Society for Cell Biology) with several Nobel laureates, rigorously peer reviewed, indexed in PubMed, and published in PubMedCentral, papers appearing in CBE deserve full recognition by departments and institutions. CBE is freely available to everyone in html and PDF formats. We do have an automated email notification system that informs registered users when new issues are available (4 times a year). Currently, we have about 2100 registered users in over 60 countries. At CBE, we intend to take advantage of our electronic medium and publish peer-reviewed electronic resources such as animations and 3D structure tutorials. Your integrated web site would be a natural for this category of publication. If you can write a description of how you used it and any form of assessment for its effectiveness (e.g. student feedback, test questions, attitudes, etc.), we'd love to see your submission. If you want to know more about the assessment part, please feel free to call me or Sally Elgin. This is the hardest part for most of us but there are many forms of assessment other than control and experimental student populations. We also want to change the climate about assessment and teaching. Assessment for many is a negative or an unknown component. We want teachers to think of their teaching the same way they think about their research. They should expect to see data that convince them the authors have a valid claim. They should measure whether a new teaching tool has improved student learning. On Wednesday, October 15, 2003, at 10:34 AM, Brian White wrote: > brian.white@umb.edu ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28036 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_Fxnr+cD4EXF+3qt9olYC8w) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_Fxnr+cD4EXF+3qt9olYC8w)-- Importance: Normal Message-Tag: 28 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <3F8D5B02.E6ECA6D1@umb.edu> <57747.193.60.81.207.1066231225.squirrel@www.mrc-dunn.cam.ac.uk> <52429.80.58.16.235.1066242706.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: =?iso-8859-1?Q?Re:_Open-source_Chime=94?= Date: Wed, 15 Oct 2003 20:25:08 +0100 (BST) To: mth@mth.com Cc: rasmol@lists.umass.edu > To help you find where the file is you might try: > locate javaplugin.so /opt/j2sdk_nb/j2sdk1.4.2/jre/plugin/i386/ns4/libjavaplugin.so > > Either copy the file or make a symbolic link to it. Put under /usr/lib/mozilla/plugins/ about:plugins File name: libjavaplugin.so Java(TM) Plug-in 1.4.2 .... > Alternatively, I *think* that if you just install the latest Sun Java rpm it will > automatically take care of this for you. For some reason it didn't even put java in my /usr/local/bin :( > (You can reply to me directly ... no reason to cc: the entire rasmol list). Thanks very much, the problem I have now is the pages referred to previously just show a blank grey square. I guess I should be seeing more? Thanks for any help you can give, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Info: This message was accepted for relay by smtp02.mrf.mail.rcn.net as the sender used SMTP authentication Message-Tag: 29 X-Trace: UmFuZG9tSVa/rxiH83cp7ctc490qQ3jKk7zu3idtzV4uZNmJEt4iZDqF5oFMGge2 ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Jmol-8, Mac OS X 10.2.8, and Safari 1.0 v85.5 Date: Wed, 15 Oct 2003 21:58:58 -0400 To: rasmol@lists.umass.edu I am brand new to jmol, but I am happy to report that the jmol-8 applet displays molecules when the embedded applet is viewed using Mac OS X 10.2.8 and Safari v85.5. Since I just downloaded the applet, I haven't tried much more than viewing molecules and running an SN1_reaction animation. But it WORKS! Chris Christopher Masi Department of Physical Science Westfield State College Westfield, MA 01086 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 30 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <3F8D5B02.E6ECA6D1@umb.edu> <57747.193.60.81.207.1066231225.squirrel@www.mrc-dunn.cam.ac.uk> <200310151730.h9FHUSd08499@boron.nrl.navy.mil> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Jmol Working - Thanks! Date: Thu, 16 Oct 2003 09:44:54 +0100 (BST) To: rasmol@lists.umass.edu Big thanks to Miguel and Mike Mehl for helping me with this problem. In the end I switched to MozillaFirebird 0.7 http://texturizer.net/firebird/news.html And linking ... /opt/j2sdk_nb/j2sdk1.4.2/jre/plugin/i386/ns610-gcc32/libjavaplugin_oji.so into my (new) plugins directory got everything working fine on all the pages I have seen so far. Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii Message-Tag: 31 X-Accept-Language: en X-OriginalArrivalTime: 16 Oct 2003 14:49:29.0057 (UTC) FILETIME=[B3931510:01C393F4] References: ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Re: Open-source Chime* Date: Thu, 16 Oct 2003 11:02:41 -0400 To: rasmol@lists.umass.edu George - Thanks for the support & info! It is great that you are willing to beta-test; I will be in touch as things progress. Brian George Helmkamp wrote: > Brian White, > I am so pleased that you are developing a Chime substitute that will > work on newer versions of Netscape and Internet Explorer. I have been > using Chime modules in my lectures and especially our accompanying > website for the past 5-6 years, teaching medical students (175-180) > aspects of protein structure/function and membrane lipid > structure/function. > See http://www.kumc.edu/biochemistry/bioc800/start.html, using Index to > get to the Proteins 1 or Membranes 1 lectures. > I would be able to be a beta-tester of your new software. > regards, George Helmkamp > > * * * * * * * * * * * * * * * * * * * * * * * * > * > George M. Helmkamp, Jr., Ph.D. > Department of Biochemistry and Molecular Biology > University of Kansas Medical Center > 3901 Rainbow Boulevard > Kansas City, Kansas 66160-7421 (USA) > > TEL: {001} 913.588.6958 > FAX: {001} 913.588.7440 > EMAIL: ghelmkam@kumc.edu > * * * * * * * * * * * * * * * * * * * * * * * * > * > > >>> brian.white@umb.edu Wed, 15 Oct 2003 >>> > Hi - > > Last summer, I e-mailed the list about creating an open-source > equivalent of the Chime plug-in. I was motivated by the following: > - the ease of use of Chime for making presentations > - the extensive use of Chime for education & research > - the lack of any potential for further development of Chime by MDL > (I > have spoken with the MDL folks & they are not interested in continuing > Chime development for free public use). > > I think that there may be a viable solution. > > Members of the jmol project, http://jmol.sourceforge.net, have > explicitly undertaken the goal of making jmol fully Chime/RasMol > compatible, to provide a modern upgrade path for current users of > Chime. > > The jmol applet will work with modern browser/platform combinations > that > are not supported by Chime. More importantly, it provides an > open-source > foundation which the user-community can enhance as our requirements > grow > and change. > > Since jmol is a java applet, users will not have to download/install a > special plug-in to be able to view jmol-based web pages. Jmol does not > have any special installation requirements and will run on most java > virtual machines, including the older Microsoft java virtual machine > that comes with Internet Explorer. Jmol will run with most browsers > 'out > of the box'. > > The development version of Jmol now implements many of Chime's > features. The developers have written a perl script, chime2jmol.pl, > which will automatically convert many chime pages to jmol. Using this > tool, we have converted one of my Chime pages (that shows some > important > features of hemoglobin - I use this in lecture) to a jmol page. The > two > pages are: > > - The original Chime page: > http://intro.bio.umb.edu/111-112/111F98Lect/hemoglobin2/hemolect.html > This is not a very sophisticated Chime presentation; we chose it > because > it uses some important Chime features. The scripts are simple & must > be > accessed in order from top to bottom or strange things will result. > There are delays built into the scripts, so wait a few seconds after > pressing a button. Viewing this page requires Chime and a > Chime-compatible browser/OS combination. > > - The converted page using jmol: > http://jmol.sf.net/demo/bwhite/hemolect.html > This has the same views as the Chime page. Note the improved > rendering > quality with jmol. Viewing this page does *not* require Chime. The > applet is automatically downloaded the first time you access the page > and subsequently stored in the web browser cache. Please note that > this > is a *development* version of jmol; more improvements are to come. > > Both pages can also be accessed via: > http://jmol.sourceforge.net/demo/bwhite/ > > Although this is not the most advanced Chime page possible, it does > demonstrate jmol's potential. Try it & see how it works! > > At this point, jmol should run on the following OS/browser > combinations: > > Linux/Unix > Netscape 4.79 + Java Plug-in 1.3.1 or better > Mozilla 1.2 + Java Plug-in 1.3.1 or better > (Konqueror has some problems) > > Win 98/ME/NT/2K/XP > Netscape 4.76 or better > IE 5.50 or better (either Microsoft JVM or Java Plug-in) > Mozilla 1.2 + Java Plug-in 1.3.1 or better > > MacOS 9 > (Performance problems on older machines with large molecules) > (600mhz or better *highly* recommended) > Netscape 4.78 > IE - no JavaScript/Java communications > > MacOS X - does not work as yet. > Netscape 7.1 - no JavaScript/Java communications > IE - no JavaScript/Java communications > Safari - no JavaScript/Java communications > > I am in the process of writing an NSF CCLI-A&I (Course, Curriculum, > and > Laboratory Improvement - Adaptation & Implementation) Grant to request > funding for one of the jmol developers. This will help ensure that the > final RasMol/Chime features get implemented in jmol in a timely > fashion. > Our goal is to develop a fully Chime-compatible version, managed as an > opensource project on sourceforge, so that the applet and application, > along with all source code, freely-available accessible for future > development. > > In order to make the grant more persuasive, we would like some > information from those who are interested; specifically: > > 1) Do you use Chime for teaching? At what level? (We need a rough > count to put in the grant). > > 2) Would you be interested in using jmol if it were fully > Chime-compatible? Please remember that the version of jmol posted at > the above link is a *development* version; the production version will > have improved compatibility, performance, etc. > > 3) We would like to have several beta-testers who would assist in the > effort by converting their chime html pages to jmol. We would provide > technical support for the changeover in return for bug reports, > feedback, suggestions, etc. Would you be willing to be a beta-tester? > > 4) Do you have any other suggestions, comments, ideas for the grant, > etc? > > Thank you for your time. > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://intro.bio.umb.edu/BW/ > -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_kfLr/HR68Z5zJsEIFZM7Zw)" Message-Tag: 33 X-scanner: scanned by Inflex 1.0.12.3 ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: =?ISO-8859-1?Q?Re:_Open-source_Chime=94?= Date: Thu, 16 Oct 2003 17:50:00 +0200 To: rasmol@lists.umass.edu --Boundary_(ID_kfLr/HR68Z5zJsEIFZM7Zw) Dear Brian, I am very pleased to hear something will happen to compensate for the=20 lack of chime functionality in MacOSX. I use chime in molecular=20 genetics course to medical students (75 people/year) and would like to=20= support funding of you jmol development project. Please let me know if you need a more "official" statement... By the way I have downloaded and installed jmol v8 and still found many=20= differences from the chime menus I was used to. Have I used a wrong=20 jmol version? Thanks Ciao Adriano Ceccarelli Prof. Adriano Ceccarelli Facolt=E0 di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex --Boundary_(ID_kfLr/HR68Z5zJsEIFZM7Zw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_kfLr/HR68Z5zJsEIFZM7Zw)-- Importance: Normal Message-Tag: 34 ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: =?iso-8859-1?Q?Re:_[Fwd:_Re:_Open-source_Chime=94]?= Date: Thu, 16 Oct 2003 19:23:25 +0200 (CEST) To: rasmol@lists.umass.edu > Miguel - > Can you answer the software questions? > Brian > Pillot Paul wrote: >> ... >> When Jmol will be fully compatible with the majors Chime commands >> use, I'll surely make a Jmol version of MolUSc. Good, I hope you won't have to wait too long. >> I gave a quick look to the Jmol pages and here are some questions for >> which I couldn't find any answer : >> - rendering of proteins : >> in your example, I saw that backbone is available. >> What about cartoon, ribbon, and trace ? Trace is currently implemented. See http://jmol.sf.net/demo/trace Cartoons and ribbons are a little more work. I expect them to be added over the next few months. In addition, there is an important issue regarding identification of protein secondary structures. Many .pdb files do not contain HELIX, TURN, and SHEET records. Therefore, I need to implement an algorithm to recognize protein secondary structures. I am not a chemist, so this is proving a bit of a challenge for me. I have read a few articles but have difficulty understanding much of the terminology (given that a few months ago I didn't know what an alpha carbon was :) In any case, I am trying to get formal permission to read the DSSP source code. I am pursuing a similar line on the GAS-P source. If anyone feels they can help me out in this area, by all means please get in touch with me. >> - Querry informations : >> does a system like messageCallback exist ? MessageCallback, LoadStructCallback, and ButtonCallback are implemented. Brian White's hemoglobin lecture uses ButtonCallback to update the text in the bottom frame. AnimFrameCallback and PickCallback are not currently implemented. They will *not* be in the next Jmol release. >> Is it possible to get a sequence from a PDB file (show sequence), >> to know the references of selected atoms, chains,... >> (show chain,...), and to know the view point ? I don't know what that is ... so it must not be implemented yet :-) I'll take a look at the RasMol doc. >> - Surfaces : >> This is a Chime specific feature, but is it possible to render >> surfaces in Jmol ? Surfaces are not currently implemented. However, this is a very important feature for the Jmol team. So it *will* be implemented. Dot surfaces *are* currently implemented ... vdw dot surface and a 'correct' rendering of a Connolly/Solvent Accessible Surface. See: http://jmol.sf.net/demo/dots >> - Files : >> Is it possible to get gzipped PDB files with Jmol, as in Chime, to >> download structures faster ? Yes, Jmol recognizes gzipped files and automatically unzips them. >> - To avoid to download the entire applet each time, is there a way to >> install it on the local computer as for a real plug-in ? Applets get cached in the local browser cache. Subsequent uses of the the applet will pull the applet from the cache (after confirming that the applet date/time/size have not changed on the web server). At least, that is the theory ... and it works correctly on the browsers I have seen :-) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 32 X-CTI-Corpmail-MailScanner-Information: Please contact the ISP for more information X-CTI-Corpmail-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: =?ISO-8859-1?Q?Re:_Open-source_Chime=94?= Date: Thu, 16 Oct 2003 11:38:24 -0400 To: rasmol@lists.umass.edu Brian, You might consider this for your CCLI. You could add this for your dissemination component. Sarah Elgin (Washington Univ in St. Louis) and I are co-Editors-in-Chief of Cell Biology Education (CBE; www.cellbioed.org). CBE is interested in articles that addresses any areas of life science education - NOT JUST CELL BIOLOGY. CBE's primary audience is undergraduate materials, but we are keen to publish K-12 school material as well. Our mission is to bring together life science researchers who teach some courses and/or train students in the lab, biology teachers at all levels, and educators (e.g. those in education departments) to a common journal. As you may know, there is good literature in the education journals but too often it is only read by educators and not those who actually teach biology courses. Furthermore, we feel the scholarly work of people like you and me deserves a higher profile form of recognition. Since CBE is published by a premier biomedical professional society (American Society for Cell Biology) with several Nobel laureates, rigorously peer reviewed, indexed in PubMed, and published in PubMedCentral, papers appearing in CBE deserve full recognition by departments and institutions. CBE is freely available to everyone in html and PDF formats. We do have an automated email notification system that informs registered users when new issues are available (4 times a year). Currently, we have about 2100 registered users in over 60 countries. At CBE, we intend to take advantage of our electronic medium and publish peer-reviewed electronic resources such as animations and 3D structure tutorials. Your integrated web site would be a natural for this category of publication. If you can write a description of how you used it and any form of assessment for its effectiveness (e.g. student feedback, test questions, attitudes, etc.), we'd love to see your submission. If you want to know more about the assessment part, please feel free to call me or Sally Elgin. This is the hardest part for most of us but there are many forms of assessment other than control and experimental student populations. We also want to change the climate about assessment and teaching. Assessment for many is a negative or an unknown component. We want teachers to think of their teaching the same way they think about their research. They should expect to see data that convince them the authors have a valid claim. They should measure whether a new teaching tool has improved student learning. ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28036 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_iWe3uDxUw1dnaZdDZBNSDQ)" Message-Tag: 36 X-scanner: scanned by Inflex 1.0.12.3 ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: =?UTF-8?Q?Re:_Open-source_Chime=C2=94?= Date: Thu, 16 Oct 2003 23:08:58 +0200 (CEST) To: rasmol@lists.umass.edu --Boundary_(ID_iWe3uDxUw1dnaZdDZBNSDQ) Dear Miguel,thanks for the info. I have looked at the suggested preview link at sourceforge and I think it looks great. But at this point I am confused, as in Brian's message there is a statement on jmol still not working in MacOSX 10.x.x Why then am I able to visualize the page in MacOSX Netscape 7.1 ? Does it mean it is working indeed, and I could think of converting my chime pages into jmol pages already?ThanksAdriano Ceccarelli _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex --Boundary_(ID_iWe3uDxUw1dnaZdDZBNSDQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_iWe3uDxUw1dnaZdDZBNSDQ)-- Importance: Normal Message-Tag: 35 References: <3F8D5B02.E6ECA6D1@umb.edu> <665F2193-FFF0-11D7-82DE-000393824920@unito.it> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: =?iso-8859-1?Q?Re:_Open-source_Chime=94?= Date: Thu, 16 Oct 2003 22:53:04 +0200 (CEST) To: rasmol@lists.umass.edu Cc: adriano.ceccarelli@unito.it, jmol-developers@lists.sourceforge.net > By the way I have downloaded and installed jmol v8 and still found many > differences from the chime menus I was used to. Have I used a wrong > jmol version? Adriano, The current public release, Jmol v8, does *not* incorporate many of the features we have developed for Chime compatibility. For example, a new 3D graphics engine has been written, but it was not included in Jmol v8. To see a few examples of the pre-release development version of the applet you can look under the link entitled 'Preview' on the Jmol home page, http://jmol.sourceforge.net Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 38 References: <3F8C3CD1.5E78DA70@austin.rr.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Bernhard Vogler Subject: Re: weblite viewer Date: Fri, 17 Oct 2003 22:11:28 -0500 To: rasmol@lists.umass.edu Would be great to have B. Vogler Department of Chemistry University of Alabama in Huntsville Huntsville, Al, 35899 At 11:22 AM 10/15/2003, you wrote: >Miguel and others, >I have weblab viewer "ViewerLite42.exe" (5MB) for a PC and the corresponding >active X files, "ViewerActiveX42.exe" (3MB), that allows one to include >molecular rotation and other features in a PowerPoint presentation. Because >of size restructions on my server these are best sent by CD or Zip disks. >If these would be of use to you please let me know. >Roger Johnson > > > >----- Original Message ----- >From: "Sondra Kamper" >To: >Sent: Tuesday, October 14, 2003 2:13 PM >Subject: weblite viewer > > > > Miguel, > > I have a saved copy of the webviewer lite v3.1.3 > > installer (Mac only I think). It is a 4.2 Mb file; > > unstuffs to 9.2 MB, about 6Mb of which is > > examples. I will email it to you in a folder. Let > > me know if you have a problem opening it. I could > > mail it to you on a CD if email doesn't work. > > - sondra Kamper > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii Message-Tag: 37 X-Accept-Language: en X-OriginalArrivalTime: 17 Oct 2003 18:23:28.0250 (UTC) FILETIME=[C2BE35A0:01C394DB] References: ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Re: Open-source =?iso-8859-1?Q?Chime=94?= Date: Fri, 17 Oct 2003 14:36:37 -0400 To: rasmol@lists.umass.edu Malcom - This is most excellent! "A.Malcolm Campbell" wrote: > Brian, > You might consider this for your CCLI. You could add this for your > dissemination component. > > Sarah Elgin (Washington Univ in St. Louis) and I are > co-Editors-in-Chief of Cell Biology Education (CBE; www.cellbioed.org). > CBE is interested in articles that addresses any areas of life science > education - NOT JUST CELL BIOLOGY. CBE's primary audience is > undergraduate materials, but we are keen to publish K-12 school > material as well. > > Our mission is to bring together life science researchers who teach > some courses and/or train students in the lab, biology teachers at all > levels, and educators (e.g. those in education departments) to a common > journal. As you may know, there is good literature in the education > journals but too often it is only read by educators and not those who > actually teach biology courses. Furthermore, we feel the scholarly work > of people like you and me deserves a higher profile form of > recognition. Since CBE is published by a premier biomedical > professional society (American Society for Cell Biology) with several > Nobel laureates, rigorously peer reviewed, indexed in PubMed, and > published in PubMedCentral, papers appearing in CBE deserve full > recognition by departments and institutions. CBE is freely available to > everyone in html and PDF formats. We do have an automated email > notification system that informs registered users when new issues are > available (4 times a year). Currently, we have about 2100 registered > users in over 60 countries. > > At CBE, we intend to take advantage of our electronic medium and > publish peer-reviewed electronic resources such as animations and 3D > structure tutorials. Your integrated web site would be a natural for > this category of publication. If you can write a description of how you > used it and any form of assessment for its effectiveness (e.g. student > feedback, test questions, attitudes, etc.), we'd love to see your > submission. If you want to know more about the assessment part, please > feel free to call me or Sally Elgin. This is the hardest part for most > of us but there are many forms of assessment other than control and > experimental student populations. I have done an evaluation of rasmol & chime - but I was not thinking of doing a formal comparison of chime & jmol. Would you be interested in just running a short blurb about jmol when it is all spiffed up? > > > We also want to change the climate about assessment and teaching. > Assessment for many is a negative or an unknown component. We want > teachers to think of their teaching the same way they think about their > research. They should expect to see data that convince them the authors > have a valid claim. They should measure whether a new teaching tool has > improved student learning. > I strongly agree - I have been working on this 'crusade' for some time now. I used to go to ABLE (assoc for biology lab education) & try to sell them on this idea, but they are still in the mode of "this is a cool lab on photosynthesis" not "what do I want them to get on photosynthesis? what is hard to get about photosyn? how can I teach those parts & see if the lab helps them to get it?" I have sent one such article (about a mol vis curriculum & it's evaluation) to biochem & mol bio ed. If I have articles relevant to cell bio, I will certainly send them your way. > > ________________________________________________________ > A. Malcolm Campbell, Ph.D. > Associate Professor of Biology > Davidson College > Director of GCAT (www.bio.davidson.edu/GCAT) > Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) > > Box 7118 (US Mail) > 209 Ridge Road (shipping) > Davidson College > Davidson, NC 28036 > 704-894-2692 (phone) > 704-894-2512 (fax) > www.bio.davidson.edu/campbell > -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 39 References: <4701342.1066338538105.JavaMail.root@ares> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: Open-source Chime Date: Sat, 18 Oct 2003 21:25:27 +0200 (CEST) To: adriano.ceccarelli@unito.it Cc: rasmol@lists.umass.edu > in Brian's message there is a statement on jmol still not > working in MacOSX 10.x.x Why then am I able to visualize the page in > MacOSX Netscape 7.1 ? (The pages in question are under http://jmol.sourceforge.net/demo) Adriano, The buttons you saw are not using JavaScript. They are applets which send scripts to the main applet. Comparable to the Chime push-button controls. The situation surrounding JavaScript/Java on MacOS X *is* confusing. (I have been trying to come up with a succinct way to describe the situation ... this is not it) - no browsers on MacOS X reliably support LiveScript communication between JavaScript and Java - this is not a Jmol issue, it applies to *every* applet - Safari is based upon the open source Konqueror and Konqueror has had LiveConnect for about a year - Apple has not released a date, and has said surprisingly little about this. - I believe they *must* introduce it into Safari in the future - Once Apple releases it, it *will* have bugs - (Send a message to Apple and tell them you *need* LiveConnect) Separately ... - The Panther release of OS X will include an X11 server - this will make it much easier to port Linux/Unix apps to OSX - I believe that someone will port Mozilla, Konqueror, etc. to OSX Therefore - I believe that the OS X situation will be quite different in 6 months > Does it mean it is working indeed, and I could > think of converting my chime pages into jmol pages already? I like your enthusiasm :-) What *is* working is the 'chime-compatible' buttons, if they do not use 'buttonCallback'. Of course, Chime does not run on OSX. So you do not lose anything by starting to move your apps to Jmol. And you gain Linux/Unix support. But ... don't start yet. We will have some 'official' test releases of Jmol v10 in November. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 40 X-scanner: scanned by Inflex 1.0.12.3 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id h9KJDwR08713 ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: Re: Open-source Chime Date: Mon, 20 Oct 2003 10:37:12 +0200 To: rasmol@lists.umass.edu MIguel, > The buttons you saw are not using JavaScript. They are applets which > send > scripts to the main applet. Comparable to the Chime push-button > controls. how sad...... > Separately ... > - The Panther release of OS X will include an X11 server > - this will make it much easier to port Linux/Unix apps to OSX > - I believe that someone will port Mozilla, Konqueror, et I am already running X11 with pymol for 3d mol vis. but as I am not a unix guru, I haven't been able to do anything with it to substitute for the lac of chime in OSX. Would it be a possible thing to do? Will Panther change this into something immediately usable, or we still have to wait for more software to be ported to OSX? > Of course, Chime does not run on OSX. So you do not lose anything by > starting to move your apps to Jmol. And you gain Linux/Unix support. > > But ... don't start yet. We will have some 'official' test releases of > Jmol v10 in November. > > In fact, following Chris Masi suggestion a few posts earlier, I tried to embed a jmol applet and open the page with safari to visualize an rRNA molecule and found that it actually works, but the performance is far away from chime. It is slower to load and to rotate, and the rendering is not as nice. Is this real or have I messed up with some settings? Will jmol v10 improve these aspects? And how about the remaining chime's functions, will they be implemented into jmol? Thanks Ciao Adriano Prof. Adriano Ceccarelli Facoltà di Medicina e Chirurgia Dip. Scienze Cliniche e Biologiche Osp. S. Luigi Gonzaga - Orbassano Torino - ITALY phone +39116708109 fax +39119038639 email adriano.ceccarelli@unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 41 ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: wanted: amino acid .pdb files Date: Mon, 20 Oct 2003 19:47:26 +0200 (CEST) To: rasmol@lists.umass.edu I am looking for a complete set of 20 amino acid .pdb files with the following characteristics: - correct nomenclature - hydrogen files Any help would be appreciated. Gracias, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 42 References: <35026.80.58.16.235.1066505127.squirrel@www.howards.org> <99CD5B38-02D8-11D8-A604-000393824920@unito.it> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: Open-source Chime Date: Mon, 20 Oct 2003 22:12:59 +0200 (CEST) To: adriano.ceccarelli@unito.it Cc: rasmol@lists.umass.edu > I tried > to embed a jmol applet and open the page with safari to visualize an > rRNA molecule and found that it actually works, but the performance is > far away from chime. It is slower to load and to rotate, and the > rendering is not as nice. Is this real or have I messed up with some > settings? The graphics engine was completely rewritten for Jmol v10. It is now significantly faster for larger molecules > Will jmol v10 improve these aspects? Yes > And how about the > remaining chime's functions, will they be implemented into jmol? Many RasMol/Chime features are implemented today in Jmol v10. Advanced graphics renderings of secondary protein structures are not. Please send me your rRNA molecule (the one with the performance problems) and I will embed it in a web page so that you can take a look at it. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 43 ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: wanted: amino acid .pdb files Date: Mon, 20 Oct 2003 19:17:59 -0400 To: rasmol@lists.umass.edu Hi, Miguel! See http://www.usm.maine.edu/~rhodes/BiochemViews/AminoAcids/index.html I hate to admit it, but I can't remember where I got these, and to whom I should give credit (don't tell my students!). Thanks to some nice person for doing them. Cheers! On Monday, October 20, 2003, at 01:47 PM, Miguel wrote: > I am looking for a complete set of 20 amino acid .pdb files with the > following characteristics: > - correct nomenclature > - hydrogen files > > Any help would be appreciated. > > Gracias, > Miguel > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Gale Rhodes, Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 44 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <52048.80.58.16.235.1066672046.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: wanted: amino acid .pdb files Date: Tue, 21 Oct 2003 07:26:08 +0100 (BST) To: rasmol@lists.umass.edu Cc: mth@mth.com Miguel said: > I am looking for a complete set of 20 amino acid .pdb files with the following > characteristics: > - correct nomenclature > - hydrogen files > > Any help would be appreciated. I like this site for AA information... http://www.imb-jena.de/IMAGE_AA.html > Gracias, > Miguel > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 45 ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: RasMol/Chime predefined sets Date: Tue, 21 Oct 2003 21:26:24 +0200 (CEST) To: rasmol@lists.umass.edu Cc: jmol-developers@lists.sourceforge.net Based upon reading the documentation, the RasMol scripting language has several ambiguities. One of them is a conflict in predefined sets. Amino acids have three letter abbreviations & 1 letter abbreviations a = ala -> alanine c = cys -> cystine g = gly -> glycine t = thr -> threonine ... I also see that the predefined sets for the 4 nucleotide bases are a -> adenosine c -> cytidine g -> guanosine t -> thymidine Can anyone shed any light on how this ambiguity is handled at run-time? In practice, do people *use* the single letter amino acid abbreviations in scripting? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Importance: Normal X-MSMail-priority: Normal Message-Tag: 46 ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: RE: wanted: amino acid .pdb files Date: Wed, 22 Oct 2003 07:02:47 -0400 To: rasmol@lists.umass.edu Miguel > I am looking for a complete set of 20 amino acid .pdb files > with the following characteristics: > - correct nomenclature > - hydrogen files > > Any help would be appreciated. Try Klotho for small molecules (including amino acids and bases) http://www.biocheminfo.org/klotho/compound_list.html. h ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 47 ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: slab mode questions Date: Wed, 22 Oct 2003 14:09:17 +0200 (CEST) To: rasmol@lists.umass.edu A few questions about slab mode: Does anyone use it a *lot* ? How important are the various slab 'modes' ? set slabmode { reject | half | hollow | solid | section } Which is most important/useful? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal Message-Tag: 48 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: slab mode questions Date: Wed, 22 Oct 2003 17:45:39 +0100 (BST) To: rasmol@lists.umass.edu Cc: mth@mth.com Miguel said: > A few questions about slab mode: > > Does anyone use it a *lot* ? > I like to look at a section about one inch wide cut in from infront and behind. p.s. my tipical rasmol screen it 5-7 inch with tipical protein = globular 300 AA. > How important are the various slab 'modes' ? > set slabmode { reject | half | hollow | solid | section } > > Which is most important/useful? > > Miguel > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: slab mode questions Date: Thu, 23 Oct 2003 15:58:25 -0400 To: rasmol@lists.umass.edu My responses to Miguel's questions: At 10/22/03, you wrote: >A few questions about slab mode: > >Does anyone use it a *lot* ? It is very useful when you need it, particularly for looking at the degree of uniformity in a hydrophobic core. Nothing else does the same job as well. >How important are the various slab 'modes' ? > set slabmode { reject | half | hollow | solid | section } Solid, the default, is very useful. Section can also be very useful by hiding rear clutter. I'm not sure the others are so important. The ability to look inside hollow surfaces would be useful, I think. Presently, slab mode does cut away the front of a rolling-probe solvent-accessible surface (in Chime) in what appears to be the correct manner. However the rear has large pieces missing so you can't see the inside shape. The slabmode's don't affect the slabbing of a surface, except that "section" hides it completely. >Which is most important/useful? Ideally there could also be a true slab mode, instead of the "semi-slab" mode implemented in RasMol 2.6 and Chime. The latter cut through the molecule only once (a single cutting plane), hiding what is in front of the cutting plane. A true slab mode cuts twice, producing a true slab, with both the front and the rear hidden (just the slab visible). Being able to set the thickness of the slab is very useful, in which case the "semi-slab" mode becomes a special case of the slab mode. >Miguel > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Message-Tag: 49 ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: slab mode questions Date: Thu, 23 Oct 2003 08:19:39 -0400 To: rasmol@lists.umass.edu Hi, Miguel! For a look at what slabbing can do, see section 7, Exploring, in http://www.usm.maine.edu/~rhodes/RasTut/index.html Cheers! On Wednesday, October 22, 2003, at 08:09 AM, Miguel wrote: > A few questions about slab mode: > > Does anyone use it a *lot* ? > > How important are the various slab 'modes' ? > set slabmode { reject | half | hollow | solid | section } > > Which is most important/useful? > > Miguel > > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Gale Rhodes, Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 10:46:56 +0200 (CEST) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu >>How important are the various slab 'modes' ? >> set slabmode { reject | half | hollow | solid | section } > Solid, the default, is very useful. Section can also be very useful by > hiding rear clutter. I'm not sure the others are so important. OK > The ability to look inside hollow surfaces would be useful, I think. It makes sense that it would be useful. (I assume that by 'surface' you mean some type of iso-surface) > Presently, slab mode does cut away the front of a rolling-probe > solvent-accessible surface (in Chime) in what appears to be the correct > manner. I have not started implementation of surfaces, so I haven't seen this yet. > However the rear has large pieces missing so you can't see the > inside shape. Without having seen it, I assume that they are not rendering the rear pixels because they are generally hidden and it would normally be a waste of CPU. > The slabmode's don't affect the slabbing of a surface, > except that "section" hides it completely. Hmmm ... I would expect it to show the iso-surface pixels that intersect the slab plane. (At some point I will probably ask someone to point me to a Chime demo of this.) >>Which is most important/useful? > Ideally there could also be a true slab mode, instead of the "semi-slab" > mode implemented in RasMol 2.6 and Chime. The latter cut through the > molecule only once (a single cutting plane), hiding what is in front of > the cutting plane. A true slab mode cuts twice, producing a true slab, > with both the front and the rear hidden (just the slab visible). Being > able to set the thickness of the slab is very useful, in which case the > "semi-slab" mode becomes a special case of the slab mode. This would be quite straightforward to implement in Jmol. To expose this functionality to the user this we will need to extend the RasMol scripting language and probably add a mouse gesture. It would be helpful to get feedback on how these changes should be implemented. First, lets talk about the scripting language. The slab command takes a positive integer from 0-100, representing the percentage of the molecule to show. We can easily extend the 'slab' (or 'set slabmode') command syntax by: - using negative integers - using floats - adding additional parameters As far as the behavior of the rear slab is concerned, two options come to mind. The first is an 'absolute' rear slab percentage. so a rear slab value of 10% would mean that the rear slab plane would cut through at 10% from the back. It would stay in the same spot independent of what happened to the front slab plane. The second is for the rear slab plane to be 'relative' to the front. So a rear slab value of 10% would mean that the rear slab plane would always stay 10% of the way behind the front slab. So that as the front slab changed you would always see 10% of the molecule. It occurs to me that the 'relative' might make more sense, especially when combined with the 'slab' CTL-LEFT mouse gesture. Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab positioning? Q: What do other programs do? I suppose it would also be easy to support a specification of the slab thickness in Angstroms (floats). Q: Would that be useful, or is % good enough? The mouse gesture question is a bit more difficult. I suppose that we could do something like CTL-SHIFT-LEFT to control the rear slab. But I fear that it will be difficult for novice users to position the rear slab ... the visual feedback will be quite different. I guess there is another possibility. I have been thinking of introducing a little 'slider' control to make it easier to specify zoom level. For 'slab' I could pop up a 'double slider', where one controls the back and the other controls the front. Something like that. Q: What kind of gestures/controls do other programs use? set slabmode : The doc doesn't say much about the various 'slabmode' values. I think I figured out what most of them do. Q: It looks to me like 'set slabmode section' is 1 pixel thick. Is my interpretation correct? slab + bond rendering : If a bond is a 'wire' then it disappears incrementally as the slab cuts through it. If a bond is a cylinder then it disappears completely if the center of either of its atoms is beyond the slab. Q: Shouldn't the two be consistent? Q: What is the desirable behavior? Finally, a very important question of priorities and timing. Q: How important is full 'slab' support relative to other things that are not currently implemented in Jmol (e.g. 'ribbons/cartoons') ? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 10:47:22 +0200 To: rasmol@lists.umass.edu Eric Martz wrote: > My responses to Miguel's questions: > ...cut... > >> Which is most important/useful? > > > > Ideally there could also be a true slab mode, instead of the > "semi-slab" mode implemented in RasMol 2.6 and Chime. The latter cut > through the molecule only once (a single cutting plane), hiding what > is in front of the cutting plane. A true slab mode cuts twice, > producing a true slab, with both the front and the rear hidden (just > the slab visible). Being able to set the thickness of the slab is very > useful, in which case the "semi-slab" mode becomes a special case of > the slab mode. > this could be done with slab 66 depth 55 which will give you 10% of the Molecule in RasMol 2.7.2.1 where depth does the back clipping. e.g. in http://www.imb-jena.de/~jr/VisAnPred/RasMol/Myoglobin/img8.gif Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <3F98E71A.6070606@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: slab mode questions & 2.7.*2* Date: Fri, 24 Oct 2003 11:10:59 +0200 (CEST) To: rasmol@lists.umass.edu Cc: jr@imb-jena.de >> Ideally there could also be a true slab mode, instead of the >> "semi-slab" mode implemented in RasMol 2.6 and Chime. The latter cut >> through the molecule only once (a single cutting plane), hiding what >> is in front of the cutting plane. A true slab mode cuts twice, >> producing a true slab, with both the front and the rear hidden (just >> the slab visible). Being able to set the thickness of the slab is very >> useful, in which case the "semi-slab" mode becomes a special case of >> the slab mode. >> > this could be done with > > slab 66 > depth 55 > > which will give you 10% of the Molecule in RasMol 2.7.2.1 where depth > does the back clipping. e.g. in > http://www.imb-jena.de/~jr/VisAnPred/RasMol/Myoglobin/img8.gif > Regards, Jan Jan, Thanks! This seems to be a new feature of 2.7.*2* So there is no mention of it in the online documentation I have been using on openrasmol.org Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <42690.80.58.16.235.1066985216.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 11:42:38 +0200 To: rasmol@lists.umass.edu Miguel wrote: > ...cut... > >>>Which is most important/useful? >>> >>> >>Ideally there could also be a true slab mode, instead of the "semi-slab" >> mode implemented in RasMol 2.6 and Chime. The latter cut through the >>molecule only once (a single cutting plane), hiding what is in front of >>the cutting plane. A true slab mode cuts twice, producing a true slab, >>with both the front and the rear hidden (just the slab visible). Being >>able to set the thickness of the slab is very useful, in which case the >>"semi-slab" mode becomes a special case of the slab mode. >> >> > >This would be quite straightforward to implement in Jmol. > >To expose this functionality to the user this we will need to extend the >RasMol scripting language and probably add a mouse gesture. It would be >helpful to get feedback on how these changes should be implemented. > >First, lets talk about the scripting language. The slab command takes a >positive integer from 0-100, representing the percentage of the molecule >to show. We can easily extend the 'slab' (or 'set slabmode') command >syntax by: > - using negative integers > - using floats > - adding additional parameters > >As far as the behavior of the rear slab is concerned, two options come to >mind. The first is an 'absolute' rear slab percentage. so a rear slab >value of 10% would mean that the rear slab plane would cut through at 10% >from the back. It would stay in the same spot independent of what happened >to the front slab plane. > > > this is like the RasMol 2.7.2.1 behaves and I would suggest to implement this. it is documented in the command line help type ? depth on the command line (on Windows you have to put the rasmol.hlp file to the right place by hand). (and even the Windows help which identifies itself as RasWin 2.6_CIF) but I have forgotten to mention depth at all in my version of the Quick Reference which I will update later today:-) http://www.imb-jena.de/~jr/VisAnPred/RasMol/RasMolv272.pdf I would like to have additional real number values meaning Angstroem units and this would in case of slab, depth mean distance from the center of the molecule chosen in that moment. >The second is for the rear slab plane to be 'relative' to the front. So a >rear slab value of 10% would mean that the rear slab plane would always >stay 10% of the way behind the front slab. So that as the front slab >changed you would always see 10% of the molecule. > > > No, not compatible with existing RasMol. >It occurs to me that the 'relative' might make more sense, especially when >combined with the 'slab' CTL-LEFT mouse gesture. > > > I prefer scripting. >Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab positioning? >Q: What do other programs do? > >I suppose it would also be easy to support a specification of the slab >thickness in Angstroms (floats). >Q: Would that be useful, or is % good enough? > > > as I mentioned above floats meaning A units would be nice, especially in case of translations, where I miss this in RasMol (you can't build a crystal in RasMol by simply loading multiple times the same asymmetric unit (this works) and rotate and translate (this is the Problem). >The mouse gesture question is a bit more difficult. I suppose that we >could do something like CTL-SHIFT-LEFT to control the rear slab. But I >fear that it will be difficult for novice users to position the rear slab >... the visual feedback will be quite different. > > > I think slabbing both sides is too difficult for mouse operations. Non of the students was able to handle the slabbing at all, when they first try. Slabbing is done in most cases by accident with the mouse and the students get confused how to reset the scene. >I guess there is another possibility. I have been thinking of introducing >a little 'slider' control to make it easier to specify zoom level. For >'slab' I could pop up a 'double slider', where one controls the back and >the other controls the front. Something like that. > >Q: What kind of gestures/controls do other programs use? > > > have a look at RasTop, but I don't use it. >set slabmode : The doc doesn't say much about the various >'slabmode' values. I think I figured out what most of them do. > > you are right (every time I have to test them all to get the desired result:-) >Q: It looks to me like 'set slabmode section' is 1 pixel thick. Is my >interpretation correct? > >slab + bond rendering : If a bond is a 'wire' then it disappears >incrementally as the slab cuts through it. If a bond is a cylinder then it >disappears completely if the center of either of its atoms is beyond the >slab. > >Q: Shouldn't the two be consistent? > > Yes >Q: What is the desirable behavior? > > > increment >Finally, a very important question of priorities and timing. > >Q: How important is full 'slab' support relative to other things that are >not currently implemented in Jmol (e.g. 'ribbons/cartoons') ? > > > cartoon is most important. Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 15:56:10 -0400 To: Miguel Cc: rasmol@lists.umass.edu At 10/24/03, you wrote: >(At some point I will probably ask someone to point me to a Chime demo of >this.) I can give you quick simple instructions to generate surfaces etc. in Protein Explorer. Using PE's buttons generates the commands automatically, which you can then copy, vary etc. I guess there is another possibility. I have been thinking of introducing >a little 'slider' control to make it easier to specify zoom level. For >'slab' I could pop up a 'double slider', where one controls the back and >the other controls the front. Something like that. Sliders would be excellent, especially accompanied by a display of the %zoom or slab position/thickness, etc. I have thought about trying to devise some to include in Protein Explorer, but not done it yet. Albion Baucom and Harry Ungar once offered some java applet sliders that interfaced with Chime, but I could never get them to work reliably. >Q: How important is full 'slab' support relative to other things that are >not currently implemented in Jmol (e.g. 'ribbons/cartoons') ? Cartoons, especially, are probably more important in general, in my opinion. I would also very much like to see inclusion of cylinders as a further simplification for alpha helices. WebLab does cylinders nicely. -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 11:45:26 -0400 To: rasmol@lists.umass.edu hi Miguel, at 10:46 am EDT on (Friday) 24 October 2003 Miguel said: > Finally, a very important question of priorities and timing. > > Q: How important is full 'slab' support relative to other things that are > not currently implemented in Jmol (e.g. 'ribbons/cartoons') ? > > since this is the most important question, I moved it to the top: cartoon rendering is much, much more important. that said, though... > >>How important are the various slab 'modes' ? > >> set slabmode { reject | half | hollow | solid | section } > > Solid, the default, is very useful. Section can also be very useful by > > hiding rear clutter. I'm not sure the others are so important. > OK > by way of disclaimer, I have only used slab (solid) a handful of times for presentation purposes, and never in animations. I have had mixed, mostly negative feedback about its utility as a teaching tool, mainly because it can be difficult to intepret visually. this is especially true in the context of 3D rotations and zooming. it is my understanding that intro and early-level student users tend to get frustrated with slab views. > > >>Which is most important/useful? > > Ideally there could also be a true slab mode, instead of the "semi-slab" > > mode implemented in RasMol 2.6 and Chime. The latter cut through the > > molecule only once (a single cutting plane), hiding what is in front of > > the cutting plane. A true slab mode cuts twice, producing a true slab, > > with both the front and the rear hidden (just the slab visible). Being > > able to set the thickness of the slab is very useful, in which case the > > "semi-slab" mode becomes a special case of the slab mode. > > This would be quite straightforward to implement in Jmol. > I can see a true slab being useful, definitely, and easier to grasp. > As far as the behavior of the rear slab is concerned, two options come to > mind. The first is an 'absolute' rear slab percentage. so a rear slab > value of 10% would mean that the rear slab plane would cut through at 10% > from the back. It would stay in the same spot independent of what happened > to the front slab plane. > > The second is for the rear slab plane to be 'relative' to the front. So a > rear slab value of 10% would mean that the rear slab plane would always > stay 10% of the way behind the front slab. So that as the front slab > changed you would always see 10% of the molecule. > > It occurs to me that the 'relative' might make more sense, especially when > combined with the 'slab' CTL-LEFT mouse gesture. > > Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab positioning? > I think the ability to control both planes independently is useful; however, I come down on the side of relative positioning for the mouse control. I think the most common use of the slab will be moving it up and back through the molecule. changing the thickness or mode should be done via commands or menus, but not the mouse. will the slab rotate and zoom with the structure, or independently? > Q: What do other programs do? > > I suppose it would also be easy to support a specification of the slab > thickness in Angstroms (floats). > Q: Would that be useful, or is % good enough? > I think supporting Angstroms is very valuable here. > The mouse gesture question is a bit more difficult. I suppose that we > could do something like CTL-SHIFT-LEFT to control the rear slab. But I > fear that it will be difficult for novice users to position the rear slab > .... the visual feedback will be quite different. > > I guess there is another possibility. I have been thinking of introducing > a little 'slider' control to make it easier to specify zoom level. For > 'slab' I could pop up a 'double slider', where one controls the back and > the other controls the front. Something like that. > I likke the idea of a slider combo for controlling the slab parameters. but again, I would steer clear of providing access to complex and visually confusing effects via the mouse. > slab + bond rendering : If a bond is a 'wire' then it disappears > incrementally as the slab cuts through it. If a bond is a cylinder then it > disappears completely if the center of either of its atoms is beyond the > slab. > > Q: Shouldn't the two be consistent? > Q: What is the desirable behavior? > > it should be consistent, and it should disappear incrementally. since we are in 3D, how about multiple simultaneous slabs? for example, one plane running in the X plane and another running in the Y. that would allow one to "peel" a globular structure like an onion by incrementally decreasing the thickness of each slab. this would be especially dramatic in animation. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 23:23:22 +0200 (CEST) To: emartz@microbio.umass.edu Cc: rasmol@lists.umass.edu > Cartoons, especially, are probably more important in general, in my > opinion. I would also very much like to see inclusion of cylinders as a > further simplification for alpha helices. WebLab does cylinders nicely. Since you brought up the subject of cylinders, I have a few questions: Q: Should the ends of the cylinders have a conic 'cap' to show the chain direction? (That will actually make them look like little rockets) Q: How can we introduce 'cylinders' (and other rendering styles) without introducing a whole series of commands? I need some suggestions for script syntax. Are these things all variants of Cartoons? Q: How important are 'strands'? Q: In beta sheets, do you want the arrows to be 'crinkled' or straight? I don't have any direct experience with other molecular visualization packages. Pointers to web images would be good. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <42690.80.58.16.235.1066985216.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 23:36:19 +0200 (CEST) To: rasmol@lists.umass.edu Cc: listsub@molvisions.com > I have had mixed, > mostly negative feedback about its utility as a teaching tool, mainly > because it can be difficult to intepret visually. this is especially > true in the context of 3D rotations and zooming. it is my understanding > that intro and early-level student users tend to get frustrated with > slab views. This is consistent with my own experience (as a novice) and the comments of Jan Reichert, who said that the students get confused when they get into slab mode. >> Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab >> positioning? >> > I think the ability to control both planes independently is useful; > however, I come down on the side of relative positioning for the mouse > control. I think the most common use of the slab will be moving it up > and back through the molecule. changing the thickness or mode should be > done via commands or menus, but not the mouse. It looks like that we are of two opinions on this, because apparently the RasMol 2.7.2 pre-release handles this in a different way. But, since 'slab' is low priority, we will table this discussion for the time being. > will the slab rotate and zoom with the structure, or independently? Hmmm ... making the slab rotate would introduce a whole new level of implementation complexity. But it is an interesting idea ... might make it easier to visualize and understand how the slab works. > since we are in 3D, how about multiple simultaneous slabs? for example, > one plane running in the X plane and another running in the Y. that > would allow one to "peel" a globular structure like an onion by > incrementally decreasing the thickness of each slab. this would be > especially dramatic in animation. We'll put that one on the shelf as a 'nice-to-have' :-) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 17:47:02 -0400 To: Miguel Cc: rasmol@lists.umass.edu At 10/24/03, Miguel wrote: > > Cartoons, especially, are probably more important in general, in my > > opinion. I would also very much like to see inclusion of cylinders as a > > further simplification for alpha helices. WebLab does cylinders nicely. > >Since you brought up the subject of cylinders, I have a few questions: > >Q: Should the ends of the cylinders have a conic 'cap' to show the chain >direction? (That will actually make them look like little rockets) Rockets are good! (directionality is important and the conic ends don't detract from the main effect) >Q: How can we introduce 'cylinders' (and other rendering styles) without >introducing a whole series of commands? I need some suggestions for script >syntax. Are these things all variants of Cartoons? New commands make sense for new capabilities. How about "rockets"? It is maybe too cute, but that makes it easy to remember. The formal word for what "cartoon" shows is "schematic" but "cartoon" is also easy to remember. Alternatively or in addition there could be 'set cartoon rockets', but I like having a direct command to make "rockets" more accessible. 'set cartoon cylinders' could be a synonym, though rather dry. >Q: How important are 'strands'? I've never found them useful. >Q: In beta sheets, do you want the arrows to be 'crinkled' or straight? > Not sure what you mean by 'crinkled' -- if you mean having them follow the actual beta strand backbone rather than being arbitrarily straight (and missing the backbone completely in some cases) I vote for 'crinkled' which I would call 'curved'. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Server: High Performance Mail Server - http://surgemail.com References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: slab mode questions Date: Sat, 25 Oct 2003 08:57:03 +1000 To: rasmol@lists.umass.edu > Sliders would be excellent, especially accompanied by a display of the > %zoom or slab position/thickness, etc. > > I have thought about trying to devise some to include in Protein Explorer, > but not done it yet. Albion Baucom and Harry Ungar once offered some java > applet sliders that interfaced with Chime, but I could never get them to > work reliably. > I you want to take a look, here is the chime toolbox adress : http://c4.cabrillo.cc.ca.us/projects/toolbox/index.html It only works with Netscape communicator As Jmol is an applet an can create its own controller, it could be possible to implement sliders as a new kind of controller, couldn't it ? Paul ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.139.6.81 References: <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <5.2.0.9.2.20031024173827.02f26620@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: slab mode questions Date: Fri, 24 Oct 2003 21:29:35 -0400 To: rasmol@lists.umass.edu To help in the discussion of slab mode and other compatability issues, I have updated the default rasmol manual at http://rasmol.org/doc/rasmol.html to the 2.7.2.1 version. Naturally, you should only use this version of the manual if you are running RasMol 2.7.2.1. The other manuals are available with the matching kits. The manual includes the depth command: ================================================================= Depth Syntax: depth {} depth The RasMol 'depth' command enables, disables or positions the back-clipping plane of the molecule. The program only draws those portions of the molecule that are closer to the viewer than the clipping plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn. This command interacts with the 'slab ' command, which clips to the front of a given z-clipping plane. ================================================================= and, of course, the slab command: ================================================================= Slab Syntax: slab {} slab The RasMol 'slab' command enables, disables or positions the z-clipping plane of the molecule. The program only draws those portions of the molecule that are further from the viewer than the slabbing plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn. This command interacts with the 'depth ' command, which clips to the rear of a given z-clipping plane. ================================================================= In addition there is documentation of the augmented centre command, the augmented set picking command, and of the shadepower, English, French, Italian and Spanish commands. -- H. J. Bernstein -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <001901c39a82$249fbc20$0408fea9@PILLOT> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: slab mode questions Date: Sat, 25 Oct 2003 10:02:04 +0200 (CEST) To: rasmol@lists.umass.edu Cc: paul.pillot@wanadoo.fr >> Sliders would be excellent, especially accompanied by a display of the >> %zoom or slab position/thickness, etc. >> >> I have thought about trying to devise some to include in Protein >> Explorer, but not done it yet. Albion Baucom and Harry Ungar once >> offered some java applet sliders that interfaced with Chime, but I >> could never get them to work reliably. >> > I you want to take a look, here is the chime toolbox adress : > http://c4.cabrillo.cc.ca.us/projects/toolbox/index.html > It only works with Netscape communicator Paul, These are excellent! > As Jmol is an applet an can create its own controller, it could be > possible to implement sliders as a new kind of controller, couldn't it ? Yes. Jmol currently has 'button' type controls that are implemented as applet classes. Essentially, these work like the Chime plug-in buttons and do not use JavaScript. I think we could quite easily add in sliders like these. (Do you have any code that you want to contribute to Jmol?) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <5.2.0.9.2.20031024173827.02f26620@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: slab mode questions Date: Sat, 25 Oct 2003 10:05:58 +0200 (CEST) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com > To help in the discussion of slab mode and other compatability > issues, I have updated the default rasmol manual at > http://rasmol.org/doc/rasmol.html to the 2.7.2.1 version. Thanks ... thats very helpful. How stable is the 2.7.2 release? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <42690.80.58.16.235.1066985216.squirrel@www.howards.org> <49727.80.58.16.235.1067031379.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Mathenge Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 03:14:11 +0900 To: rasmol@lists.umass.edu This probably going to sad a tad heretical, this being primarily a Rasmol/chime mailing list, but most of the functions Miguel mentionioned in his recent postings, except of ccourse the "onion peeling" one (seebottom of this post ),which would really be something worth seeng done from, a artistic as well as a didactic point of view) All the other functions currenly being discussed on theis list are contained in a small though powerful program called MOLMOL http://www.mol.biol.ethz.ch/wuthrich/software/molmol/, it has Slabmode galore, sliders for thickness, depth and all (if you can figure out what does what) slab mode is both relative and independent of selection,this used in conjunction with thickness control can make for som very intersting displays. On teh whole the MOLMOL toolset of features would make any one using Insight II green with envy, primarily because MOLMOL is free, (or at least it has been until present.) But considering the attention its been getting from authours publishing in major molecular modelling journals it will probably be moving into the private sector any time soon (or Not, any one know what the boys at Zurich are up to?). This would probably be a good time to add that MOLMOL is NOTOURIOUSLY quirky and incredibly difficult to get to understand fully. However once you grasp the fundamental idiosyncracies (and there are still a few despite massive improvements in the latest release) then the sheer visual quality of the programs virually realtime high quality renders are a joy to behold. And Oh did I mention its FREE?. Edward. PS. My appologies to any one offended by this post. I just thought an put in my two-bits. ----- Original Message ----- Sent: Saturday, October 25, 2003 6:36 AM From: "Miguel" Subject: Re: slab mode questions To: Cc: > > I have had mixed, > > mostly negative feedback about its utility as a teaching tool, mainly > > because it can be difficult to intepret visually. this is especially > > true in the context of 3D rotations and zooming. it is my understanding > > that intro and early-level student users tend to get frustrated with > > slab views. > > This is consistent with my own experience (as a novice) and the comments > of Jan Reichert, who said that the students get confused when they get > into slab mode. > > >> Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab > >> positioning? > >> > > I think the ability to control both planes independently is useful; > > however, I come down on the side of relative positioning for the mouse > > control. I think the most common use of the slab will be moving it up > > and back through the molecule. changing the thickness or mode should be > > done via commands or menus, but not the mouse. > It looks like that we are of two opinions on this, because apparently the > RasMol 2.7.2 pre-release handles this in a different way. > > But, since 'slab' is low priority, we will table this discussion for the > time being. > > > will the slab rotate and zoom with the structure, or independently? > Hmmm ... making the slab rotate would introduce a whole new level of > implementation complexity. > > But it is an interesting idea ... might make it easier to visualize and > understand how the slab works. > > > since we are in 3D, how about multiple simultaneous slabs? for example, > > one plane running in the X plane and another running in the Y. that > > would allow one to "peel" a globular structure like an onion by > > incrementally decreasing the thickness of each slab. this would be > > especially dramatic in animation. > We'll put that one on the shelf as a 'nice-to-have' :-) > > Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: slab mode questions Date: Sat, 25 Oct 2003 21:58:06 -0400 To: rasmol@lists.umass.edu hi Edward, at 3:14 am EDT on (Sunday) 26 October 2003 Edward Mathenge said: > This probably going to sad a tad heretical, this being primarily a > Rasmol/chime mailing list, but most of the functions Miguel mentionioned in > his recent postings, except of ccourse the "onion peeling" one (seebottom of > this post ),which would really be something worth seeng done from, a > artistic as well as a didactic point of view) All the other functions > currenly being discussed on theis list are contained in a small though > powerful program called MOLMOL > http://www.mol.biol.ethz.ch/wuthrich/software/molmol/, I don't think it heretical in the least; MolMol is a valuable program in its own right and, if it handles slab as you describe below, would be a good example for constructing slab features in JMol. > it has Slabmode galore, sliders for thickness, depth and all (if you can > figure out what does what) slab mode is both relative and independent of > selection,this used in conjunction with thickness control can make for som > very intersting displays. On teh whole the MOLMOL toolset of features > would make any one using Insight II green with envy, primarily because > MOLMOL is free, (or at least it has been until present.) But considering the > attention its been getting from authours publishing in major molecular > modelling journals it will probably be moving into the private sector any > time soon (or Not, any one know what the boys at Zurich are up to?). This > would probably be a good time to add that MOLMOL is NOTOURIOUSLY quirky and > incredibly difficult to get to understand fully. However once you grasp the > fundamental idiosyncracies (and there are still a few despite massive > improvements in the latest release) then the sheer visual quality of the > programs virually realtime high quality renders are a joy to behold. And Oh > did I mention its FREE?. > IMO, "incredibly difficult to understand" and "quirky" outweigh MolMol's usefulness for routine use. for me, there are many programs that fall into this category, unfortunately. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-KCL-MailScanner: Found to be CLEAN ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Sydney Shall" Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 12:08:54 +0000 To: rasmol@lists.umass.edu Cc: "Dr. Sydney Shall" Can MOLMOL be compiled on the Macintosh MAC OS X operating System? Sydney On Saturday, October 25, 2003, at 07:14 pm, Edward Mathenge wrote: > This probably going to sad a tad heretical, this being primarily a > Rasmol/chime mailing list, but most of the functions Miguel > mentionioned in > his recent postings, except of ccourse the "onion peeling" one > (seebottom of > this post ),which would really be something worth seeng done from, a > artistic as well as a didactic point of view) All the other functions > currenly being discussed on theis list are contained in a small though > powerful program called MOLMOL > http://www.mol.biol.ethz.ch/wuthrich/software/molmol/, > it has Slabmode galore, sliders for thickness, depth and all (if you > can > figure out what does what) slab mode is both relative and independent > of > selection,this used in conjunction with thickness control can make > for som > very intersting displays. On teh whole the MOLMOL toolset of features > would make any one using Insight II green with envy, primarily because > MOLMOL is free, (or at least it has been until present.) But > considering the > attention its been getting from authours publishing in major molecular > modelling journals it will probably be moving into the private sector > any > time soon (or Not, any one know what the boys at Zurich are up to?). > This > would probably be a good time to add that MOLMOL is NOTOURIOUSLY > quirky and > incredibly difficult to get to understand fully. However once you > grasp the > fundamental idiosyncracies (and there are still a few despite massive > improvements in the latest release) then the sheer visual quality of > the > programs virually realtime high quality renders are a joy to behold. > And Oh > did I mention its FREE?. > > > Edward. > > PS. My appologies to any one offended by this post. I just thought an > put in > my two-bits. > > ----- Original Message ----- > From: "Miguel" > To: > Cc: > Sent: Saturday, October 25, 2003 6:36 AM > Subject: Re: slab mode questions > > >>> I have had mixed, >>> mostly negative feedback about its utility as a teaching tool, mainly >>> because it can be difficult to intepret visually. this is especially >>> true in the context of 3D rotations and zooming. it is my >>> understanding >>> that intro and early-level student users tend to get frustrated with >>> slab views. >> >> This is consistent with my own experience (as a novice) and the >> comments >> of Jan Reichert, who said that the students get confused when they get >> into slab mode. >> >>>> Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab >>>> positioning? >>>> >>> I think the ability to control both planes independently is useful; >>> however, I come down on the side of relative positioning for the >>> mouse >>> control. I think the most common use of the slab will be moving it >>> up >>> and back through the molecule. changing the thickness or mode >>> should be >>> done via commands or menus, but not the mouse. >> It looks like that we are of two opinions on this, because apparently >> the >> RasMol 2.7.2 pre-release handles this in a different way. >> >> But, since 'slab' is low priority, we will table this discussion for >> the >> time being. >> >>> will the slab rotate and zoom with the structure, or independently? >> Hmmm ... making the slab rotate would introduce a whole new level of >> implementation complexity. >> >> But it is an interesting idea ... might make it easier to visualize >> and >> understand how the slab works. >> >>> since we are in 3D, how about multiple simultaneous slabs? for >>> example, >>> one plane running in the X plane and another running in the Y. that >>> would allow one to "peel" a globular structure like an onion by >>> incrementally decreasing the thickness of each slab. this would be >>> especially dramatic in animation. >> We'll put that one on the shelf as a 'nice-to-have' :-) >> >> Miguel >> >> >> >> > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Professor Sydney Shall Department of Molecular Medicine GKT Medical School The Rayne Institute 123 Coldharbour Lane SE5 9NU LONDON E-mail:sydney.shall@kcl.ac.uk Tel:020 7 848 5901 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Virus-Scanned: Symantec AntiVirus Scan Engine ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 09:05:31 -0500 To: rasmol@lists.umass.edu It should be available through Fink (http://fink.sourceforge.net/), but could also be compiled manually with the source code. Doug On Sunday, October 26, 2003, at 07:08 AM, Dr. Sydney Shall wrote: > Can MOLMOL be compiled on the Macintosh MAC OS X operating System? > > > Sydney > > > On Saturday, October 25, 2003, at 07:14 pm, Edward Mathenge wrote: > >> This probably going to sad a tad heretical, this being primarily a >> Rasmol/chime mailing list, but most of the functions Miguel >> mentionioned in >> his recent postings, except of ccourse the "onion peeling" one >> (seebottom of >> this post ),which would really be something worth seeng done from, a >> artistic as well as a didactic point of view) All the other functions >> currenly being discussed on theis list are contained in a small >> though >> powerful program called MOLMOL >> http://www.mol.biol.ethz.ch/wuthrich/software/molmol/, >> it has Slabmode galore, sliders for thickness, depth and all (if >> you can >> figure out what does what) slab mode is both relative and >> independent of >> selection,this used in conjunction with thickness control can make >> for som >> very intersting displays. On teh whole the MOLMOL toolset of features >> would make any one using Insight II green with envy, primarily >> because >> MOLMOL is free, (or at least it has been until present.) But >> considering the >> attention its been getting from authours publishing in major molecular >> modelling journals it will probably be moving into the private sector >> any >> time soon (or Not, any one know what the boys at Zurich are up to?). >> This >> would probably be a good time to add that MOLMOL is NOTOURIOUSLY >> quirky and >> incredibly difficult to get to understand fully. However once you >> grasp the >> fundamental idiosyncracies (and there are still a few despite massive >> improvements in the latest release) then the sheer visual quality of >> the >> programs virually realtime high quality renders are a joy to behold. >> And Oh >> did I mention its FREE?. >> >> >> Edward. >> >> PS. My appologies to any one offended by this post. I just thought an >> put in >> my two-bits. >> >> ----- Original Message ----- >> From: "Miguel" >> To: >> Cc: >> Sent: Saturday, October 25, 2003 6:36 AM >> Subject: Re: slab mode questions >> >> >>>> I have had mixed, >>>> mostly negative feedback about its utility as a teaching tool, >>>> mainly >>>> because it can be difficult to intepret visually. this is >>>> especially >>>> true in the context of 3D rotations and zooming. it is my >>>> understanding >>>> that intro and early-level student users tend to get frustrated with >>>> slab views. >>> >>> This is consistent with my own experience (as a novice) and the >>> comments >>> of Jan Reichert, who said that the students get confused when they >>> get >>> into slab mode. >>> >>>>> Q: Thoughts/feedback on 'relative' vs. 'absolute' rear slab >>>>> positioning? >>>>> >>>> I think the ability to control both planes independently is useful; >>>> however, I come down on the side of relative positioning for the >>>> mouse >>>> control. I think the most common use of the slab will be moving it >>>> up >>>> and back through the molecule. changing the thickness or mode >>>> should be >>>> done via commands or menus, but not the mouse. >>> It looks like that we are of two opinions on this, because >>> apparently the >>> RasMol 2.7.2 pre-release handles this in a different way. >>> >>> But, since 'slab' is low priority, we will table this discussion for >>> the >>> time being. >>> >>>> will the slab rotate and zoom with the structure, or independently? >>> Hmmm ... making the slab rotate would introduce a whole new level of >>> implementation complexity. >>> >>> But it is an interesting idea ... might make it easier to visualize >>> and >>> understand how the slab works. >>> >>>> since we are in 3D, how about multiple simultaneous slabs? for >>>> example, >>>> one plane running in the X plane and another running in the Y. that >>>> would allow one to "peel" a globular structure like an onion by >>>> incrementally decreasing the thickness of each slab. this would be >>>> especially dramatic in animation. >>> We'll put that one on the shelf as a 'nice-to-have' :-) >>> >>> Miguel >>> >>> >>> >>> >> >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> ---------------------------------------------------------------- >> rasmol-- >> >> > Professor Sydney Shall > Department of Molecular Medicine > GKT Medical School > The Rayne Institute > 123 Coldharbour Lane > SE5 9NU > LONDON > E-mail:sydney.shall@kcl.ac.uk > Tel:020 7 848 5901 > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Scope of this "MolVis Freeware" EMail List Date: Sun, 26 Oct 2003 10:06:20 -0500 To: rasmol@lists.umass.edu Edward Mathenge feared sounding "heretical" when he brought up MolMol. On the contrary, as the founder of this list in 1995 and its maintainer ever since, I would like to encourage discussion of any molvis freeware of interest to the subscribership (which has plateaued near 600 for the past couple of years). That is why I renamed this list from the "RasMol EMail List" to the "Molecular Visualization Freeware EMail List" several years ago (http://www.umass.edu/microbio/rasmol/raslist.htm). Of course many programs, including MolMol and DeepView, have their own email lists for bug reports and highly technical questions. But Edward's comparison of MolMol with other software is just what I hope to see more of on this list as hopefully we are able to evolve away from the limitations that Chime imposes upon many of us. molvisindex.org has a category for molvis freeware which presently indexes 47 programs. Miguel -- please add Jmol! Also please add the Jmol screenshots page to the Galleries category. Brief, infrequent, factual announcements of commercial software packages, as well as comparisons involving commercial packages, are also welcome. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <42690.80.58.16.235.1066985216.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 08:14:00 -0800 To: rasmol@lists.umass.edu Miguel, The keyword "depth" was first introduced in RasTop 1.3, then latter adopted in the RasMol 2.7. series. You also want to check RasTop (www.geneinfinity.org/rastop), which is another member of the "rasmol" family and is compatible with rasmol scripting language. We should also address the question of adding new keywords to the "standard" rasmol set that have been requested for a long period of time. I remember about a different color coding schema that is used in Chime - but I do not use Chime, so I do not know the details, and there was also something related to pausing, maybe like "pause " where number indicates the number of seconds (or milliseconds?) to wait before executing the next command. What is the point on these two commands? Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <42690.80.58.16.235.1066985216.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime's superset of RasMol script commands & reference manuals Date: Sun, 26 Oct 2003 12:46:50 -0500 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com On 10/26/03, Philippe Valadon wrote: >We should also address the question of adding new keywords to the "standard" >rasmol set that have been requested for a long period of time. I remember >about a different color coding schema that is used in Chime - but I do not >use Chime, so I do not know the details, and there was also something >related to pausing, maybe like "pause " where number indicates the >number of seconds (or milliseconds?) to wait before executing the next >command. What is the point on these two commands? MDL offers nearly complete documentation on the commands added to Chime that are not in RasMol 2.6. Unfortunately, they change their website often and have recently made it unnecessarily difficult to find the documentation, as well as quite annoying to download Chime itself. Nevertheless, with a little patience and persistence it is all available free. To download Chime, you have to login with a random password that they email to you, and that you cannot change. This, of course, makes the password virtually impossible to remember and very inconvenient. Nevertheless, they have recently made old versions of Chime downloadable as well as the current versions, a large improvement especially for Irix users and during transitions after new versions are released. At www.mdl.com, click on DOWNLOADS on the top menu, then login, then select Chime. You won't find the Chime reference manuals linked to the Chime download page, as they were for the previous 5 years or so. Instead, at www.mdl.com, at the top main menu, open the Support menu and click on Developer Support, and then look under Developer Tools, particularly for "Embed Tags" and "RasMol Scripts" (sic). The command that Philippe is thinking of is "delay" rather than "pause". Although Tim Maffett (principal architect of Chime) included "pause" and "unpause" at my request, I think they could be eliminated. The inclusion of the "delay" and "move" commands that operate independently (as much as possible) of the hardware speed of the client computer are huge improvements over what could be done in RasMol 2.6. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.139.6.81 References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <42690.80.58.16.235.1066985216.squirrel@www.howards.org> <002801c39bdc$2a9f4fe0$7339cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 13:01:33 -0500 To: rasmol@lists.umass.edu RasTop is a nice MS-windows wrapper for RasMol. Philippe is right. It would be a good idea to add functionality to the RasMol command set. However, please be very careful if you extract any command from Chime -- remember that "no reverse engineering" clause in the Chime license. We must work purely from functional specs, not from the details as to how anything is done in Chime. I know this creates a serious problem for users who would like compatable functionality, but unless MDL grants permission, I cannot see any alternative. That is the bad news. The good news is that I suspect that, if we started creating a real alternative to Chime for people for browser-embedded windows, and people started moving away from Chime, MDL would find it in their interests to be more cooperative, so that if they resumed support of Chime, people who wanted to could move back easily. -- HJB At 8:14 AM -0800 10/26/03, Philippe wrote: >Miguel, > >The keyword "depth" was first introduced in RasTop 1.3, then latter adopted >in the RasMol 2.7. series. You also want to check RasTop >(www.geneinfinity.org/rastop), which is another member of the "rasmol" >family and is compatible with rasmol scripting language. > >We should also address the question of adding new keywords to the "standard" >rasmol set that have been requested for a long period of time. I remember >about a different color coding schema that is used in Chime - but I do not >use Chime, so I do not know the details, and there was also something >related to pausing, maybe like "pause " where number indicates the >number of seconds (or milliseconds?) to wait before executing the next >command. What is the point on these two commands? > >Philippe Valadon > > > > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-language: en Content-disposition: inline X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: PHILLIP W BARAK Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 13:11:41 -0600 To: rasmol@lists.umass.edu > The good news is that I suspect that, if we started creating a real > alternative to Chime for people for browser-embedded windows, and > peoplestarted moving away from Chime, MDL would find it in their > intereststo be more cooperative, so that if they resumed support > of Chime, > people who wanted to could move back easily. From: "Herbert J. Bernstein" Just so this possibility, MDL resuming support of Chime, can be put in perspective, my recollection is that they have not added any significant feature to Chime in the last five years. In that time, their "updates" and "service packs" have consisted largely of rewritten installers for an ever-diminishing number of browsers and operating systems (we're now down to WinNT/2000/XP and IE5.5/6, having shed irix, mac, and netscape while ignoring linux, osx, safari, mozilla, opera). I believe that we have heard that all MDL's original Chime team has moved on and their website claims that they don't have the resources (even though now owned by Elsevier, so read that as inclination) to test all combinations for compatibility. With MS making noises about yet unspecified modifications to future versions of IE regarding handling of plugins to comply with the sweeping intellectual property rights of Eolas, MDL Chime will once again have to respond to these changes, or not. Don't get me wrong. MDL has provided an invaluable service to the educational & scientific community, putting chemical plugins into webpages relatively early in the game. So great is their contribution, that all newcomers must at least measure up to the bar that they have set. Further, the jmol developers explicitly recognize that migration paths for Chime content must be established lest we have to reinvent thousands of tutorials. Somewhere in all of this, sooner rather than later, I hear a goodbye. Phillip Barak Assoc Prof, Soil Science University of Wisconsin-Madison ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.139.6.81 References: <10937610a1d5.10a1d5109376@wiscmail.wisc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: slab mode questions Date: Sun, 26 Oct 2003 17:17:23 -0500 To: rasmol@lists.umass.edu I agree that the future for Chime looks grim. Maybe if we were all to say "pretty please" in unison, MDl would release the Chime source for incorporation into supported open source programs, such as RasMol and Jmol, or at least relax their license terms to permit us to ensure external compatability of fuctionally equivalent extensions. -- HJB At 1:11 PM -0600 10/26/03, PHILLIP W BARAK wrote: >From: "Herbert J. Bernstein" >> The good news is that I suspect that, if we started creating a real >> alternative to Chime for people for browser-embedded windows, and >> peoplestarted moving away from Chime, MDL would find it in their >> intereststo be more cooperative, so that if they resumed support >> of Chime, >> people who wanted to could move back easily. > >Just so this possibility, MDL resuming support of Chime, can be put >in perspective, my recollection is that they have not added any >significant feature to Chime in the last five years. In that time, >their "updates" and "service packs" have consisted largely of >rewritten installers for an ever-diminishing number of browsers and >operating systems (we're now down to WinNT/2000/XP and IE5.5/6, >having shed irix, mac, and netscape while ignoring linux, osx, >safari, mozilla, opera). I believe that we have heard that all MDL's >original Chime team has moved on and their website claims that they >don't have the resources (even though now owned by Elsevier, so read >that as inclination) to test all combinations for compatibility. >With MS making noises about yet unspecified modifications to future >versions of IE regarding handling of plugins to comply with the >sweeping intellectual property rights of Eolas, MDL Chime will once >again have to respond to these changes, or not. > >Don't get me wrong. MDL has provided an invaluable service to the >educational & scientific community, putting chemical plugins into >webpages relatively early in the game. So great is their >contribution, that all newcomers must at least measure up to the bar >that they have set. Further, the jmol developers explicitly >recognize that migration paths for Chime content must be established >lest we have to reinvent thousands of tutorials. > >Somewhere in all of this, sooner rather than later, I hear a goodbye. > >Phillip Barak >Assoc Prof, Soil Science >University of Wisconsin-Madison > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Recent development of Chime by MDL Date: Sun, 26 Oct 2003 18:51:11 -0500 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com At 10/26/03, Philip Barak wrote: >Just so this possibility, MDL resuming support of Chime, can be put in >perspective, my recollection is that they have not added any significant >feature to Chime in the last five years. In the main, I agree completely with Philip Barak. Although the pace of Chime development and bug fixes has been much less than the users of Chime would like, MDL has made a few crucial improvements in the past 5 years. In fact, Chime would not work at all in IE 6.0 were it not for changes MDL made in 2001. To clarify: Jan 1999, Chime 2.0.3: Fixed a bug that precluded loading PDB files with long URL's in Windows, including PDB files from the Protein Data Bank! Jan 2000, Chime 2.6: At my request, MDL added a new command to Chime, "show pdbheader". This has been crucial for the subsequent development path of Protein Explorer. Jan 2001, Chime 2.6 SP3: During summer 2001, Microsoft suddenly removed "plugin" support from IE 5.5 SP2 and all subsequent versions. Chime would not work in IE anymore. MDL quickly managed to modify Chime to enable it to continue to work in IE. Oct 2002, Chime 2.6 SP4: At my request, MDL fixed the "show version" command, making is possible for the first time for IE to tell what version of Chime is installed. Further, they corrected a disastrous bug in the installer that made Chime fail to work in IE under certain circumstances. The above are only the changes that directly affected my work. They probably represent only a small portion of the total changes. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <42690.80.58.16.235.1066985216.squirrel@www.howards.org> <5.2.0.9.2.20031026122836.021f5020@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Sun, 26 Oct 2003 21:52:01 -0800 To: rasmol@lists.umass.edu Eric, I found a set of commands called "RasMol Scripts" at http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp. Is-it the one you are talking about? Some of these commands would be relatively simple to implement; I see for example the slab +|- that was mentionned earlier. I wonder if a copyright claim can be made on this set of keywords. I have some doubts, but I am not a layer. Maybe MDL could clarify its position here. Question? I see a few keywords related to animation (anim, interrup, unpause, and spin). How are these commands used in a single script? Do we first set a delay, let say 10 s, then start an animation that will go on by itself during 10 s until the end of the delay, then pass to the next command? Are the entire set of commands really used from a pratical standpoint? For example the command "view" sounds complicated and one could do the same with the commands "save script" and "script" already implemented. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en References: <2CBE2C19-0553-11D8-82B7-0003939F0932@usm.maine.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Anton Feenstra Subject: Re: slab mode questions Date: Mon, 27 Oct 2003 14:04:41 +0100 To: rasmol@lists.umass.edu Gale Rhodes wrote: > Hi, Miguel! > > For a look at what slabbing can do, see section 7, Exploring, in > > http://www.usm.maine.edu/~rhodes/RasTut/index.html I noticed your page only sets background color. As default my foreground color is light (yellow, actually), it doesn't display well on your light yellow-ish background. Perhaps it would be better if you either specify both fore- and background color, or no specification at all. (The reason I post this is that I encounter this absurdly often...) -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Room P275 Tel: +31 20 44 47608 Fax: +31 20 44 47610 | | | Feenstra@chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "Everybody is Smashing Things Down" (Offspring) | |_____________|_______________________________________________________| ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 X-Accept-Language: en-us, en References: <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <44263.80.58.16.235.1066824557.squirrel@www.howards.org> <5.2.0.9.2.20031023153938.021da350@marlin.bio.umass.edu> <5.2.0.9.2.20031024154614.00a73550@marlin.bio.umass.edu> <51022.80.58.16.235.1067030602.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Anton Feenstra Subject: Re: slab mode questions Date: Mon, 27 Oct 2003 14:18:32 +0100 To: rasmol@lists.umass.edu Miguel wrote: >>Cartoons, especially, are probably more important in general, in my >>opinion. I would also very much like to see inclusion of cylinders as a >>further simplification for alpha helices. WebLab does cylinders nicely. > > > Since you brought up the subject of cylinders, I have a few questions: > > Q: Should the ends of the cylinders have a conic 'cap' to show the chain > direction? (That will actually make them look like little rockets) That would defenitely be a nice option to have. > Q: How can we introduce 'cylinders' (and other rendering styles) without > introducing a whole series of commands? I need some suggestions for script > syntax. Are these things all variants of Cartoons? Perhaps similar to what MolScript uses as 'graphics state parameters', you could 'set cartoons helix screw' or 'set cartoons helix cylinder' or 'set cartoons helix capped' > Q: How important are 'strands'? Very. > Q: In beta sheets, do you want the arrows to be 'crinkled' or straight? Both options would be good, depending on the amount of structural detail wanted/needed in the picture. > I don't have any direct experience with other molecular visualization > packages. Pointers to web images would be good. You could take the options and syntax of molscript as a reference? http://www.avatar.se/molscript/doc/molscript.html -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Room P275 Tel: +31 20 44 47608 Fax: +31 20 44 47610 | | | Feenstra@chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "Everybody is Smashing Things Down" (Offspring) | |_____________|_______________________________________________________| ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MailScanner-Information: Please contact the ISP for more information X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: slab mode questions Date: Mon, 27 Oct 2003 08:58:08 -0500 To: rasmol@lists.umass.edu On Sunday, October 26, 2003, at 11:14 AM, Philippe wrote: > > We should also address the question of adding new keywords to the > "standard" > rasmol set that have been requested for a long period of time. I > remember > about a different color coding schema that is used in Chime - but I do > not > use Chime, so I do not know the details, and there was also something > related to pausing, maybe like "pause " where number indicates > the > number of seconds (or milliseconds?) to wait before executing the next > command. What is the point on these two commands? I have used the delay command extensively in Chime scripts. Delaying between small changes in rendering is necessary to allow authors to "fade" between two representations, say, from spacefill to ball and stick, so that the viewer can watch the transformation and understand intuitively the relationship between the two displays. Without a delay issued between each command, a series of commands that shrinks a spacefill representation will be seen as a jump to the last spacefill size given, not as a gradual fade. The fade scripts that Tim Driscoll generously made available to the molvis community some time ago use delay to create their effect. Another important use of delay is to provide a pause between two move commands. Without the pause, two sequential moves are often too quick for the viewer to retain a sense of where they are in the molecule. To see both these effects in Chime animations, visit http://www.worthpublishers.com/lehninger3d/ or http://www.MoleculesInMotion.com In summary, the delay command is an important part of what makes Chime so animation-friendly. There are probably other ways that the same effects could be implemented if changes were made to "move" and other commands, but at present, "delay" is how it is done. hth, Frieda Frieda Reichsman, PhD Educational Multimedia Specialist Molecules in Motion Interactive Molecular Structures http://www.MoleculesInMotion.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 27 Oct 2003 15:20:34.0231 (UTC) FILETIME=[DDD94C70:01C39C9D] References: <10937610a1d5.10a1d5109376@wiscmail.wisc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Re: slab mode questions Date: Mon, 27 Oct 2003 10:34:04 -0500 To: rasmol@lists.umass.edu I have talked with the Chime folks & this seems EXTREMELY unlikely. "Herbert J. Bernstein" wrote: > I agree that the future for Chime looks grim. > > Maybe if we were all to say "pretty please" in unison, MDl would release > the Chime source for incorporation into supported open source programs, such > as RasMol and Jmol, or at least relax their license terms to permit us > to ensure external compatability of fuctionally equivalent extensions. > > -- HJB > > At 1:11 PM -0600 10/26/03, PHILLIP W BARAK wrote: > >From: "Herbert J. Bernstein" > >> The good news is that I suspect that, if we started creating a real > >> alternative to Chime for people for browser-embedded windows, and > >> peoplestarted moving away from Chime, MDL would find it in their > >> intereststo be more cooperative, so that if they resumed support > >> of Chime, > >> people who wanted to could move back easily. > > > >Just so this possibility, MDL resuming support of Chime, can be put > >in perspective, my recollection is that they have not added any > >significant feature to Chime in the last five years. In that time, > >their "updates" and "service packs" have consisted largely of > >rewritten installers for an ever-diminishing number of browsers and > >operating systems (we're now down to WinNT/2000/XP and IE5.5/6, > >having shed irix, mac, and netscape while ignoring linux, osx, > >safari, mozilla, opera). I believe that we have heard that all MDL's > >original Chime team has moved on and their website claims that they > >don't have the resources (even though now owned by Elsevier, so read > >that as inclination) to test all combinations for compatibility. > >With MS making noises about yet unspecified modifications to future > >versions of IE regarding handling of plugins to comply with the > >sweeping intellectual property rights of Eolas, MDL Chime will once > >again have to respond to these changes, or not. > > > >Don't get me wrong. MDL has provided an invaluable service to the > >educational & scientific community, putting chemical plugins into > >webpages relatively early in the game. So great is their > >contribution, that all newcomers must at least measure up to the bar > >that they have set. Further, the jmol developers explicitly > >recognize that migration paths for Chime content must be established > >lest we have to reinvent thousands of tutorials. > > > >Somewhere in all of this, sooner rather than later, I hear a goodbye. > > > >Phillip Barak > >Assoc Prof, Soil Science > >University of Wisconsin-Madison > > > > -- > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://intro.bio.umb.edu/BW/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-language: en Content-disposition: inline X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: PHILLIP W BARAK Subject: Re: Recent development of Chime by MDL Date: Mon, 27 Oct 2003 15:06:17 -0600 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com And this would be about the right spot in the conversation for the MDL team to "chime" in with what they have in mind for the Chime plugin for the next year, two years, and five--what new features to be added, what level of commitment to specific browsers and operating systems, etc. --Phil Barak ----- Original Message ----- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Recent development of Chime by MDL Date: Sunday, October 26, 2003 5:51 pm > At 10/26/03, Phillip Barak wrote: > >Just so this possibility, MDL resuming support of Chime, can be > put in > >perspective, my recollection is that they have not added any > significant > >feature to Chime in the last five years. > > In the main, I agree completely with Philip Barak. > > Although the pace of Chime development and bug fixes has been much > less > than the users of Chime would like, MDL has made a few crucial > improvements > in the past 5 years. In fact, Chime would not work at all in IE > 6.0 were it > not for changes MDL made in 2001. To clarify: > > Jan 1999, Chime 2.0.3: Fixed a bug that precluded loading PDB > files with > long URL's in Windows, including PDB files from the Protein Data Bank! > > Jan 2000, Chime 2.6: At my request, MDL added a new command to > Chime, "show > pdbheader". This has been crucial for the subsequent development > path of > Protein Explorer. > > Jan 2001, Chime 2.6 SP3: During summer 2001, Microsoft suddenly > removed > "plugin" support from IE 5.5 SP2 and all subsequent versions. > Chime would > not work in IE anymore. MDL quickly managed to modify Chime to > enable it to > continue to work in IE. > > Oct 2002, Chime 2.6 SP4: At my request, MDL fixed the "show > version" > command, making is possible for the first time for IE to tell what > version > of Chime is installed. Further, they corrected a disastrous bug in > the > installer that made Chime fail to work in IE under certain > circumstances. > The above are only the changes that directly affected my work. > They > probably represent only a small portion of the total changes. > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: > http://molvisindex.orgConSurf - Find Conserved Patches in > Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: Recent development of Chime by MDL Date: Mon, 27 Oct 2003 17:20:19 -0800 To: "'PHILLIP W BARAK'" , rasmol@lists.umass.edu Cc: chime-team@mdli.com Dear Phil: We have a service pack planned for Chime/Chime Pro for the end of this year. This service pack will correct the following: *An important issue that affects structure searching on the Thomson Derwent website for Kanji (Japanese) Desktop 2.5 and 2.4 users *Abbreviations incorrectly written as expanded structures in V3000 format *Several issues that involve amino acid sequence group abbreviation display *Proprietary header with NMR spectra in a JCAMP format that is not recognized and causes a shift in the display *IE 5.5 SP2 not supported on Windows 98 Beyond SP5, we don't have any plans for upgrading to new browsers or operating systems. We will continue to provide special releases for Chime Pro customers as we consider them necessary. Chime/Chime Pro will eventually be replaced by MDL Draw. We expect to phase out Chime completely by sometime in 2007; however, that date is subject to change. Regards, Bob Dickey -----Original Message----- Sent: Monday, October 27, 2003 1:06 PM From: PHILLIP W BARAK [mailto:pwbarak@facstaff.wisc.edu] Subject: Re: Recent development of Chime by MDL To: rasmol@lists.umass.edu Cc: chime-team@mdli.com And this would be about the right spot in the conversation for the MDL team to "chime" in with what they have in mind for the Chime plugin for the next year, two years, and five--what new features to be added, what level of commitment to specific browsers and operating systems, etc. --Phil Barak ----- Original Message ----- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Recent development of Chime by MDL Date: Sunday, October 26, 2003 5:51 pm > At 10/26/03, Phillip Barak wrote: > >Just so this possibility, MDL resuming support of Chime, can be > put in > >perspective, my recollection is that they have not added any > significant > >feature to Chime in the last five years. > > In the main, I agree completely with Philip Barak. > > Although the pace of Chime development and bug fixes has been much > less > than the users of Chime would like, MDL has made a few crucial > improvements > in the past 5 years. In fact, Chime would not work at all in IE > 6.0 were it > not for changes MDL made in 2001. To clarify: > > Jan 1999, Chime 2.0.3: Fixed a bug that precluded loading PDB > files with > long URL's in Windows, including PDB files from the Protein Data Bank! > > Jan 2000, Chime 2.6: At my request, MDL added a new command to > Chime, "show > pdbheader". This has been crucial for the subsequent development > path of > Protein Explorer. > > Jan 2001, Chime 2.6 SP3: During summer 2001, Microsoft suddenly > removed > "plugin" support from IE 5.5 SP2 and all subsequent versions. > Chime would > not work in IE anymore. MDL quickly managed to modify Chime to > enable it to > continue to work in IE. > > Oct 2002, Chime 2.6 SP4: At my request, MDL fixed the "show > version" > command, making is possible for the first time for IE to tell what > version > of Chime is installed. Further, they corrected a disastrous bug in > the > installer that made Chime fail to work in IE under certain > circumstances. > The above are only the changes that directly affected my work. > They > probably represent only a small portion of the total changes. > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: > http://molvisindex.orgConSurf - Find Conserved Patches in > Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: Recent development of Chime by MDL Date: Tue, 28 Oct 2003 05:01:39 -0500 To: rasmol@lists.umass.edu at 5:20 pm EDT on (Monday) 27 October 2003 Robert Dickey said: > Dear Phil: > > We have a service pack planned for Chime/Chime Pro for the end of this year. > > > > Beyond SP5, we don't have any plans for upgrading to new browsers or > operating systems. We will continue to provide special releases for Chime > Pro customers as we consider them necessary. Chime/Chime Pro will > eventually be replaced by MDL Draw. We expect to phase out Chime > completely by sometime in 2007; however, that date is subject to change. > > can we then look forward to the Chime source being made available? :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > > -----Original Message----- > From: PHILLIP W BARAK [mailto:pwbarak@facstaff.wisc.edu] > Sent: Monday, October 27, 2003 1:06 PM > To: rasmol@lists.umass.edu > Cc: chime-team@mdli.com > Subject: Re: Recent development of Chime by MDL > > > And this would be about the right spot in the conversation for the MDL team > to "chime" in with what they have in mind for the Chime plugin for the next > year, two years, and five--what new features to be added, what level of > commitment to specific browsers and operating systems, etc. > > --Phil Barak > > ----- Original Message ----- > From: Eric Martz > Date: Sunday, October 26, 2003 5:51 pm > Subject: Recent development of Chime by MDL > > > At 10/26/03, Phillip Barak wrote: > > >Just so this possibility, MDL resuming support of Chime, can be > > put in > > >perspective, my recollection is that they have not added any > > significant > > >feature to Chime in the last five years. > > > > In the main, I agree completely with Philip Barak. > > > > Although the pace of Chime development and bug fixes has been much > > less > > than the users of Chime would like, MDL has made a few crucial > > improvements > > in the past 5 years. In fact, Chime would not work at all in IE > > 6.0 were it > > not for changes MDL made in 2001. To clarify: > > > > Jan 1999, Chime 2.0.3: Fixed a bug that precluded loading PDB > > files with > > long URL's in Windows, including PDB files from the Protein Data Bank! > > > > Jan 2000, Chime 2.6: At my request, MDL added a new command to > > Chime, "show > > pdbheader". This has been crucial for the subsequent development > > path of > > Protein Explorer. > > > > Jan 2001, Chime 2.6 SP3: During summer 2001, Microsoft suddenly > > removed > > "plugin" support from IE 5.5 SP2 and all subsequent versions. > > Chime would > > not work in IE anymore. MDL quickly managed to modify Chime to > > enable it to > > continue to work in IE. > > > > Oct 2002, Chime 2.6 SP4: At my request, MDL fixed the "show > > version" > > command, making is possible for the first time for IE to tell what > > version > > of Chime is installed. Further, they corrected a disastrous bug in > > the > > installer that made Chime fail to work in IE under certain > > circumstances. > > The above are only the changes that directly affected my work. > > They > > probably represent only a small portion of the total changes. > > > > -Eric > > > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > > Protein Explorer - 3D Visualization: http://proteinexplorer.org > > Workshops: http://www.umass.edu/molvis/workshop > > World Index of Molecular Visualization Resources: > > http://molvisindex.orgConSurf - Find Conserved Patches in > > Proteins: http://consurf.tau.ac.il > > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > > PDB Lite Macromolecule Finder: http://pdblite.org > > Molecular Visualization EMail List: > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > Eric Martz, Professor (Immunology), Dept Microbiology > > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > > http://www.umass.edu/molvis/martz > > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-language: en Content-disposition: inline X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: PHILLIP W BARAK Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Tue, 28 Oct 2003 09:53:57 -0600 To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net ----- Original Message ----- ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Sunday, October 26, 2003 11:52 pm > Eric, > > I found a set of commands called "RasMol Scripts" at > http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp. > Is-it the one you are talking about? Some of these commands would be > relatively simple to implement; I see for example the slab +|- > that was > mentionned earlier. I wonder if a copyright claim can be made on > this set of > keywords. I have some doubts, but I am not a lawyer. This question sounds a bit like the Lotus/Borland look-and-feel of the Quatto menu in Lotus-emulation mode violated U.S. copyright. For discussion, see "1990-1995: The Lotus look and feel suits" at http://www.swiss.ai.mit.edu/6805/articles/int-prop/software-copyright.html --Phil Barak ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <10b425110fc8.110fc810b425@wiscmail.wisc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Tue, 28 Oct 2003 22:35:58 -0800 To: rasmol@lists.umass.edu > This question sounds a bit like the Lotus/Borland look-and-feel of the Quatto menu in Lotus-emulation mode violated U.S. copyright. For discussion, see "1990-1995: The Lotus look and feel suits" at http://www.swiss.ai.mit.edu/6805/articles/int-prop/software-copyright.html Thanks Phillip for pointing out this page. It seems to me that this story relates more on how the buttons are disposed rather than on what is written on them. Chime scripts use a scripting language; programming languages are made of keywords and a set of keywords makes a sentence. As far as my understanding goes, sentences are copyrightable. Therefore if we add the same set of keywords to rasmol or jmol, it appears to me that we are in position to be sued on copyright issues dealing with the original Chime manual. The risk sounds minor, but not null It is unlikely that Chime tags will be conserved as-is in the post-Chime era and, therefore, it is a good time to talk about the one we like. Unless... of course MDL put the Chime manual in the public domain. I think actually they might find good reasons to do so. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Recent development of Chime by MDL Date: Wed, 29 Oct 2003 11:36:13 -0500 To: rasmol@lists.umass.edu [At Tom Blackadar's request, I am posting this to the list to circumvent technical difficulties. -Eric Martz] I'd like to add a few comments to the recent messages about the future of Chime. MDL has no committed plan to discontinue support for Chime on any specific date. Although all technology generations eventually reach an end, we at MDL are extremely conscious of our responsibility to provide the best support we can for Chime for as long as that is possible in this world of changing browsers and plug-in architectures. The upcoming service pack is an example of our support. With over a million downloads to date, we know how much our customers and the community depend on Chime. There may come a time sooner or later when the current product becomes unsupportable, but when that happens, we will make that decision reluctantly and with as much warning as possible. On the more general questions posed in recent days, we are aware that the community needs to move forward in directions that may or may not match our strategic plans for Chime and related products. Some of these directions may mesh with our new for-sale products like MDL Draw, while others might involve independent efforts in the open-source community. MDL would be happy to have a dialogue with appropriate representatives of the community to see how we can be as supportive as we can within our constraints as a for-profit business. Our primary interest is seeing the scientific community served by the best software possible. Thank you all for your continued interest in Chime and the future of molecular visualization software. Tom Blackadar Director, MDL Discovery Framework (and a member of the original Chime team!) MDL Information Systems, Inc. t.blackadar@mdl.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Wed, 29 Oct 2003 09:50:27 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net There are two major problems in basing revisions to Jmol on Chime-related material: 1. The general body of law protecting intellectual property. 2. The license that everyone who uses Chime agreed to Now, unless someone has a very large pot of money to mount a spirited legal fight to carve out whatever exceptions can be carved out to get around these problems, the best course forward is to steer clear of basing anything that is intended to be open source on anything in any way derived from Chime as opposed to being derived from RasMol, except to the extent that MDL provides written permission. Therefore, I suggest that we ask Eric Martz, who has the best connections of any of us to MDL to ask them for explicit permission to do designs of extensions to open source molecular graphics programs based on 1. The currently availble supply of scripts using the Chime command set, and 2. The Chime documentation Naturally, in exchange we would agree to give MDL a nice credit for their community spirit in the documentation of the programs using that material. My guess is that that will agree to our use of item 1, provided the scripts in question were not authored by MDL staff and we have permission of the person who is the author, but that they will not agree to item 2. However, we won't know until and unless the question is asked. Eric, how about it? -- think how nice it would be if PE could slide smoothly and easily over to Jmol as a base when Chime breathes its last breath. Java may not be perfect, but at least it has a future and it works on a wide range of platforms. And, as a bonus, if such permission were granted I might be able to reduce the gap in command sets between RasMol and Chime. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 28 Oct 2003, PHILLIP W BARAK wrote: > ----- Original Message ----- > From: Philippe > Date: Sunday, October 26, 2003 11:52 pm > Subject: Re: Chime's superset of RasMol script commands & reference manuals > > > Eric, > > > > I found a set of commands called "RasMol Scripts" at > > http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp. > > Is-it the one you are talking about? Some of these commands would be > > relatively simple to implement; I see for example the slab +|- > > that was > > mentionned earlier. I wonder if a copyright claim can be made on > > this set of > > keywords. I have some doubts, but I am not a lawyer. > > This question sounds a bit like the Lotus/Borland look-and-feel of the Quatto menu in Lotus-emulation mode violated U.S. copyright. For discussion, see "1990-1995: The Lotus look and feel suits" at http://www.swiss.ai.mit.edu/6805/articles/int-prop/software-copyright.html > > --Phil Barak > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Wed, 29 Oct 2003 11:20:16 -0600 (CST) To: rasmol@lists.umass.edu Hi, If you idea holds then this would probably make all Chime specific scripts illegal. Chime was built on RasMol and a version of RasMol is now available under a different license. Therefore, I don't believe that copyright argument applies to the keywords not present in the open source version of RasMol. I think the 'derivative works' argument will apply to the scripting language. In the extreme, this would either make the words okay or take the scripting language out of the open source version of RasMol. Second you are allowed to do reverse engineering. In terms of names, I doubt that these are covered by copyright. For example, how many programs (in many operating systems) have 'File or Edit' as menu names that have the same function? Things like this do need legal council for every country concerned. Regards Bruce On Tue, 28 Oct 2003, Philippe wrote: > > This question sounds a bit like the Lotus/Borland look-and-feel of the > Quatto menu in Lotus-emulation mode violated U.S. copyright. For discussion, > see "1990-1995: The Lotus look and feel suits" at > http://www.swiss.ai.mit.edu/6805/articles/int-prop/software-copyright.html > > Thanks Phillip for pointing out this page. It seems to me that this story > relates more on how the buttons are disposed rather than on what is written > on them. Chime scripts use a scripting language; programming languages are > made of keywords and a set of keywords makes a sentence. As far as my > understanding goes, sentences are copyrightable. Therefore if we add the > same set of keywords to rasmol or jmol, it appears to me that we are in > position to be sued on copyright issues dealing with the original Chime > manual. The risk sounds minor, but not null > It is unlikely that Chime tags will be conserved as-is in the post-Chime > era and, therefore, it is a good time to talk about the one we like. > Unless... of course MDL put the Chime manual in the public domain. I think > actually they might find good reasons to do so. > > Philippe Valadon > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Wed, 29 Oct 2003 15:07:48 -0500 To: rasmol@lists.umass.edu I am sorry, but you are mistaken. In general you are allowed to do reverse engineering _unless_ you have made an agreement not to do reverse engineering, and one of the clauses in the Chime license has users of Chime agreeing not to do reverse engineering. That is why I, as the current maintainer of RasMol, do not use Chime. That way there is no question of even "accidental" reverse engineering. The more important issue is, however, not to waste time and money on a legal battle. If MDL claims proprietary rights to Chime, then it is a lot easier to avoid a legal fight and work with functional specs of what the community needs based on RasMol, rather than potentially tying up Jmol or RasMol in a legal battle by making use without MDL's permission of whatever MDL claims is their intellectual property. If we are very careful and Eric Martz cooperates, and does not have an agreement with MDL preventing him from doing so, he can re-originate his functional specifications of commands that he asked MDL to add to the original RasMol command set, and we can at least get those commands in in a compatible form. One can make all kind of arguments about individual words not being subject to copyright, but there is not a very clear trail of email messages making it clear that the composite use to which all these words are to be put is to achieve similar functionality in Jmol as is not being offered by Chime. We avoid legal hassles by taking one of two simple approaches: 1. Base the new functionality of RasMol, rather than Chime, so that there is no question of Jmol somehow being called a derivative work of Chime; or 2. Get MDL's permission to make Jmol as a derivative work from certain aspect of Chime. At 11:20 AM -0600 10/29/03, southey@ux1.cso.uiuc.edu wrote: >Hi, >If you idea holds then this would probably make all Chime specific scripts >illegal. > >Chime was built on RasMol and a version of RasMol is now available under a >different license. Therefore, I don't believe that copyright argument >applies to the keywords not present in the open source version of RasMol. >I think the 'derivative works' argument will apply to the scripting >language. In the extreme, this would either make the words okay or take >the scripting language out of the open source version of RasMol. > >Second you are allowed to do reverse engineering. > >In terms of names, I doubt that these are covered by copyright. For >example, how many programs (in many operating systems) have 'File or Edit' >as menu names that have the same function? > >Things like this do need legal council for every country concerned. > >Regards >Bruce > >On Tue, 28 Oct 2003, Philippe wrote: > >> > This question sounds a bit like the Lotus/Borland look-and-feel of the >> Quatto menu in Lotus-emulation mode violated U.S. copyright. For discussion, >> see "1990-1995: The Lotus look and feel suits" at >> http://www.swiss.ai.mit.edu/6805/articles/int-prop/software-copyright.html >> >> Thanks Phillip for pointing out this page. It seems to me that this story >> relates more on how the buttons are disposed rather than on what is written >> on them. Chime scripts use a scripting language; programming languages are >> made of keywords and a set of keywords makes a sentence. As far as my >> understanding goes, sentences are copyrightable. Therefore if we add the >> same set of keywords to rasmol or jmol, it appears to me that we are in >> position to be sued on copyright issues dealing with the original Chime >> manual. The risk sounds minor, but not null >> It is unlikely that Chime tags will be conserved as-is in the post-Chime >> era and, therefore, it is a good time to talk about the one we like. >> Unless... of course MDL put the Chime manual in the public domain. I think >> actually they might find good reasons to do so. >> >> Philippe Valadon >> >> >> >> >> > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Wed, 29 Oct 2003 16:39:17 -0500 To: rasmol@lists.umass.edu at 9:50 am EDT on (Wednesday) 29 October 2003 Herbert J. Bernstein said: > There are two major problems in basing revisions to Jmol on Chime-related > material: > > 1. The general body of law protecting intellectual property. > 2. The license that everyone who uses Chime agreed to > > Now, unless someone has a very large pot of money to mount a spirited > legal fight to carve out whatever exceptions can be carved out to > get around these problems, the best course forward is to steer clear > of basing anything that is intended to be open source on anything > in any way derived from Chime as opposed to being derived from RasMol, > except to the extent that MDL provides written permission. > someone feel free to correct me, but... I can't think of any feature implemented in Chime that does not already exist in one or many other software titles. I don't see how MDL could step forward and purport that they own the ideas of molecular surfaces, timed delays, and object position tweening, even though these features are the key differences between RasMol and Chime. these are neither Chime derivatives nor original MDL ideas. as long as JMol does not delve into the Chime source to find out how they do these things, I can't seriously see any infringement issues based on their EUL. the implementation of them in Chime is MDL property, but the concepts themselves are not. but to sidestep the entire issue, I think the way Chime handles movement and time is not user-friendly. I would like to see JMol handle it differently, something more in line with the average user's mental image of a movie. then a chime2jmol.pl type of converter could make short work of any compatibility issues. if JMol could offer features like tweening and key frames, for example, that would be a wonderful paradigm shift in molecular animations. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Chime's superset of RasMol script commands & reference manuals Date: Wed, 29 Oct 2003 23:03:19 -0800 To: rasmol@lists.umass.edu Cc: t.blackadar@mdl.com > > In terms of names, I doubt that these are covered by copyright. For > example, how many programs (in many operating systems) have 'File or Edit' > as menu names that have the same function? > > Things like this do need legal council for every country concerned. > Yes, maybe, surely even. In fact it does not matter. It is not the future user who is in trouble here, most probably not, but the programmer who will put its authorship tag on the keyword translation. Let's put it clearly, nobody will start a systematic implementation of Chime's specificities without prior MDL's consent. Jmol is based on a powerfull Java technology, together with the help of the rasmol community, it will certainely generate grant money to become an outstanding replacement of Chime. Therefore it is to the Chime community to make its choice, and before all to MDL. Jmol is offered under a generous LGPL license, which gives plenty of room for a corporate already in place to develop. I suggest MDL to release the specifications of its scripting language under both the GPL and the LGPL, publication to this list should be sufficient, and I do not think that this is asking to much. Philippe Valadon cc: t.blackadar@mdl.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en X-cmbi-MailScanner-Information: Please contact the ISP for more information X-cmbi-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Elmar Krieger Subject: YASARA now available for free download Date: Mon, 03 Nov 2003 12:01:59 +0100 To: rasmol@lists.umass.edu Dear all, after 10 years of development, we are happy to announce the release of YASARA - a molecular graphics, -modeling and -simulation program for Linux and Windows. Free download from http://www.yasara.org Why yet another one? - A new approach to OpenGL graphics, up to 35 times faster than usually: atoms are truly round, and you can even walk through the ribosome (100000 atoms) fluently, also in stereo. - Lots of multimedia elements: display text in 3D letters, load and animate images including alpha channel/transparency, create your own molecular movies and presentations. People use it instead of PowerPoint when giving a talk. See http://www.yasara.org/movies for examples. - New molecular dynamics force fields, optimized for maximum accuracy required in protein structure prediction: http://www.yasara.org/yamber - Interactive real-time simulations: just pull atoms and molecules around during a simulation, and work with dynamic models instead of static pictures. - Publication-quality ray-traced images including labels and arrows. No Photoshop post-processing required, label the atoms directly in YASARA. http://www.yasara.org/raytrace - Intuitive user interface with context menus and a sequence selector that zooms in on your favorite residues. - Lots of analysis and molecular modeling functions. Building, contacts, RMSDs.. - Program your own plugins in Python to extend YASARA with new functions. - Powerful macro language (Yanaconda) and selection syntax. That's it for the most important features, many thanks to Eric Martz for the invitation to post here! Best greetings and hope to see you soon (in the download log ;-), Elmar Elmar Krieger Center for Molecular and Biomolecular Informatics Toernooiveld 1 NL-6525ED Nijmegen The Netherlands Ww c(@@)c ================()==OUu============ =WHAT IF YASARA knows the answer?!= =----- http://www.yasara.org -----= =- http://www.cmbi.kun.nl/whatif -= ============OOo==================== () () _/ /_ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: YASARA now available for free download Date: Mon, 03 Nov 2003 06:20:13 -0500 To: rasmol@lists.umass.edu at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: > Dear all, > > after 10 years of development, we are happy to announce the release of > YASARA - a molecular graphics, -modeling and -simulation program for > Linux and Windows. > > Free download from http://www.yasara.org > hi Elmar, I checked out your site and would love to try yasara. any plans for an OSX port in the near future? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 boundary="Boundary_(ID_D0KartbleT7cxqorjQ21jw)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: Interesting program Date: Wed, 05 Nov 2003 22:23:48 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_D0KartbleT7cxqorjQ21jw) The below listed links should prove interesting for anyone reading this list from the point of view of open-source plug-in programming. http://witanweb.ca/ICE_Teachers/ www.witanweb.ca/ICE/ Welcome to eclipse.org Eclipse is a kind of universal tool platform - an open extensible IDE for anything and nothing in particular. Find out what eclipse is all about - check out the white paper (requires Acrobat Reader 6.0 or later), read some technical articles, visit the newsgroups, take a look at the projects, and pick up the latest downloads. Don't forget to check out the Eclipse Project FAQ and online documentation. You can find out about eclipse-related events, projects, plug-ins and websites on the Community page. For software licensing, website terms of use, and legal FAQs, please see our legal stuff page. Eclipse logos and graphics are found on our artwork page. Lewis Edgel --Boundary_(ID_D0KartbleT7cxqorjQ21jw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_D0KartbleT7cxqorjQ21jw)-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <3FA635A7.D0F74827@cmbi.kun.nl> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: YASARA now available for free download Date: Thu, 06 Nov 2003 12:28:46 +0000 (GMT) To: rasmol@lists.umass.edu Cc: molvisions@mac.com I found this software extreemly slow to use (user interface) Is something wrong with my system? Menus slowly fade in and out, so it was hard to get to grips with any of the functions. My PC is not old. timothy driscoll said: > > at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: > >> Dear all, >> >> after 10 years of development, we are happy to announce the release of YASARA - >> a molecular graphics, -modeling and -simulation program for Linux and Windows. >> >> Free download from http://www.yasara.org >> > > hi Elmar, > > I checked out your site and would love to try yasara. any plans for an OSX port > in the near future? > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en X-cmbi-MailScanner-Information: Please contact the ISP for more information X-cmbi-MailScanner: Found to be clean References: <3FA635A7.D0F74827@cmbi.kun.nl> <49821.193.60.81.207.1068121726.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Elmar Krieger Subject: Re: YASARA now available for free download Date: Thu, 06 Nov 2003 15:23:29 +0100 To: rasmol@lists.umass.edu Hi Dan! > I found this software extreemly slow to use (user interface) > Is something wrong with my system? Yes, your OpenGL driver uses software rendering instead of hardware-acceleration. As there are ~600 people in this list, it's best to post YASARA related technical questions at http://www.yasara.org/contact , click on 'Report a problem'. Then there's the YASARA user forum at http://yasara3.cmbi.kun.nl/pipermail/forum/2003/thread.html for non-technical, scientific questions. I'll contact you off the list to solve your OpenGL issue. Greetings, Elmar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "CPHL - Platt, Steven" Subject: RE: YASARA now available for free download Date: Thu, 06 Nov 2003 13:21:14 +0000 To: "'rasmol@lists.umass.edu'" Cc: molvisions@mac.com I found the same thing! ... and my PCs quite high spec too. Rotating menus are a novelty for the first 10 seconds, after which they very quickly become frustrating. I only spent a few minutes with this as it doesn't seem particularly intuitive. Other (completely) free software is just as functional, if not more so, and does not sacrifice substance over style. Steve -----Original Message----- Sent: 06 November 2003 12:29 From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] Subject: Re: YASARA now available for free download To: rasmol@lists.umass.edu Cc: molvisions@mac.com I found this software extreemly slow to use (user interface) Is something wrong with my system? Menus slowly fade in and out, so it was hard to get to grips with any of the functions. My PC is not old. timothy driscoll said: > > at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: > >> Dear all, >> >> after 10 years of development, we are happy to announce the release of YASARA - >> a molecular graphics, -modeling and -simulation program for Linux and Windows. >> >> Free download from http://www.yasara.org >> > > hi Elmar, > > I checked out your site and would love to try yasara. any plans for an OSX port > in the near future? > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <427DA33A6101484BA7A72934AF90DF7303C91558@exchange1.phls.org.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: fredie Subject: Re: YASARA now available for free download Date: Thu, 06 Nov 2003 18:01:50 -0800 To: rasmol@lists.umass.edu YASARA Everything worked fine for me. I have an Xp PC with 1Gig memory 2.8 G hz and an ATI 9600, 2 monitor card. In fact, I found the program so good I ordered the upgraded version. The software is super fast, the renderings superb. I have tried just about all the other programs on the net. It's a novel way of doing things, I think you guys need to upgrade to the proper hardware to really appreciate what this software can do. Fredie UCLA ----- Original Message ----- Sent: Thursday, November 06, 2003 5:21 AM From: "CPHL - Platt, Steven" Subject: RE: YASARA now available for free download To: Cc: > I found the same thing! ... and my PCs quite high spec too. > > Rotating menus are a novelty for the first 10 seconds, after which they very > quickly become frustrating. > I only spent a few minutes with this as it doesn't seem particularly > intuitive. Other (completely) free software is just as functional, if not > more so, and does not sacrifice substance over style. > > Steve > > > -----Original Message----- > From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] > Sent: 06 November 2003 12:29 > To: rasmol@lists.umass.edu > Cc: molvisions@mac.com > Subject: Re: YASARA now available for free download > > > > I found this software extreemly slow to use (user interface) > Is something wrong with my system? > > Menus slowly fade in and out, so it was hard to get to grips > with any of the functions. > > My PC is not old. > > timothy driscoll said: > > > > at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: > > > >> Dear all, > >> > >> after 10 years of development, we are happy to announce the release of > YASARA - > >> a molecular graphics, -modeling and -simulation program for Linux and > Windows. > >> > >> Free download from http://www.yasara.org > >> > > > > hi Elmar, > > > > I checked out your site and would love to try yasara. any plans for an > OSX port > > in the near future? > > > > > > regards, > > > > :tim > > > > -- > > timothy driscoll > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <427DA33A6101484BA7A72934AF90DF7303C91558@exchange1.phls.org.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Mathenge Subject: Re: YASARA normal "buggery" Date: Fri, 07 Nov 2003 11:04:04 +0900 To: rasmol@lists.umass.edu Every first software release will have at least as many bugs as the calender date on which it was released "The Kleinhoeffers predicate 1983" I would have to agree that there are configuration issues (that will hopefully soon be resolved) and the initial release is incredibly slow on even hi-spec systems (P4 3.09GHz HT, 2GB RAM, Matrox P750 w/ 64MB VRAM under WIN 2K). If Elmar Krieger could find general solutions to the windows OpenGL configuration issue (at least for the major cards to start with) and post it on the YASARA site I'm sure everyone would be a lot happier. Perhaps then we could all take a shot at critiquing the software rather than cutting it down before reviewing it in the form which the author intended. I for one got to see a sneak preview, 2 years ago when I visited the Vreind group at CMBI,. Under Linux the Molecular dynamics module is truly something to behold, unbelievable speed with real-time recalculation under sculpt-mode-like conditions and all this with fully rendered CPK spheres. (teh effect is some what like looking at a nest of coral snakes)Truly an intuitive way to approach the problem as well as a wonderful environment to work in not to mention its teaching and demonstration value. I'm hoping the rest of the program line will have the same functionality and speed. I hope Yasara act quickly, personally I can wait to have it running on my system. sincerely Edward G.M. Mathenge Nagasaki University Sakamoto 1-12-4 Nagasaki city Japan 852-8523 Tel Office. +81-95-849-7829 Tel Home. +81-95-849-6080 e_mathenge@hotmail.com eddy_mathenge@yahoo.com ----- Original Message ----- Sent: Thursday, November 06, 2003 10:21 PM From: "CPHL - Platt, Steven" Subject: RE: YASARA now available for free download To: Cc: > I found the same thing! ... and my PCs quite high spec too. > > Rotating menus are a novelty for the first 10 seconds, after which they very > quickly become frustrating. > I only spent a few minutes with this as it doesn't seem particularly > intuitive. Other (completely) free software is just as functional, if not > more so, and does not sacrifice substance over style. > > Steve > > > -----Original Message----- > From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] > Sent: 06 November 2003 12:29 > To: rasmol@lists.umass.edu > Cc: molvisions@mac.com > Subject: Re: YASARA now available for free download > > > > I found this software extreemly slow to use (user interface) > Is something wrong with my system? > > Menus slowly fade in and out, so it was hard to get to grips > with any of the functions. > > My PC is not old. > > timothy driscoll said: > > > > at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: > > > >> Dear all, > >> > >> after 10 years of development, we are happy to announce the release of > YASARA - > >> a molecular graphics, -modeling and -simulation program for Linux and > Windows. > >> > >> Free download from http://www.yasara.org > >> > > > > hi Elmar, > > > > I checked out your site and would love to try yasara. any plans for an > OSX port > > in the near future? > > > > > > regards, > > > > :tim > > > > -- > > timothy driscoll > > molvisions - molecular graphics & visualization > > > > usa:north carolina:wake forest > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <427DA33A6101484BA7A72934AF90DF7303C91558@exchange1.phls.org.uk> <000a01c3a4d3$1c2298f0$1802a8c0@maya> ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Mathenge Subject: Re: YASARA, is Win XP the solution? Date: Fri, 07 Nov 2003 14:07:17 +0900 To: rasmol@lists.umass.edu Thanks for the tip Fredie I just installed windows XP on my system and tried installing Yasara on that, and it works fine now. Smooth, fast operation with no glitches (so far). The rotating menus are a nice touch, though the serious user may want to turn those off at some point, and only switch them on when necessary, (eg when that cute research assistant from Biochem comes by, they can be an excellent conversation starter ;)). It it possible that the earlier problems experienced were due to some specific default parameter in the Win 2K, system. Anyway its working and now I can take a real look at it at last. Edward G.M. Mathenge Nagasaki University Sakamoto 1-12-4 Nagasaki city Japan 852-8523 Tel Office. +81-95-849-7829 Tel Home. +81-95-849-6080 e_mathenge@hotmail.com eddy_mathenge@yahoo.com ----- Original Message ----- Sent: Friday, November 07, 2003 11:01 AM From: "fredie" Subject: Re: YASARA now available for free download To: > YASARA > > Everything worked fine for me. I have an Xp PC with 1Gig memory 2.8 G hz > and > an ATI 9600, 2 monitor card. In fact, I found the program so good I ordered > the upgraded > version. The software is super fast, the renderings superb. I have tried > just about all the other programs on the net. It's a novel way of doing > things, I think you guys need to upgrade to the proper hardware to really > appreciate what this software can do. > > Fredie UCLA > ----- Original Message ----- > From: "CPHL - Platt, Steven" > To: > Cc: > Sent: Thursday, November 06, 2003 5:21 AM > Subject: RE: YASARA now available for free download > > > > I found the same thing! ... and my PCs quite high spec too. > > > > Rotating menus are a novelty for the first 10 seconds, after which they > very > > quickly become frustrating. > > I only spent a few minutes with this as it doesn't seem particularly > > intuitive. Other (completely) free software is just as functional, if not > > more so, and does not sacrifice substance over style. > > > > Steve > > > > > > -----Original Message----- > > From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] > > Sent: 06 November 2003 12:29 > > To: rasmol@lists.umass.edu > > Cc: molvisions@mac.com > > Subject: Re: YASARA now available for free download > > > > > > > > I found this software extreemly slow to use (user interface) > > Is something wrong with my system? > > > > Menus slowly fade in and out, so it was hard to get to grips > > with any of the functions. > > > > My PC is not old. > > > > timothy driscoll said: > > > > > > at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: > > > > > >> Dear all, > > >> > > >> after 10 years of development, we are happy to announce the release of > > YASARA - > > >> a molecular graphics, -modeling and -simulation program for Linux and > > Windows. > > >> > > >> Free download from http://www.yasara.org > > >> > > > > > > hi Elmar, > > > > > > I checked out your site and would love to try yasara. any plans for an > > OSX port > > > in the near future? > > > > > > > > > regards, > > > > > > :tim > > > > > > -- > > > timothy driscoll > > > molvisions - molecular graphics & visualization > > > > > > usa:north carolina:wake forest > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <427DA33A6101484BA7A72934AF90DF7303C91558@exchange1.phls.org.uk> <000a01c3a4d3$1c2298f0$1802a8c0@maya> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: YASARA now available for free download Date: Fri, 07 Nov 2003 08:50:28 +0000 (GMT) To: rasmol@lists.umass.edu Cc: fredie2@prodigy.net Yup, it is a problem with my graphics card acceleration.... I am trying to patch my kernel at the moment... Sorry for the confusion, Dan. fredie said: > YASARA > > Everything worked fine for me. I have an Xp PC with 1Gig memory 2.8 G hz and > an ATI 9600, 2 monitor card. In fact, I found the program so good I ordered the > upgraded > version. The software is super fast, the renderings superb. I have tried > just about all the other programs on the net. It's a novel way of doing things, I > think you guys need to upgrade to the proper hardware to really appreciate what > this software can do. > > Fredie UCLA > ----- Original Message ----- > From: "CPHL - Platt, Steven" > To: > Cc: > Sent: Thursday, November 06, 2003 5:21 AM > Subject: RE: YASARA now available for free download > > >> I found the same thing! ... and my PCs quite high spec too. >> >> Rotating menus are a novelty for the first 10 seconds, after which they > very >> quickly become frustrating. >> I only spent a few minutes with this as it doesn't seem particularly intuitive. >> Other (completely) free software is just as functional, if not more so, and does >> not sacrifice substance over style. >> >> Steve >> >> >> -----Original Message----- >> From: Dan Bolser [mailto:dmb@mrc-dunn.cam.ac.uk] >> Sent: 06 November 2003 12:29 >> To: rasmol@lists.umass.edu >> Cc: molvisions@mac.com >> Subject: Re: YASARA now available for free download >> >> >> >> I found this software extreemly slow to use (user interface) >> Is something wrong with my system? >> >> Menus slowly fade in and out, so it was hard to get to grips >> with any of the functions. >> >> My PC is not old. >> >> timothy driscoll said: >> > >> > at 12:01 pm EDT on (Monday) 3 November 2003 Elmar Krieger said: >> > >> >> Dear all, >> >> >> >> after 10 years of development, we are happy to announce the release of >> YASARA - >> >> a molecular graphics, -modeling and -simulation program for Linux and >> Windows. >> >> >> >> Free download from http://www.yasara.org >> >> >> > >> > hi Elmar, >> > >> > I checked out your site and would love to try yasara. any plans for an >> OSX port >> > in the near future? >> > >> > >> > regards, >> > >> > :tim >> > >> > -- >> > timothy driscoll >> > molvisions - molecular graphics & visualization >> > >> > usa:north carolina:wake forest >> > >> >> >> >> > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en X-cmbi-MailScanner-Information: Please contact the ISP for more information X-cmbi-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Elmar Krieger Subject: Rotating menus.. Date: Fri, 07 Nov 2003 11:29:03 +0100 To: rasmol@lists.umass.edu Dear Steven Platt, >Rotating menus are a novelty for the first 10 seconds, after which they very >quickly become frustrating. Citing from the email that contained your YASARA download link: "If you don't like the rotating windows, go to Window > Animation" I thank you for pointing out the potential risk that not reading the email can cause enough frustration to stop using YASARA and tell ~600 people about it ;-) To make sure that this doesn't happen again, the new YASARA available for download now disables rotating menus (and thus part of the fun ;-) by default. I added 2.5 Euros to your account as a reward for reporting this inconvenience. >I only spent a few minutes with this as it doesn't seem particularly >intuitive. Other (completely) free software is just as functional, if not >more so, and does not sacrifice substance over style. The email also suggested to click on "Help > Play help movie > Working with YASARA". This will start an interactive tutorial, which gives you an overview of the things you can do with YASARA. Have fun! Elmar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <3FAB73EF.5B484E5E@cmbi.kun.nl> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Rotating menus.. Date: Fri, 07 Nov 2003 11:59:44 +0000 (GMT) To: rasmol@lists.umass.edu Cc: elmar.krieger@cmbi.kun.nl Just to let ~600 people know YASARA is now running fine on my system (after a slow start). Cheers, Dan. Elmar Krieger said: > Dear Steven Platt, > >>Rotating menus are a novelty for the first 10 seconds, after which they very >> quickly become frustrating. > > Citing from the email that contained your YASARA download link: > > "If you don't like the rotating windows, go to Window > Animation" > > I thank you for pointing out the potential risk that not reading the email can > cause enough frustration to stop using YASARA and tell ~600 people about it ;-) > > To make sure that this doesn't happen again, the new YASARA available for download > now disables rotating menus (and thus part of the fun ;-) by default. I added 2.5 > Euros to your account as a reward for reporting this inconvenience. > >>I only spent a few minutes with this as it doesn't seem particularly intuitive. >> Other (completely) free software is just as functional, if not more so, and does >> not sacrifice substance over style. > > The email also suggested to click on "Help > Play help movie > Working with > YASARA". This will start an interactive tutorial, which gives you an overview of > the things you can do with YASARA. > > Have fun! > > Elmar > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MailScanner-Information: Please contact the ISP for more information X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: software to make PE demo Date: Wed, 19 Nov 2003 17:38:28 -0500 To: rasmol@lists.umass.edu Dear List, I am planning to create a demo that will introduce Protein Explorer to new users, and am seeking feedback on the best software to use for creating it. The PE demo will show a new user how to use the basic features of PE, from loading a molecule to displaying it using QuickViews. The demo will consist of the PE interface (static except for features activated by the demo itself), a moving cursor that demonstrates where to click and how to enter information such as a pdb ID code, and text-based and voice-over instructions. The PE demo will be available from PE by clicking a button to activate it. It must be downloadable, cross-platform, browser-compatible, etc., etc. The software I am currently considering is RoboDemo, which publishes a Flash file (.swf and .fla). I would appreciate hearing from anyone who has used RoboDemo, or any other means to make a demo, preferably with voice-over capability. Thanks in advance, Frieda Frieda Reichsman, PhD Educational Multimedia Specialist Molecules in Motion Interactive Molecular Structures http://www.MoleculesInMotion.com 94 Pratt Corner Road Shutesbury, MA 01072 413-253-2405 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Originating-IP: [12.77.140.179] X-Originating-Email: [pat_ohern@hotmail.com] X-OriginalArrivalTime: 20 Nov 2003 13:17:53.0207 (UTC) FILETIME=[B4402C70:01C3AF68] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: software to make PE demo Date: Thu, 20 Nov 2003 13:17:52 +0000 To: rasmol@lists.umass.edu Hi, Frieda- I have a Ph.D. in biochemistry, an AA in Multimedia and Web Design, and have been developing computer-based training products (including molecular animations) for academic and government clients for almost 4 years. I took a quick look at the "RoboDemo" Website, and it appears to be primarily a screen-capture program. You have to export the RoboDemo images into Flash and finish the animation and compression there. That may work well for you, but be aware that you will have to purchase and know how to use both RoboDemo and Flash to do your project. On the other hand, you could write a script to have RasMol or Chime rotate molecular images and automatically "save as gif" and then import them directly into Flash or Quicktime. There was a posting about doing that on this board a year or so ago. Maybe Tim Driscoll can advise you on that. Your PE demo is a great idea and will be extremely useful. Please keep us posted on your progress. Pat O'Hern Patricia A. O'Hern, Ph.D. CyberScience Design Computer-based Training and Accessibility Engineering 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 www.cybersciencedesign.com pat.ohern@cybersciencedesign.com _________________________________________________________________ >From the hottest toys to tips on keeping fit this winter, you’ll find a range of helpful holiday info here. http://special.msn.com/network/happyholidays.armx ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 boundary="Boundary_(ID_0kLsXr2uNEqAqSizPViijw)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: software to make PE demo Date: Thu, 20 Nov 2003 14:50:25 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_0kLsXr2uNEqAqSizPViijw) SCREEN CAPTURE? In the windows environment, you should have the window you want to capture "active"... then press the "ALT" and "PRINT SCREEN" buttons simultaneously. That captures the screen to your "clipboard". I recommend using Photoshop, but most windows programs made to manipulate images can import directly from the clipboard. (See you documentation.) For example in Windows 2000 (my current OS), I use the ALT/PRINT SCREEN combination and capture the current window I see as I am writing this message. When I open Photoshop, I mouse "click" on the file menu and choose "new". Photoshop automatically checks for image content on the clipboard and sizes a "proposed" blank window based on the pixel dimensions of the captured image. (In this case, it is 1152X835 or 1152X864 minus the W2K toolbar.) Unless you change the pixels per inch ratio, it stays at the standard 72 pixels per inch that monitors use. I recommend changing that to at least 100 pixels per inch, but simple images can have the pixel count really reduced and still be effective. It is easiest to accept the proposed window dimensions. The go to the "edit" toolbar and scroll down to "paste" (or CTRL+V) and the captured image will be placed in the window. Resize and reset proportional values as needed and save the file in a "standard" format like .jpg, tif, or gif.. If you need anymore help with this sort of thing, email me at lewis.edgel@comhem.se and I will be glad to take you through the process of going from your image series to, for example, Powerpoint.... Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Pat O'Hern Sent: den 20 november 2003 14:18 From: owner-rasmol@lists.umass.edu Subject: Re: software to make PE demo To: rasmol@lists.umass.edu Hi, Frieda- I have a Ph.D. in biochemistry, an AA in Multimedia and Web Design, and have been developing computer-based training products (including molecular animations) for academic and government clients for almost 4 years. I took a quick look at the "RoboDemo" Website, and it appears to be primarily a screen-capture program. You have to export the RoboDemo images into Flash and finish the animation and compression there. That may work well for you, but be aware that you will have to purchase and know how to use both RoboDemo and Flash to do your project. On the other hand, you could write a script to have RasMol or Chime rotate molecular images and automatically "save as gif" and then import them directly into Flash or Quicktime. There was a posting about doing that on this board a year or so ago. Maybe Tim Driscoll can advise you on that. Your PE demo is a great idea and will be extremely useful. Please keep us posted on your progress. Pat O'Hern Patricia A. O'Hern, Ph.D. CyberScience Design Computer-based Training and Accessibility Engineering 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 www.cybersciencedesign.com pat.ohern@cybersciencedesign.com _________________________________________________________________ >From the hottest toys to tips on keeping fit this winter, you'll find a range of helpful holiday info here. http://special.msn.com/network/happyholidays.armx --Boundary_(ID_0kLsXr2uNEqAqSizPViijw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_0kLsXr2uNEqAqSizPViijw)-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: software to make PE demo Date: Thu, 20 Nov 2003 09:57:54 -0600 (CST) To: rasmol@lists.umass.edu Hi, The problem with good demos is that they really need a functional version of the program. Luckily PE is somewhat amiable to this since PE is just an open source interface between the user and Chime. So PE always knows what the user has entered or clicked and therefore PE can decide if the action is valid or not. (Note that Paul Pillot's MolUsc maybe a better choice because it is somewhat simplier.) If you have a good Javascipt programmer (I am not one but I do program) then it should fairly easy to modify PE to achieve this. At least then you have a functional PE on the computer and browser that the user will be using. At the very least, you can disable certain PE functions that you don't want the user to have access to. Further, you can adapt PE in such a way to be able to demo anything you want! One simple way to achieve this is adding extra information (ie flags and an error statement) to each function in PE. Once the correct step has been done in the correct order a new function becomes valid, an old function become invalid and some variable is updated to indicate a successful completion of that step. When an incorrect step occurs, PE sends an 'error' message and doesn't do anything else. The modifications (as I currently see them) are: 1) This is the hard part! Add a function that determines the correct order statements that must be carried out. This would determine validity of a relevant PE instruction. Note that probably only functions that determine user input need to be modified. Initially it would be hard coded but eventually it should be external such as reading a Chime script so it is completely flexible. 2a) Add a statement to each relevant PE function that checks the validity of the statement. It should refer to the code in step one. If the function corresponds to an incorrect option then provide an 'error' statement to the user. Otherwise continue with the function. 2b) Add a statement to each relevant PE function to indicate that the step was completed and update the information of what steps have been completed. Regards Bruce Southey ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Server: High Performance Mail Server - http://surgemail.com References: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: software to make PE demo Date: Fri, 21 Nov 2003 06:31:21 +1100 To: rasmol@lists.umass.edu Hello, A free french software, called Touroperator, allows you to make screen captures and to play them as a sliding show in a browser. For each slide, the position of the cursor is memorized and its deplacement are replayed during the show. You can add notes, and comments on each slide. Presentations use javascript and are only compatible with IE. You can also make presentation using a java applet, the compatibility range with other browsers is then broader. To take a look at an applet demo of Touroperator about Touroperator : http://martial.tarizzo.free.fr/TourOp/TourOperator/TourOpApplet.htm To download Touroperator : http://martial.tarizzo.free.fr/TourOp/TourOp.0.3.47.zip (4 Mo) Touroperator was intended to offer a replacement to viewlet Builder, a non-free software http://www.qarbon.com/ Paul ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MailScanner-Information: Please contact the ISP for more information X-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: software to make PE demo Date: Fri, 21 Nov 2003 08:23:42 -0500 To: rasmol@lists.umass.edu Thanks to everyone who replied to my query about software for making demos. Unless there is a general interest on the list in reading discussion about these alternatives, I will be replying in a more detailed fashion to each responder off-list, since this is a bit off-topic for molvis. I can also cc anyone who is more interested, if you let me know. Frieda Frieda Reichsman, PhD Educational Multimedia Specialist Molecules in Motion Interactive Molecular Structures http://www.MoleculesInMotion.com 94 Pratt Corner Road Shutesbury, MA 01072 413-253-2405 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Best, Catherine" Subject: RE: software to make PE demo Date: Fri, 21 Nov 2003 08:54:48 -0500 To: "'rasmol@lists.umass.edu'" Hi, Please Cc me. I am very interested -thank you, Catherine -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Frieda Reichsman Sent: Friday, November 21, 2003 8:24 AM From: owner-rasmol@lists.umass.edu Subject: Re: software to make PE demo To: rasmol@lists.umass.edu Thanks to everyone who replied to my query about software for making demos. Unless there is a general interest on the list in reading discussion about these alternatives, I will be replying in a more detailed fashion to each responder off-list, since this is a bit off-topic for molvis. I can also cc anyone who is more interested, if you let me know. Frieda Frieda Reichsman, PhD Educational Multimedia Specialist Molecules in Motion Interactive Molecular Structures http://www.MoleculesInMotion.com 94 Pratt Corner Road Shutesbury, MA 01072 413-253-2405 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: petrocor Subject: Re: software to make PE demo Date: Fri, 21 Nov 2003 16:31:40 +0200 To: rasmol@lists.umass.edu Please Cc me Regards ----- Original Message ----- Sent: Friday, November 21, 2003 3:23 PM From: "Frieda Reichsman" Subject: Re: software to make PE demo To: > Thanks to everyone who replied to my query about software for making > demos. Unless there is a general interest on the list in reading > discussion about these alternatives, I will be replying in a more > detailed fashion to each responder off-list, since this is a bit > off-topic for molvis. I can also cc anyone who is more interested, if > you let me know. > > Frieda > > > Frieda Reichsman, PhD > Educational Multimedia Specialist > > Molecules in Motion > Interactive Molecular Structures > http://www.MoleculesInMotion.com > > 94 Pratt Corner Road > Shutesbury, MA 01072 > 413-253-2405 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Darrell Brooks Subject: Re: software to make PE demo Date: Fri, 21 Nov 2003 16:41:42 +0000 To: rasmol Hi Frieda I am a fairly passive recipient of the discussion list but I would be interested in your discussion Could you CC me please? D >>> friedar@biochem.umass.edu 11/21/03 01:23pm >>> Thanks to everyone who replied to my query about software for making demos. Unless there is a general interest on the list in reading discussion about these alternatives, I will be replying in a more detailed fashion to each responder off-list, since this is a bit off-topic for molvis. I can also cc anyone who is more interested, if you let me know. Frieda Frieda Reichsman, PhD Educational Multimedia Specialist Molecules in Motion Interactive Molecular Structures http://www.MoleculesInMotion.com 94 Pratt Corner Road Shutesbury, MA 01072 413-253-2405 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: software to make PE demo Date: Fri, 21 Nov 2003 12:04:52 -0500 To: rasmol@lists.umass.edu hey Frieda, might as well keep the discussion on list, if nobody minds - I'm interested, too :-) regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest at 4:41 pm EDT on (Friday) 21 November 2003 Darrell Brooks said: > Hi Frieda > > I am a fairly passive recipient of the discussion list but I would be > interested in your discussion Could you CC me please? > > D > > >>> friedar@biochem.umass.edu 11/21/03 01:23pm >>> > Thanks to everyone who replied to my query about software for making > demos. Unless there is a general interest on the list in reading > discussion about these alternatives, I will be replying in a more > detailed fashion to each responder off-list, since this is a bit > off-topic for molvis. I can also cc anyone who is more interested, if > you let me know. > > Frieda > > > Frieda Reichsman, PhD > Educational Multimedia Specialist > > Molecules in Motion > Interactive Molecular Structures > http://www.MoleculesInMotion.com > > 94 Pratt Corner Road > Shutesbury, MA 01072 > 413-253-2405 > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: help with PDB Date: Fri, 21 Nov 2003 13:02:09 -0500 To: rasmol@lists.umass.edu Can anyone explain why the alpha helices of this structure look non-equivalent: http://biology.kenyon.edu/slonc/1CZZ.pdb The "prong" of the button-like structure has three alpha helices, but only one of them goes into a "ribbon" under Ribbons or Cartoons. The others stay like telephone cord. Please let me know what's wrong with this file, and if we can fix it. Thanks, Joan Joan L. Slonczewski Professor of Biology Higley Hall, 202 N. College Drive Kenyon College Gambier, OH 43022 http://biology.kenyon.edu/slonc/slonc.htm slonczewski@kenyon.edu Phone: 740-427-5397 Fax: 740-427-5741 "The Doctor is In" Howard Dean for America: deanforamerica.com timothy driscoll wrote: >hey Frieda, > >might as well keep the discussion on list, if nobody minds - I'm >interested, too :-) > >regards, > >:tim > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en X-MailScanner-Information: Please contact the ISP for more information X-MailScanner: Found to be clean X-MailScanner-SpamCheck: not spam, SpamAssassin (score=-4.9, required 5, BAYES_00 -4.90) References: <3FBE5321.5040700@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: david marcey Subject: Re: help with PDB Date: Fri, 21 Nov 2003 12:15:53 -0800 To: rasmol@lists.umass.edu Joan, The "helix" record for residues 316-348 are missing from the pdb for chains A and B only (C is ok). You can modify the pdb directly in word, save and things will be fine, but you should put in a remark in your new pdb file indicating the change you have made. Cheers, David Joan Slonczewski wrote: > Can anyone explain why the alpha helices of this structure look > non-equivalent: > http://biology.kenyon.edu/slonc/1CZZ.pdb > The "prong" of the button-like structure has three alpha helices, but > only one of them goes into a "ribbon" under Ribbons or Cartoons. The > others stay like telephone cord. > Please let me know what's wrong with this file, and if we can fix it. > Thanks, > Joan > > Joan L. Slonczewski > Professor of Biology > Higley Hall, 202 N. College Drive > Kenyon College > Gambier, OH 43022 > http://biology.kenyon.edu/slonc/slonc.htm > slonczewski@kenyon.edu > Phone: 740-427-5397 > Fax: 740-427-5741 > "The Doctor is In" Howard Dean for America: deanforamerica.com > > > > > > timothy driscoll wrote: > >> hey Frieda, >> >> might as well keep the discussion on list, if nobody minds - I'm >> interested, too :-) >> >> regards, >> >> :tim >> >> >> > > > > -- <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> David Marcey Fletcher Jones Professor of Developmental Biology CLU Department of Biology, MC3700 60 W. Olsen Rd. Thousand Oaks, CA 91360 (805)-493-3263, 3590 marcey@clunet.edu <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> -- *** Incoming / Outgoing Mail scanned for known Viruses by CLUnet *** ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id hALNprN23527 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: help with PDB Date: Fri, 21 Nov 2003 18:37:53 -0500 To: rasmol@lists.umass.edu At 11/21/03, you wrote: >Can anyone explain why the alpha helices of this structure look >non-equivalent: >http://biology.kenyon.edu/slonc/1CZZ.pdb >The "prong" of the button-like structure has three alpha helices, but only >one of them goes into a "ribbon" under Ribbons or Cartoons. The others >stay like telephone cord. >Please let me know what's wrong with this file, and if we can fix it. >Thanks, >Joan > >Joan L. Slonczewski >Kenyon College Dear Joan: David Marcey's suggestion is a good one. Alternatively, when you press the "Secondary" (2°) button in Protein Explorer's QuickViews, the following is displayed automatically in the middle help window (you'd need to scroll down a bit to see this paragraph): "Even when the PDB file authors have specified secondary structure, you can force Chime to ignore the PDB-specified secondary structure with the command "structure". It will then assign secondary structure objectively with the built-in routine, after which you need to press the 2° button again to see the changes." Indeed, entering "structure" in the command slot, followed by re-applying the cartoon display and secondary structure colors, shows all three of the "stalk" helices as red ribbons. This works in RasMol, Chime or PE. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Spam-Level: References: <5.2.0.9.2.20031121183302.0224cc60@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: Re: help with PDB Date: Sat, 22 Nov 2003 12:34:31 +0200 To: rasmol@lists.umass.edu Scrambled message report (after Fatal Error): Error is: [ERROR: Msg 1 neither a new gap nor fits an existing gap!] Message is [773 atoms selected!] [debug_unscramble_tape is disabled] Please tell me what you were doing when the error occurred, how reproducible it is, and what version of PE you are using (or URL). ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_y0+N/zS/A4plrghSR7DBxg)" ++++------+------+------+------+------+------+------+------+------+------+ From: Herve Bizot Subject: hydrophobic scale and display of biopolymers surface Date: Mon, 24 Nov 2003 12:33:21 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_y0+N/zS/A4plrghSR7DBxg) Dear all, possibly related to hydroxyls exposure and orientation is there a tool to=20 display and identify what might be improperly called hydrophobic surfaces=20 of polysaccharides ? I admit I have not gone through most documentation. Salutations Cordiales / Best regards / ;-) ****************************************************************************= *********************************** Herv=E9 Bizot / Unit=E9 de Physico-chimie des Macromol=E9cules / Inst. Nat.= =20 Recherche Agronomique / rue de la G=E9raudi=E8re/ BP# 71627 /44316 NANTES C=E9dex 03 / FRANCE Tel.: 33 (0)2 40 67 50 00 / FAX.: 33 (0)2 40 67 50 43 or 50 05 / E-Mail := =20 bizot@nantes.inra.fr http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm ****************************************************************************= **************************************. --Boundary_(ID_y0+N/zS/A4plrghSR7DBxg) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_y0+N/zS/A4plrghSR7DBxg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Herve Bizot Subject: hydrophobic scale and display of biopolymers surface Date: Mon, 24 Nov 2003 16:48:42 +0100 To: rasmol@lists.umass.edu Dear all, possibly related to hydroxyls exposure and orientation is there a tool to display and identify what might be improperly called hydrophobic surfaces of polysaccharides ? I admit I have not gone through most documentation. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: ssbond questions Date: Thu, 27 Nov 2003 14:58:36 +0100 (CET) To: jmol-users@lists.sourceforge.net, rasmol@lists.umass.edu I have the following questions about the RasMol script command 'ssbonds' My general problem is that I do not understand why these bonds are treated specially in RasMol. I understand that they are connections in the sidechain, and that makes them interesting. I believe I was told that these S-S bonds are regular covalent bonds (unlike hbonds). The questions below are predicated on this assumption. (Simple answers are better ... I'm not a chemist :-) Q: Why aren't these S-S bonds created as regular covalent bonds automatically during the autobond process? Q: RasMol shows these bonds as dotted lines. What is the motivation for doing this if they are regular covalent bonds? Thanks in advance, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Coulson Subject: Re: ssbond questions Date: Thu, 27 Nov 2003 15:25:15 +0000 To: rasmol@lists.umass.edu Good questions, to which I'm afraid the answers may only be 'it seemed a good idea at the time'. Unless Roger knows better? Andrew Coulson At 13:58 27/11/2003, you wrote: >I have the following questions about the RasMol script command 'ssbonds' > >My general problem is that I do not understand why these bonds are treated >specially in RasMol. I understand that they are connections in the >sidechain, and that makes them interesting. > >I believe I was told that these S-S bonds are regular covalent bonds >(unlike hbonds). The questions below are predicated on this assumption. >(Simple answers are better ... I'm not a chemist :-) > > >Q: Why aren't these S-S bonds created as regular covalent bonds >automatically during the autobond process? > >Q: RasMol shows these bonds as dotted lines. What is the motivation for >doing this if they are regular covalent bonds? > > >Thanks in advance, >Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> <6.0.0.22.2.20031127150546.01d40b28@staffmail.ed.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: ssbond questions Date: Thu, 27 Nov 2003 16:44:41 +0100 (CET) To: rasmol@lists.umass.edu > Good questions, to which I'm afraid the answers may only be 'it seemed a > good idea at the time'. Unless Roger knows better? :-) Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Atom specification behavior Date: Thu, 27 Nov 2003 16:43:15 +0100 (CET) To: jmol-users@lists.sourceforge.net, rasmol@lists.umass.edu I have a detailed question about the behavior of atom specifications in RasMol expressions. We think we understand what is intended by the expressions select *.fe and select *.ca Presumably, the first selects all iron atoms and the second selects alpha carbons. But the second case gets a little more interesting if you put a calcium atom in the file. Q: There is a calcium atom in the .pdb file and we evaluate the expression 'select *.ca' ... Should the calcium atom be selected? Q: Is the *desirable* behavior different from the RasMol/Chime *compatible* behavior? The problem is that the atom name field in the .pdb file is 4 characters long. Given less than 4 characters to 'pattern match', the challenge is to figure out how to do the comparison. Q: For compatibility with existing RasMol/Chime scripts, is my concern about this issue even warranted? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <3819.212.128.142.25.1069947795.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: Atom specification behavior Date: Thu, 27 Nov 2003 16:55:09 +0100 To: rasmol@lists.umass.edu Miguel Howard wrote: >I have a detailed question about the behavior of atom specifications in >RasMol expressions. > > > >We think we understand what is intended by the expressions > select *.fe >and > select *.ca > > > we do this with select iron select calcium select *.ca & carbon >Presumably, the first selects all iron atoms and the second selects >alpha carbons. But the second case gets a little more interesting if you >put a calcium atom in the file. > >Q: There is a calcium atom in the .pdb file and we evaluate the >expression 'select *.ca' ... Should the calcium atom be selected? > > rasmol atom expressions simply are the non blank part of the PDB atom name field >Q: Is the *desirable* behavior different from the RasMol/Chime >*compatible* behavior? > > Hmm, I don't think it could be made better with those difficult data in the PDB I suggest to keep it, but we need a good element type estimator. >The problem is that the atom name field in the .pdb file is 4 characters >long. Given less than 4 characters to 'pattern match', the challenge is >to figure out how to do the comparison. > >Q: For compatibility with existing RasMol/Chime scripts, is my concern >about this issue even warranted? > I'm not a compatibility slave, but as I wrote, we need a primitive discussion. Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: ssbond questions Date: Thu, 27 Nov 2003 09:01:36 -0700 (MST) To: rasmol@lists.umass.edu On Thu, 27 Nov 2003, Andrew Coulson wrote: > >Q: Why aren't these S-S bonds created as regular covalent bonds > >automatically during the autobond process? > > > >Q: RasMol shows these bonds as dotted lines. What is the motivation for > >doing this if they are regular covalent bonds? > > Good questions, to which I'm afraid the answers may only be 'it seemed a > good idea at the time'. Unless Roger knows better? Alas, this is an artifact of RasMol's (and the PDB's) history... Many protein visualization programs originate from a biochemistry background rather than a general organic chemistry background. One assumption that is frequently made is that all elements have the same covalent bonding radius, so that any two atoms are bonded together if they are closer than a single "universal" distance threshold. Clearly such an algorithm is advantageous for PDB files, where (i) the file format doesn't normally specify the connection table, (ii) there are often tens of thousands of atoms that need to have their connectivity determined, and (iii) X-ray crystallography of biomolecules doesn't resolve hydrogen/proton positions, and therefore the assumption that carbon, nitrogen and oxygen all have the same covalent radius is fairly accurate. Hence for speed many molecular graphics programs use a single distance threshold in bonding calculations. This works fine for the proteins and nucleic acids found in PDB files, with one single exception, that sulphur-sulphur bonds (i.e. disulphide bridges) are too long. Indeed I believe that this is *the* reason why PDB files contains SSBOND records, and why the only CONECT records in, for example, pdb1crn.ent, describe these disulphide linkages. Now, the good news. RasMol actually contains two connectivity algorithms, the one above for "speed" that is the default if a molecule contains over 255 atoms, and a second more accurate algorithm, which is the default below 256 atoms. This second algorithm uses a different distance threshold for each element-element bond distance, based on covalent radii. This makes the algorithm suitable for the functionalized (fluoro-, seleno-, bromo-, etc...) compounds found in medicinal chemistry, zeolites and even gallium-arsenide semiconductor lattices. Running the command "connect true", forces use of this more accurate algorithm. When applied to a protein such as 1CRN, the ssbonds do indeed show up as real covalent bonds able to be displayed as wireframe. As Andrew will remember, when RasMol was developed over ten years ago, the typical machines running it were 20MHz PCs with either 4 or 8 Mbytes of memory. Loading pdb1gd1.ent with over 10,000 atoms (the second file I ever loaded into RasMol :), required a fast, approximate, heuristic algorithm. Times, and particularly computer performance, have changed and perhaps now that we 3GHz PCs with 1Gbyte of memory, it's probably reasonable to now make the "accurate" algorithm the default. The other hint is that using the RasMol command "ssbonds 1", the disulphide linkages will be displayed as solid lines, identical to wireframes. Treating them like hbonds by default and displaying them as dashed lines, "just seemed like a good idea at the time". As to why biochemists are so interested in disulphide bridges, and why, of the 337 bonds in crambin, the three ssbonds are the most interesting structurally, I'll leave to the better qualified experts on this list :> Happy Thanksgiving, Roger -- Roger Sayle, E-mail: roger@eyesopen.com OpenEye Scientific Software, WWW: http://www.eyesopen.com/ Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: ssbond questions Date: Thu, 27 Nov 2003 11:38:32 -0500 To: mth@mth.com, rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net Disufide bridges are very important in macromolecular structural studies. These bonds are neither part of the normal intra-residue connectivity, nor part of the normal linear backbone connectivity. When they occur they act as structural scaffolding for a protein, adding support to hold pieces of protein in relative positions they might not hold without the extra support. Therefore it is helpful to be able to mark these bonds differently (just as it is helpful to be able to mark hydrogen bonds). Yes, a disulfide bridge is a covalent bond. To quote from http://www.ndif.org/Terms/disulfide_bond.html it is a "strong covalent bond, -S-S-, important in linking polypeptide chains in proteins, the linkage arising as a result of the oxidation of the sulfhydryl (SH) groups of two molecules of cysteine". If you use the ssbonds command with a small value, the disulfide bridges will be drawn as narrow cylinders instead of with dotted lines, and will look like ordinary covalent bonds. For example, if you are looking at a wireframe display and do "ssbonds 1", the disulfide bridges will be inserted just like the rest of the bonds. If you are looking at a stick display, then "ssbonds 80" will put the disulfide bridges in inconspicuously. For ball and stick displays "ssbonds 40" does the trick. Many people, however, like to have their disulfide bridges stand out and will pick a large value, and combine that with a cartoon display. -- Herbert At 2:58 PM +0100 11/27/03, Miguel Howard wrote: >I have the following questions about the RasMol script command 'ssbonds' > >My general problem is that I do not understand why these bonds are treated >specially in RasMol. I understand that they are connections in the >sidechain, and that makes them interesting. > >I believe I was told that these S-S bonds are regular covalent bonds >(unlike hbonds). The questions below are predicated on this assumption. >(Simple answers are better ... I'm not a chemist :-) > > >Q: Why aren't these S-S bonds created as regular covalent bonds >automatically during the autobond process? > >Q: RasMol shows these bonds as dotted lines. What is the motivation for >doing this if they are regular covalent bonds? > > >Thanks in advance, >Miguel > > > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Server: High Performance Mail Server - http://surgemail.com References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: ssbond questions Date: Fri, 28 Nov 2003 06:13:27 +1100 To: rasmol@lists.umass.edu Miguel, it's only an hypothesis, but SSbonds can exist between two different chains, whereas regular covalent bonds never does. It can be also more convenient to consider these bonds as specific ones, because when you display your model in backbones (or trace, cartoon,...), you are still able to view the s-s bonds between two chains (it's the same for h bonds). Paul ----- Original Message ----- Sent: Friday, November 28, 2003 12:58 AM From: "Miguel Howard" Subject: ssbond questions To: ; > I have the following questions about the RasMol script command 'ssbonds' > > My general problem is that I do not understand why these bonds are treated > specially in RasMol. I understand that they are connections in the > sidechain, and that makes them interesting. > > I believe I was told that these S-S bonds are regular covalent bonds > (unlike hbonds). The questions below are predicated on this assumption. > (Simple answers are better ... I'm not a chemist :-) > > > Q: Why aren't these S-S bonds created as regular covalent bonds > automatically during the autobond process? > > Q: RasMol shows these bonds as dotted lines. What is the motivation for > doing this if they are regular covalent bonds? > > > Thanks in advance, > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: ssbond questions Date: Thu, 27 Nov 2003 08:54:17 -0800 To: rasmol@lists.umass.edu ----- Original Message ----- > > Q: Why aren't these S-S bonds created as regular covalent bonds > automatically during the autobond process? > From: "Miguel Howard" Disulfide bridges are not supposed to exist inside the cell, which is a chemically reducing enviroment. Their formation takes place inside the endoplasmic reticulum and concerns secreted proteins and proteins exposed to the outer side of the plasma membrane. Any algotrythm will fail on that and two cysteines even very close might not be crosslinked in vivo. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> ++++------+------+------+------+------+------+------+------+------+------+ From: "IKEHATA, Akihisa" Subject: Re: hydrophobic scale and display of biopolymers surface Date: Fri, 28 Nov 2003 11:34:58 +0900 To: rasmol@lists.umass.edu Dear Mr.? Hervé Bizot I received your e-mail and tried visiting the link; http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm , but it has been out. I would like to know the hydrophobic scale. I would appreciate it if you could tell me the appropriate address. Regards ********************************** (Mr.) IKEHATA, Akihisa Graduate School of Integrated Sciences Yokohama City University Science of Supramolecular Systems Affiliated with RIKEN Yokohama Institute ikehata_a@tsurumi.yokohama-cu.ac.jp ********************************** ----- Original Message ----- Sent: Monday, November 24, 2003 8:33 PM From: "Herve Bizot" Subject: hydrophobic scale and display of biopolymers surface To: Dear all, possibly related to hydroxyls exposure and orientation is there a tool to display and identify what might be improperly called hydrophobic surfaces of polysaccharides ? I admit I have not gone through most documentation. Salutations Cordiales / Best regards / ;-) **************************************************************************** *********************************** Hervé Bizot / Unité de Physico-chimie des Macromolécules / Inst. Nat. Recherche Agronomique / rue de la Géraudière/ BP# 71627 /44316 NANTES Cédex 03 / FRANCE Tel.: 33 (0)2 40 67 50 00 / FAX.: 33 (0)2 40 67 50 43 or 50 05 / E-Mail : bizot@nantes.inra.fr http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm **************************************************************************** **************************************. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <6.0.0.22.2.20031127150546.01d40b28@staffmail.ed.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: ssbond questions Date: Fri, 28 Nov 2003 09:45:38 +0100 (CET) To: rasmol@lists.umass.edu Many thanks to all who took the time to respond to my questions regarding SSBOND behavior in RasMol. The responses I received were all informative, giving me some insight into the importance of S-S bonds and the rationale behind RasMol behavior. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en X-MailScanner-Information-cryst-bbk: Please contact CCSG (http://www.cryst.bbk.ac.uk/CCSG/) more information X-MailScanner-cryst-bbk: Found to be clean X-MailScanner-SpamCheck-cryst-bbk: not spam, SpamAssassin (score=-38.1, required 9, BAYES_01, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, REPLY_WITH_QUOTES, SIGNATURE_LONG_SPARSE, USER_AGENT_MOZILLA_UA) References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> <001101c3b507$1d0a5200$2907cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Nicholas Keep Subject: Re: ssbond questions Date: Fri, 28 Nov 2003 10:11:08 +0000 To: rasmol@lists.umass.edu True, but they can form in a crystal for example in our structure 1gwn is a cytosolic protein expressed in the e.coli cytosol, but an advantitous disulphide bond has formed in the crystal, despite modest 1mM DTT. In the paper we state we do not have any reason to believe this is physiological and another structure of the same protein from another group in another space group does not have this bond (but there is no real difference in the structure apart from the CG posistion) Similarly a structure of a secreted protein may have some of the S-S bonds reduced depending on the reducing conditions the protein was exposed to during purification. I don't think it is the job of the molecular graphics package to extrapolate to in vivo, although that is of course a matter one could debate. Best wishes Nick > ----- Original Message ----- > From: "Miguel Howard" > >>> >>> Q: Why aren't these S-S bonds created as regular covalent bonds >>> automatically during the autobond process? >>> > > > Disulfide bridges are not supposed to exist inside the cell, which is a > chemically reducing enviroment. Their formation takes place inside the > endoplasmic reticulum and concerns secreted proteins and proteins exposed to > the outer side of the plasma membrane. Any algotrythm will fail on that and > two cysteines even very close might not be crosslinked in vivo. > > Philippe Valadon -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G59 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Server: High Performance Mail Server - http://surgemail.com References: <3819.212.128.142.25.1069947795.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: [Jmol-users] Atom specification behavior Date: Sat, 29 Nov 2003 09:28:53 +1100 To: rasmol@lists.umass.edu > Q: There is a calcium atom in the .pdb file and we evaluate the > expression 'select *.ca' ... Should the calcium atom be selected? > > Q: Is the *desirable* behavior different from the RasMol/Chime > *compatible* behavior? > > The problem is that the atom name field in the .pdb file is 4 characters > long. Given less than 4 characters to 'pattern match', the challenge is > to figure out how to do the comparison. As calcium doesn't take part in amino-acids, whereas carbon alpha does, the comparison between both atom in the PDB file might be done in combination with the residue name field. In my opinion this ambiguity must be fixed in the "desirable behavior". Paul ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.4) Gecko/20030630 X-Accept-Language: fr, en-us, en References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> <001101c3b507$1d0a5200$2907cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: yves Meyer Subject: Re: ssbond questions Date: Fri, 28 Nov 2003 08:07:15 +0100 To: rasmol@lists.umass.edu Philippe wrote: >----- Original Message ----- >From: "Miguel Howard" > > >>Q: Why aren't these S-S bonds created as regular covalent bonds >>automatically during the autobond process? >> >> >> > >Disulfide bridges are not supposed to exist inside the cell, which is a >chemically reducing enviroment. Their formation takes place inside the >endoplasmic reticulum and concerns secreted proteins and proteins exposed to >the outer side of the plasma membrane. Any algotrythm will fail on that and >two cysteines even very close might not be crosslinked in vivo. > >Philippe Valadon > > > > > > > Sorry the idea that disulfide bonds does not exist within the cell is completly false. The best demonstration is that every organism contain thioredoxins and glutaredoxins presents in the cytosol, mitochondries and chlorooplasts which functions are to reduce disulfide bridges. To make short, two types of reversible disulfide bridges exist within the cells: -some reductases get their reducing power on a cystein pair which switch from disulfure to dithiol to get reducing power from thioredoxins or glutaredoxins. The electrons are then transfered within the protein to reduce the substrat and the disulfure bridge is reformed. As example ribonucleotide reductase, peroxiredoxins, methionine sulfoxide reductases, PAPS reductases .... - a lot of proteins including enzymes, kinases, transcription factors ... have a pair of cysteins which plays a regulatory role. One form reduced or oxidized is active while the other form is inactive. The activity of these proteins are regulated by thioredoxins or glutaredoxins. Examples NF kappa B, Kinases implicated in apoptosis, numerous Calvin cycle enzymes in the chloroplast .... Sincerely Yves -- Yves Meyer Génome et développement des plantes UMR 5096 CNRS-UP-IRD Université Av de VIlleneuve F 66860 Perpignan Cedex Tel 33 4 68662225 (labo) 33 4 68668848 (standard) Fax 33 4 68668499 Mail ymeyer@univ-perp.fr ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <44536.80.58.16.235.1069941516.squirrel@www.howards.org> <001101c3b507$1d0a5200$2907cb40@Tranquilo> <3FC6F423.4000103@univ-perp.fr> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: ssbond questions Date: Fri, 28 Nov 2003 23:27:58 -0800 To: rasmol@lists.umass.edu I must agree that this is a common belief, but not without some ground. Try for example to express antibodies intracellularly, even parts of them. Actually you can now buy bacterial strains at the corner that express proteins intracellularly with all their disulfide bridges. Same way, disulfide briges are also well-described in thermophiles. From you examples, it seems that extra-cellular disulfides are more involved into architechtural roles whereas intracellular one would be more involved in regulatory functions or in enzymatic reactions. I am curious to know if disulfide bridges implicated either in stability or in multimerization of intracellular proteins have been described (apart extremophiles). Any idea? Philippe Valadon ----- Original Message ----- Sent: Thursday, November 27, 2003 11:07 PM > > > Sorry the idea that disulfide bonds does not exist within the cell is > completly false. The best demonstration is that every organism contain > thioredoxins and glutaredoxins presents in the cytosol, mitochondries > and chlorooplasts which functions are to reduce disulfide bridges. > To make short, two types of reversible disulfide bridges exist within > the cells: > -some reductases get their reducing power on a cystein pair which switch > from disulfure to dithiol to get reducing power from thioredoxins or > glutaredoxins. The electrons are then transfered within the protein to > reduce the substrat and the disulfure bridge is reformed. As example > ribonucleotide reductase, peroxiredoxins, methionine sulfoxide > reductases, PAPS reductases .... > - a lot of proteins including enzymes, kinases, transcription factors > ... have a pair of cysteins which plays a regulatory role. One form > reduced or oxidized is active while the other form is inactive. The > activity of these proteins are regulated by thioredoxins or > glutaredoxins. Examples NF kappa B, Kinases implicated in apoptosis, > numerous Calvin cycle enzymes in the chloroplast .... From: "yves Meyer" Subject: Re: ssbond questions To: ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: ssbond questions Date: Sat, 29 Nov 2003 05:10:35 -0500 To: rasmol@lists.umass.edu at 10.11a EDT on 2003 November 28 Friday Nicholas Keep said: [...] > I don't think it is the job of the molecular graphics package to > extrapolate to in vivo, although that is of course a matter one could > debate. > hi Nick, I agree. however, then it begs the question: given two cys sulfurs in close proximity, how can a mol vis program distinguish between two sulfur atoms that have formed a SS bond, and two that have not? I believe the common behavior is for software to simply assume that cys sulfurs within a certain distance could form an ssbond (this is similar to the behavior regarding hbonds). this may be why "it was a good idea at the time" for rasmol to treat ssbonds separately from 'regular' covalent bonds - if there is no way at the atomic level for software to make the distinction between SS and SH HS, it should be left up to the user. Jmol should follow suit, in my opinion. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > > ----- Original Message ----- > > From: "Miguel Howard" > > > >>> > >>> Q: Why aren't these S-S bonds created as regular covalent bonds > >>> automatically during the autobond process? > >>> > > > > > > Disulfide bridges are not supposed to exist inside the cell, which is > > a chemically reducing enviroment. Their formation takes place inside > > the endoplasmic reticulum and concerns secreted proteins and proteins > > exposed to the outer side of the plasma membrane. Any algotrythm will > > fail on that and two cysteines even very close might not be > > crosslinked in vivo. > > > > Philippe Valadon > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en X-MailScanner-Information-cryst-bbk: Please contact CCSG (http://www.cryst.bbk.ac.uk/CCSG/) more information X-MailScanner-cryst-bbk: Found to be clean X-MailScanner-SpamCheck-cryst-bbk: not spam, SpamAssassin (score=-27.9, required 9, BAYES_01, IN_REP_TO, RCVD_IN_OSIRUSOFT_COM, REFERENCES, SIGNATURE_LONG_SPARSE, USER_AGENT_MOZILLA_UA) References: ++++------+------+------+------+------+------+------+------+------+------+ From: Nicholas Keep Subject: Re: ssbond questions Date: Mon, 01 Dec 2003 10:24:59 +0000 To: rasmol@lists.umass.edu There is a significant difference in geometry between a pair of cysteines that form an S-S bond and ones that do not. At reasonable resolution , I think that X-ray crystallography would distinguish the case. In out refinement of the structure with the S-S bonds in the cytosolic protein we tried to force SH SH chemistry and the refined structure was not compatible with the electron density. The S-S bond has a bond length of 2.031 and torsion CB-SG-SG-CB of 90 and angles of CB-SG-SG of 110 with fairly tight consrtraints see http://www.ccp4.ac.uk/dist/html/mon_lib.html Testing for closeness to this should define whether there is an S-S bond or not. Best wishes Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G59 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: ssbond questions Date: Mon, 01 Dec 2003 09:00:45 -0500 (EST) To: rasmol@lists.umass.edu On Sat, 29 Nov 2003, timothy driscoll wrote: ... > hi Nick, > > I agree. however, then it begs the question: given two cys sulfurs in > close proximity, how can a mol vis program distinguish between two sulfur > atoms that have formed a SS bond, and two that have not? > > I believe the common behavior is for software to simply assume that cys > sulfurs within a certain distance could form an ssbond (this is similar to > the behavior regarding hbonds). this may be why "it was a good idea at > the time" for rasmol to treat ssbonds separately from 'regular' covalent > bonds - if there is no way at the atomic level for software to make the > distinction between SS and SH HS, it should be left up to the user. Jmol > should follow suit, in my opinion. > > :tim ... I would suggest a three-fold answer: 1. Start with the connectivity given explicitly in the entry, and implicitly given by standard residue connectvity and standard backbone connectvity. If the user is happy with the result, leave it at that. 2. Allow the user to request the program to rebond the entry based on distances. If the user is happy, leave it at that. 3. Allow the user to add and subtract various bonds "by hand". Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: ssbond questions Date: Mon, 01 Dec 2003 10:17:01 -0500 (EST) To: rasmol@lists.umass.edu I think that some history might be useful here in explaining bonds are represented in PDB entries. When the current format was originally designed in the 1970's computers were much more limited in speed and memory. Molecular graphics programmers wanted to have all the CONECT records included to allow for quick displays but that would have almost doubled the size of each entry, which was unacceptable in terms of disk space. The decision was made to include CONECT records for all bonds that could not be implied from the atom names and the sequence. Each standard residue has atoms with standard names given in consistent order. Thus the connectivity of atoms within a residue could be generated rapidly, without doing any distance calculations. The connectivity between residues is standard and can be generated on the fly. (Originally atom numbers were omitted for missing residues so the connectivity could be generated automatically. That is no longer done so a quick distance calculation must now be done to see if two residues that are adjacent in the atom list are actually bonded.) The CONECT records in a PDB entry thus contain only the bonds that cannot be implied from the residue name and sequence: namely, het groups, links between the protein (or dna) and het groups, disulfides, salt bridges, and hydrogen bonds. Note that there is an old Fortran program that generates a complete set of CONECT records given the partial information on CONECT records in an entry (see conect.for at ftp://ftp.rcsb.org/pub/pdb/software/bnl_software/) Thus, combining the residue names, sequence, and CONECT records yields full connectivity but only in numeric form in terms of atom numbers. There was a demand from the community to also include this information in symbolic form which led to the creation of SSBOND, LINK, HYDBND, and SLTBRG records. At present, connectivity information is thus available both in symbolic and numeric form. The specification of disulfides is done by the depositor. While I was processing data for the PDB at BNL (1974 - 1998) we checked this information during entry preparation to confirm that the S-S distances were reasonable and that none were missed. I assume that RCSB continues to carry out such checks but this should be confirmed with them. Frances P.S. Checking disulfide distances occasionally led to the discovery that the depositor had forgotten to constrain those distances during refinement. This led to data sets being replaced before release. In a general sense, this is the purpose of having both automated and manual checking of an entry before it is released and is, in my opinion, the greatest value-added contribution of the PDB. ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Mon, 1 Dec 2003, Herbert J. Bernstein wrote: > On Sat, 29 Nov 2003, timothy driscoll wrote: > ... > > hi Nick, > > > > I agree. however, then it begs the question: given two cys sulfurs in > > close proximity, how can a mol vis program distinguish between two sulfur > > atoms that have formed a SS bond, and two that have not? > > > > I believe the common behavior is for software to simply assume that cys > > sulfurs within a certain distance could form an ssbond (this is similar to > > the behavior regarding hbonds). this may be why "it was a good idea at > > the time" for rasmol to treat ssbonds separately from 'regular' covalent > > bonds - if there is no way at the atomic level for software to make the > > distinction between SS and SH HS, it should be left up to the user. Jmol > > should follow suit, in my opinion. > > > > :tim > ... > > I would suggest a three-fold answer: > > 1. Start with the connectivity given explicitly in the entry, and > implicitly given by standard residue connectvity and standard backbone > connectvity. If the user is happy with the result, leave it at that. > 2. Allow the user to request the program to rebond the entry based > on distances. If the user is happy, leave it at that. > 3. Allow the user to add and subtract various bonds "by hand". > > Regards, > Herbert > ===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu > ===================================================== > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eugenia Polverini Subject: Re: ssbond questions Date: Tue, 02 Dec 2003 11:34:45 +0100 To: rasmol@lists.umass.edu Hi! Have a look at the 1pmp file of the pdb databank: two cys are near enough, but they cannot form the SS-bridge due to the torsion angle of one of them. And RasMol does not build the SS-bridge! Best wishes Eugenia At 11:24 AM 12/1/2003, you wrote: >There is a significant difference in geometry between a pair of cysteines >that form an S-S bond and ones that do not. >At reasonable resolution , I think that X-ray crystallography would >distinguish the case. In out refinement of the >structure with the S-S bonds in the cytosolic protein we tried to force SH >SH chemistry and the refined structure was not compatible with the >electron density. The S-S bond has a bond length of 2.031 and torsion >CB-SG-SG-CB of 90 >and angles of CB-SG-SG of 110 with fairly tight consrtraints see >http://www.ccp4.ac.uk/dist/html/mon_lib.html >Testing for closeness to this should define whether there is an S-S bond >or not. >Best wishes >Nick >-- >Dr Nicholas H. Keep >School of Crystallography, >Birkbeck, University of London, >Malet Street, >Bloomsbury >LONDON >WC1E 7HX > >email n.keep@mail.cryst.bbk.ac.uk >Telephone 020-7631-6852 (Room G59 Office) > 020-7631-6868 (Rosalind Franklin Laboratory) > 020-7631-6800 (Department Office) >Fax 020-7631-6803 >If you want to access me in person you have to come to the crystallography >entrance >and ring me or the department office from the internal phone by the door > > Eugenia Polverini, Ph. D. Dept. of Physics University of Parma Parco Area delle Scienze, 7/A 43100 Parma Italy Phone: +39 521 905254 Fax: +39 521 905223 E-mail: eugenia.polverini@fis.unipr.it ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <5.1.0.14.0.20031202112409.00ad73a8@galileo.fis.unipr.it> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: ssbond questions Date: Tue, 02 Dec 2003 17:57:16 +0100 To: rasmol@lists.umass.edu Eugenia Polverini wrote: > Hi! > Have a look at the 1pmp file of the pdb databank: two cys are near > enough, but they cannot form the SS-bridge due to the torsion angle of > one of them. And RasMol does not build the SS-bridge! with more than 4.3 A they are to far apart for a covalent bound. Regards, Jan > Best wishes > Eugenia > > At 11:24 AM 12/1/2003, you wrote: > >> There is a significant difference in geometry between a pair of >> cysteines that form an S-S bond and ones that do not. >> At reasonable resolution , I think that X-ray crystallography would >> distinguish the case. In out refinement of the >> structure with the S-S bonds in the cytosolic protein we tried to >> force SH SH chemistry and the refined structure was not compatible >> with the electron density. The S-S bond has a bond length of 2.031 >> and torsion CB-SG-SG-CB of 90 >> and angles of CB-SG-SG of 110 with fairly tight consrtraints see >> http://www.ccp4.ac.uk/dist/html/mon_lib.html >> Testing for closeness to this should define whether there is an S-S >> bond or not. >> Best wishes >> Nick >> -- >> Dr Nicholas H. Keep >> School of Crystallography, >> Birkbeck, University of London, >> Malet Street, >> Bloomsbury >> LONDON >> WC1E 7HX >> >> email n.keep@mail.cryst.bbk.ac.uk >> Telephone 020-7631-6852 (Room G59 Office) >> 020-7631-6868 (Rosalind Franklin Laboratory) >> 020-7631-6800 (Department Office) >> Fax 020-7631-6803 >> If you want to access me in person you have to come to the >> crystallography entrance >> and ring me or the department office from the internal phone by the door >> >> > > Eugenia Polverini, Ph. D. > Dept. of Physics > University of Parma > Parco Area delle Scienze, 7/A > 43100 Parma > Italy > > Phone: +39 521 905254 > Fax: +39 521 905223 > E-mail: eugenia.polverini@fis.unipr.it > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: ssbond questions Date: Tue, 02 Dec 2003 12:20:24 -0500 To: rasmol@lists.umass.edu at 10.17a EDT on 2003 December 01 Monday Frances C. Bernstein said: > I think that some history might be useful here in explaining > bonds are represented in PDB entries. > [...] hi Frances, despite having deleted this one for the sake of brevity, I find these historical explanations extremely helpful. Can you, or someone else, recommend an authoritative a book on the subject? I have a handful of saved emails and Web bookmarks, but I still feel paper is the best storage medium. [...] > Thus, combining the residue names, sequence, and CONECT > records yields full connectivity but only in numeric form in terms > of atom numbers. There was a demand from the community to also > include this information in symbolic form which led to the creation > of SSBOND, LINK, HYDBND, and SLTBRG records. At present, connectivity > information is thus available both in symbolic and numeric form. > unfortunately, many programs create custom "pdb" files without the CONECT records. :-( regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PDBj Viewer? Date: Tue, 02 Dec 2003 13:23:43 -0500 To: rasmol@lists.umass.edu Recently, the World Wide Protein Data Bank was announced (www.wwpdb.org). The Japanese PDB (PDBj), linked to wwpdb, offers PDBj Viewer, a molecular visualization applet. Has anyone tried it out? If so, what is your impression? How does it compare with Jmol? -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: PDBj Viewer? Date: Tue, 02 Dec 2003 20:53:21 +0100 (CET) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu > The Japanese PDB (PDBj), linked to wwpdb, offers PDBj Viewer, a > molecular visualization applet. > Has anyone tried it out? If so, what is your impression? How does it > compare with Jmol? A quick look at the PDBjViewer web pages says that it requires the client to have a relatively new Java Plug-in (1.4.1) and the Java 3D API installed. These requirements are probably OK for professional users in a controlled environment. However, casual users with regular web browsers will not be able to use the applet. The big problem is the Java 3D API. It seems to me that the Java 3D API never got much traction/momentum behind it. Therefore, it is not part of the standard Java installation; it is a separate package that you need to install. Plus, I am under the impression that it has relatively limited video card support. (To be clear, I have never actually used the Java 3D API and don't have it installed on my machine ... because I don't think I have the right hardware.) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <34157.80.58.16.235.1070394801.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: PDBj Viewer? Date: Wed, 03 Dec 2003 09:15:44 +0000 (GMT) To: rasmol@lists.umass.edu Cc: mth@mth.com, emartz@microbio.umass.edu > (To be clear, I have never actually used the Java 3D API and don't have it > installed on my machine ... because I don't think I have the right hardware.) I also heard that Java 3D API has a problem (possibly licencing) with max 0S X, however, what you just said is good news for my collegues on max regarding Jmol. Cheers, Dan. > > > Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: PDBj Viewer? Date: Wed, 03 Dec 2003 05:07:27 -0500 To: rasmol@lists.umass.edu at 9.15a EDT on 2003 December 03 Wednesday Dan Bolser said: > > you forgot to close this tag, Dan. ;-) > > (To be clear, I have never actually used the Java 3D API and don't > > have it installed on my machine ... because I don't think I have the > > right hardware.) > > I also heard that Java 3D API has a problem (possibly licencing) with > max 0S X, however, what you just said is good news for my collegues on > max regarding Jmol. > anecdotally, I have read some unhappy things about support for Java3D into the future. if I can scare up the exact ref I will post it. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <49262.193.60.81.207.1070442944.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: PDBj Viewer? Date: Wed, 03 Dec 2003 10:36:07 +0000 (GMT) To: rasmol@lists.umass.edu Cc: molvisions@mac.com > > > at 9.15a EDT on 2003 December 03 Wednesday Dan Bolser said: > >> >> > you forgot to close this tag, Dan. ;-) The inner mind of my mailer is a mystery to me... hmmmmm > >> > (To be clear, I have never actually used the Java 3D API and don't have it >> installed on my machine ... because I don't think I have the right hardware.) >> >> I also heard that Java 3D API has a problem (possibly licencing) with max 0S X, >> however, what you just said is good news for my collegues on max regarding Jmol. >> > anecdotally, I have read some unhappy things about support for Java3D into the > future. if I can scare up the exact ref I will post it. > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: boris gorelik Subject: piping to rasmol from c++ program Date: Thu, 04 Dec 2003 14:59:02 +0200 (IST) To: rasmol@lists.umass.edu Hi, In order to make a simple visualisation of my calculations, which were made in a C++ program, I decided to write a pipe to rasmol. it is very simple (see attached file). When I run this program, a rasmol window is opened, but no structures are displayed in it. I suspect the problem is with buffering, but I can't see any solution. I tried to flush the stream, append to it ends or endl. nothing helps. Can anyone give any idea what's wrong? Thanks in advance. PS. I know a similar solution written in Perl (with open2 function) works perfect. /*rasmolPipe.cpp*/ //////////////////////////////////////// #include #include #include #include #include #include using namespace std; class RasmolPipe { public: string RASMOL_BINARY; string TEMP_DIR; private: string tempFileName; mutable procbuf pb; public: /**create an object, use the specified PDB file*/ RasmolPipe(string fileName); /**send a command to the pipe*/ void sendCommand (string command) const; }; /**create an object, use the specified PDB file*/ RasmolPipe::RasmolPipe(string fileName){ RASMOL_BINARY="/usr/X11R6/bin/rasmol"; TEMP_DIR="/tmp"; ostrstream os; os<>temp; return 0; } /********** END OF FILE ***************/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,pdf References: <3F8C3CD1.5E78DA70@austin.rr.com> <003601c39338$9930a6e0$48953181@pnb.sunysb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Jeffrey Lerner Subject: Re: weblite viewer Date: Fri, 05 Dec 2003 10:16:39 -0500 To: rasmol@lists.umass.edu "Roger A. Johnson" wrote: > > Miguel and others, > I have weblab viewer "ViewerLite42.exe" (5MB) for a PC and the corresponding > active X files, "ViewerActiveX42.exe" (3MB), that allows one to include > molecular rotation and other features in a PowerPoint presentation. Because > of size restructions on my server these are best sent by CD or Zip disks. > If these would be of use to you please let me know. > Roger Johnson > > ----- Original Message ----- > From: "Sondra Kamper" > To: > Sent: Tuesday, October 14, 2003 2:13 PM > Subject: weblite viewer > > > Miguel, > > I have a saved copy of the webviewer lite v3.1.3 > > installer (Mac only I think). It is a 4.2 Mb file; > > unstuffs to 9.2 MB, about 6Mb of which is > > examples. I will email it to you in a folder. Let > > me know if you have a problem opening it. I could > > mail it to you on a CD if email doesn't work. > > - sondra Kamper > > > > > > > Dear Roger, I would be interested in obtaining a zip or CD of the ViewerLite42.exe file. Here is my address: Jeffrey Lerner 21 Beeching St. Worcester, MA 01602 USA Thank you very much. Best regards, Jeff Lerner Ph.D. candidate Dept. of Microbiology University of Massachusetts Amherst, MA 01003 USA ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 boundary="Boundary_(ID_41n7sAJNB4oLcKa7/IrPVw)" X-MSMail-priority: Normal References: <3F8C3CD1.5E78DA70@austin.rr.com> <003601c39338$9930a6e0$48953181@pnb.sunysb.edu> <3FD0A157.E8B54356@worldnet.att.net> ++++------+------+------+------+------+------+------+------+------+------+ From: petrocor Subject: Re: weblite viewer Date: Fri, 05 Dec 2003 19:10:08 +0200 To: jeffreylerner@worldnet.att.net, rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_41n7sAJNB4oLcKa7/IrPVw) You can download website viewer from http://www.dfh.dk/orgkemi/ViewerLite42.exe Gideon harnoy Petrocor, Inc. ----- Original Message ----- Sent: Friday, December 05, 2003 5:16 PM From: "Jeffrey Lerner" Subject: Re: weblite viewer To: > "Roger A. Johnson" wrote: > > > > Miguel and others, > > I have weblab viewer "ViewerLite42.exe" (5MB) for a PC and the corresponding > > active X files, "ViewerActiveX42.exe" (3MB), that allows one to include > > molecular rotation and other features in a PowerPoint presentation. Because > > of size restructions on my server these are best sent by CD or Zip disks. > > If these would be of use to you please let me know. > > Roger Johnson > > > > ----- Original Message ----- > > From: "Sondra Kamper" > > To: > > Sent: Tuesday, October 14, 2003 2:13 PM > > Subject: weblite viewer > > > > > Miguel, > > > I have a saved copy of the webviewer lite v3.1.3 > > > installer (Mac only I think). It is a 4.2 Mb file; > > > unstuffs to 9.2 MB, about 6Mb of which is > > > examples. I will email it to you in a folder. Let > > > me know if you have a problem opening it. I could > > > mail it to you on a CD if email doesn't work. > > > - sondra Kamper > > > > > > > > > > > > > Dear Roger, > I would be interested in obtaining a zip or CD of the ViewerLite42.exe > file. > Here is my address: > Jeffrey Lerner > 21 Beeching St. > Worcester, MA 01602 USA > > Thank you very much. > Best regards, > Jeff Lerner > Ph.D. candidate > Dept. of Microbiology > University of Massachusetts > Amherst, MA 01003 USA > > --Boundary_(ID_41n7sAJNB4oLcKa7/IrPVw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_41n7sAJNB4oLcKa7/IrPVw)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> ++++------+------+------+------+------+------+------+------+------+------+ From: petrocor Subject: Re: hydrophobic scale and display of biopolymers surface Date: Fri, 05 Dec 2003 22:04:16 +0200 To: rasmol@lists.umass.edu Cc: "'harnoy'" Your request Gideon harnoy Petrocor, Inc. Hydrophobicity Scales Kyte-Doolittle Hopp-Woods Alanine 1.8 -0.5 Arginine -4.5 3.0 Asparagine -3.5 0.2 Aspartic acid -3.5 3.0 Cysteine 2.5 -1.0 Glutamine -3.5 0.2 Glutamic acid -3.5 3.0 Glycine -0.4 0.0 Histidine -3.2 -0.5 Isoleucine 4.5 -1.8 Leucine 3.8 -1.8 Lysine -3.9 3.0 Methionine 1.9 -1.3 Phenylalanine 2.8 -2.5 Proline -1.6 0.0 Serine -0.8 0.3 Threonine -0.7 -0.4 Tryptophan -0.9 -3.4 Tyrosine -1.3 -2.3 Valine 4.2 -1.5 ----- Original Message ----- Sent: Friday, November 28, 2003 4:34 AM From: "IKEHATA, Akihisa" Subject: Re: hydrophobic scale and display of biopolymers surface To: > Dear Mr.? Hervé Bizot > > I received your e-mail and tried visiting the link; > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > , but it has been out. I would like to know the hydrophobic scale. I would > appreciate it if you could tell me the appropriate address. > > Regards > > ********************************** > (Mr.) IKEHATA, Akihisa > Graduate School of Integrated Sciences > Yokohama City University > Science of Supramolecular Systems > Affiliated with RIKEN Yokohama Institute > ikehata_a@tsurumi.yokohama-cu.ac.jp > ********************************** > > ----- Original Message ----- > From: "Herve Bizot" > To: > Sent: Monday, November 24, 2003 8:33 PM > Subject: hydrophobic scale and display of biopolymers surface > > > Dear all, > possibly related to hydroxyls exposure and orientation is there a tool to > display and identify what might be improperly called hydrophobic surfaces > of polysaccharides ? > I admit I have not gone through most documentation. > > > Salutations Cordiales / Best regards / ;-) > **************************************************************************** > *********************************** > Hervé Bizot / Unité de Physico-chimie des Macromolécules / Inst. Nat. > Recherche Agronomique / > rue de la Géraudière/ BP# 71627 /44316 NANTES Cédex 03 / FRANCE > Tel.: 33 (0)2 40 67 50 00 / FAX.: 33 (0)2 40 67 50 43 or 50 05 / E-Mail : > bizot@nantes.inra.fr > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > **************************************************************************** > **************************************. > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne Decatur Subject: evaluating atom or residue distance from generated surface Date: Fri, 05 Dec 2003 13:55:43 -0800 (PST) To: rasmol@lists.umass.edu I am now wondering if it is possible to determine the distance to other atoms once you generated a surface? Chime/Raslmo has predefined commands called 'surface' and 'buried' but they seem to just are amino aicds that tend to be in these sites. Also, I was looking at this paper below about atom depth and naively thought it might be easy to use Chime or Rasmol to color/list residues based on atom depth. (It is especially interesting since in general more conserved residues usually tend to be solvent inaccessible.) I tried to come up with a script that would start color coding based on atom depth but realized the problem was that after I had calculated the water accessible surface area I couldn't figure out the command to select residues within a certain distance from the calculated surface. I looked at MDL's info on surface stuff but couldn't figure it out. Is it possible? The paper I mentionned: Atom depth in protein structure and function Alessandro Pintar, Oliviero Carugo and Sandor Pongor Atom depth, originally defined as the distance between a protein atom and the nearest water molecule surrounding a protein, is a simple but valuable geometrical descriptor of the protein interior. http://reviews.bmn.com/journals/atoz/latest?pii=S0968000403002287&node=TOC%40%40TIBS%40028%4011%40028_11 Thanks, Wayne Decatur Department of Biochemistry and Molecular Biology UMass Amherst __________________________________ Do you Yahoo!? Protect your identity with Yahoo! Mail AddressGuard http://antispam.yahoo.com/whatsnewfree ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> <000801c3bb6a$f675f940$0101c80a@gideon> ++++------+------+------+------+------+------+------+------+------+------+ From: "IKEHATA, Akihisa" Subject: Re: hydrophobic scale and display of biopolymers surface Date: Sun, 07 Dec 2003 12:35:56 +0900 To: rasmol@lists.umass.edu Hi Thanks for sending us the scale. I would also like to know the source of the scale; the original paper. Thank you for your time. Akihisa ----- Original Message ----- Sent: Saturday, December 06, 2003 5:04 AM From: "petrocor" Subject: Re: hydrophobic scale and display of biopolymers surface To: Cc: "'harnoy'" > Your request > > Gideon harnoy > Petrocor, Inc. > > Hydrophobicity Scales > Kyte-Doolittle Hopp-Woods > > Alanine 1.8 -0.5 > Arginine -4.5 3.0 > Asparagine -3.5 0.2 > Aspartic acid -3.5 3.0 > Cysteine 2.5 -1.0 > Glutamine -3.5 0.2 > Glutamic acid -3.5 3.0 > Glycine -0.4 0.0 > Histidine -3.2 -0.5 > Isoleucine 4.5 -1.8 > Leucine 3.8 -1.8 > Lysine -3.9 3.0 > Methionine 1.9 -1.3 > Phenylalanine 2.8 -2.5 > Proline -1.6 0.0 > Serine -0.8 0.3 > Threonine -0.7 -0.4 > Tryptophan -0.9 -3.4 > Tyrosine -1.3 -2.3 > Valine 4.2 -1.5 > > > > > > ----- Original Message ----- > From: "IKEHATA, Akihisa" > To: > Sent: Friday, November 28, 2003 4:34 AM > Subject: Re: hydrophobic scale and display of biopolymers surface > > > > Dear Mr.? Hervé Bizot > > > > I received your e-mail and tried visiting the link; > > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > > , but it has been out. I would like to know the hydrophobic scale. I would > > appreciate it if you could tell me the appropriate address. > > > > Regards > > > > ********************************** > > (Mr.) IKEHATA, Akihisa > > Graduate School of Integrated Sciences > > Yokohama City University > > Science of Supramolecular Systems > > Affiliated with RIKEN Yokohama Institute > > ikehata_a@tsurumi.yokohama-cu.ac.jp > > ********************************** > > > > ----- Original Message ----- > > From: "Herve Bizot" > > To: > > Sent: Monday, November 24, 2003 8:33 PM > > Subject: hydrophobic scale and display of biopolymers surface > > > > > > Dear all, > > possibly related to hydroxyls exposure and orientation is there a tool to > > display and identify what might be improperly called hydrophobic surfaces > > of polysaccharides ? > > I admit I have not gone through most documentation. > > > > > > Salutations Cordiales / Best regards / ;-) > > > **************************************************************************** > > *********************************** > > Hervé Bizot / Unité de Physico-chimie des Macromolécules / Inst. Nat. > > Recherche Agronomique / > > rue de la Géraudière/ BP# 71627 /44316 NANTES Cédex 03 / FRANCE > > Tel.: 33 (0)2 40 67 50 00 / FAX.: 33 (0)2 40 67 50 43 or 50 05 / E-Mail : > > bizot@nantes.inra.fr > > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > > > **************************************************************************** > > **************************************. > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> <000801c3bb6a$f675f940$0101c80a@gideon> <009301c3bc73$3f425ac0$d72da8c0@HP13792165820> ++++------+------+------+------+------+------+------+------+------+------+ From: petrocor Subject: Re: hydrophobic scale and display of biopolymers surface Date: Sun, 07 Dec 2003 17:41:54 +0200 To: rasmol@lists.umass.edu Cc: "'harnoy'" Try http://arbl.cvmbs.colostate.edu/molkit/hydropathy/scales.html Good luck g. ----- Original Message ----- Sent: Sunday, December 07, 2003 5:35 AM From: "IKEHATA, Akihisa" Subject: Re: hydrophobic scale and display of biopolymers surface To: > Hi > > Thanks for sending us the scale. I would also like to know the source of > the scale; the original paper. > > Thank you for your time. > > Akihisa > ----- Original Message ----- > From: "petrocor" > To: > Cc: "'harnoy'" > Sent: Saturday, December 06, 2003 5:04 AM > Subject: Re: hydrophobic scale and display of biopolymers surface > > > > Your request > > > > Gideon harnoy > > Petrocor, Inc. > > > > Hydrophobicity Scales > > Kyte-Doolittle Hopp-Woods > > > > Alanine 1.8 -0.5 > > Arginine -4.5 3.0 > > Asparagine -3.5 0.2 > > Aspartic acid -3.5 3.0 > > Cysteine 2.5 -1.0 > > Glutamine -3.5 0.2 > > Glutamic acid -3.5 3.0 > > Glycine -0.4 0.0 > > Histidine -3.2 -0.5 > > Isoleucine 4.5 -1.8 > > Leucine 3.8 -1.8 > > Lysine -3.9 3.0 > > Methionine 1.9 -1.3 > > Phenylalanine 2.8 -2.5 > > Proline -1.6 0.0 > > Serine -0.8 0.3 > > Threonine -0.7 -0.4 > > Tryptophan -0.9 -3.4 > > Tyrosine -1.3 -2.3 > > Valine 4.2 -1.5 > > > > > > > > > > > > ----- Original Message ----- > > From: "IKEHATA, Akihisa" > > To: > > Sent: Friday, November 28, 2003 4:34 AM > > Subject: Re: hydrophobic scale and display of biopolymers surface > > > > > > > Dear Mr.? Hervé Bizot > > > > > > I received your e-mail and tried visiting the link; > > > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > > > , but it has been out. I would like to know the hydrophobic scale. I > would > > > appreciate it if you could tell me the appropriate address. > > > > > > Regards > > > > > > ********************************** > > > (Mr.) IKEHATA, Akihisa > > > Graduate School of Integrated Sciences > > > Yokohama City University > > > Science of Supramolecular Systems > > > Affiliated with RIKEN Yokohama Institute > > > ikehata_a@tsurumi.yokohama-cu.ac.jp > > > ********************************** > > > > > > ----- Original Message ----- > > > From: "Herve Bizot" > > > To: > > > Sent: Monday, November 24, 2003 8:33 PM > > > Subject: hydrophobic scale and display of biopolymers surface > > > > > > > > > Dear all, > > > possibly related to hydroxyls exposure and orientation is there a tool > to > > > display and identify what might be improperly called hydrophobic > surfaces > > > of polysaccharides ? > > > I admit I have not gone through most documentation. > > > > > > > > > Salutations Cordiales / Best regards / ;-) > > > > > > **************************************************************************** > > > *********************************** > > > Hervé Bizot / Unité de Physico-chimie des Macromolécules / Inst. Nat. > > > Recherche Agronomique / > > > rue de la Géraudière/ BP# 71627 /44316 NANTES Cédex 03 / FRANCE > > > Tel.: 33 (0)2 40 67 50 00 / FAX.: 33 (0)2 40 67 50 43 or 50 05 / E-Mail > : > > > bizot@nantes.inra.fr > > > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > > > > > > **************************************************************************** > > > **************************************. > > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: ABRIATA Subject: Compiling / DDE linking Date: Mon, 08 Dec 2003 00:51:54 -0300 To: rasmol@lists.umass.edu I wonder if any of you can give me a hand with the following 2 topics: - Compiling RasMol with MS Visual C++ (I tried doing it as explained in OpenRasmol.org, but it didn't work) - Linking Rasmol to Visual Basic through DDE (I also tried doing it as explained, but it didn't work) Thanks a lot for your time, Luciano ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: ca X-Spam-Status: No, hits=0.0 required=5.0 tests=none autolearn=no version=2.60 X-Spam-Checker-Version: SpamAssassin 2.60 (1.212-2003-09-23-exp) on gregal.xtec.es X-Virus-Scanned: TAMIZ 2.3 + McAfee en gregal.xtec.es X-XTEC-MailScanner: Sembla que estigui net X-XTEC-MailScanner-SpamCheck: no es spam, SpamAssassin (puntuaci*n=0, requerido 5) References: <002c01c3bd3f$018ccd60$545346c8@123> ++++------+------+------+------+------+------+------+------+------+------+ From: Antonio Parra Subject: Re: Compiling / DDE linking Date: Mon, 08 Dec 2003 18:49:02 +0100 To: rasmol@lists.umass.edu > - Linking Rasmol to Visual Basic through DDE I used Chime instead. Messages are sent to the browser to show the desired file. In Pascal: L:=GlobalAddAtom(A); SendMessage(H,WM_DOIT,0,L); GlobalDeleteAtom(L); where A is a nil ended string, L is an atom, and H is a handle to the browser window. -- Antonio Parra http://www.xtec.es/~aparra1/index.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: <002c01c3bd3f$018ccd60$545346c8@123> <3FD4B98E.27B3D28C@pie.xtec.es> ++++------+------+------+------+------+------+------+------+------+------+ From: ABRIATA Subject: Re: Compiling / DDE linking Date: Mon, 08 Dec 2003 09:25:16 -0300 To: rasmol@lists.umass.edu Thanks a lot for your answer! Would you mind to give me some more advise? What I don't understand is the following: I have the VB app, which has a WebBrowser control navigating at URL = my molecule. I did it, and it works. But then, how do I do DDE with the chime object inside the WebBrowser control? Again, thanks for your time. Yours sincerely, Luciano ----- Original Message ----- Sent: Monday, December 08, 2003 2:49 PM From: "Antonio Parra" Subject: Re: Compiling / DDE linking To: > > - Linking Rasmol to Visual Basic through DDE > > I used Chime instead. Messages are sent to the browser to show the desired > file. > In Pascal: > L:=GlobalAddAtom(A); > SendMessage(H,WM_DOIT,0,L); > GlobalDeleteAtom(L); > where A is a nil ended string, L is an atom, and H is a handle to the > browser window. > -- > Antonio Parra > > http://www.xtec.es/~aparra1/index.htm > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> <000801c3bb6a$f675f940$0101c80a@gideon> <009301c3bc73$3f425ac0$d72da8c0@HP13792165820> <000c01c3bcd8$a46e3670$0101c80a@gideon> ++++------+------+------+------+------+------+------+------+------+------+ From: "IKEHATA, Akihisa" Subject: Re: hydrophobic scale and display of biopolymers surface Date: Thu, 11 Dec 2003 13:50:56 +0900 To: rasmol@lists.umass.edu Thanks a lot, for reply Akihisa ----- Original Message ----- Sent: Monday, December 08, 2003 12:41 AM From: "petrocor" Subject: Re: hydrophobic scale and display of biopolymers surface To: Cc: "'harnoy'" > Try > > http://arbl.cvmbs.colostate.edu/molkit/hydropathy/scales.html > > Good luck > > g. > ----- Original Message ----- > From: "IKEHATA, Akihisa" > To: > Sent: Sunday, December 07, 2003 5:35 AM > Subject: Re: hydrophobic scale and display of biopolymers surface > > > > Hi > > > > Thanks for sending us the scale. I would also like to know the source of > > the scale; the original paper. > > > > Thank you for your time. > > > > Akihisa > > ----- Original Message ----- > > From: "petrocor" > > To: > > Cc: "'harnoy'" > > Sent: Saturday, December 06, 2003 5:04 AM > > Subject: Re: hydrophobic scale and display of biopolymers surface > > > > > > > Your request > > > > > > Gideon harnoy > > > Petrocor, Inc. > > > > > > Hydrophobicity Scales > > > Kyte-Doolittle Hopp-Woods > > > > > > Alanine 1.8 -0.5 > > > Arginine -4.5 3.0 > > > Asparagine -3.5 0.2 > > > Aspartic acid -3.5 3.0 > > > Cysteine 2.5 -1.0 > > > Glutamine -3.5 0.2 > > > Glutamic acid -3.5 3.0 > > > Glycine -0.4 0.0 > > > Histidine -3.2 -0.5 > > > Isoleucine 4.5 -1.8 > > > Leucine 3.8 -1.8 > > > Lysine -3.9 3.0 > > > Methionine 1.9 -1.3 > > > Phenylalanine 2.8 -2.5 > > > Proline -1.6 0.0 > > > Serine -0.8 0.3 > > > Threonine -0.7 -0.4 > > > Tryptophan -0.9 -3.4 > > > Tyrosine -1.3 -2.3 > > > Valine 4.2 -1.5 > > > > > > > > > > > > > > > > > > ----- Original Message ----- > > > From: "IKEHATA, Akihisa" > > > To: > > > Sent: Friday, November 28, 2003 4:34 AM > > > Subject: Re: hydrophobic scale and display of biopolymers surface > > > > > > > > > > Dear Mr.? Hervé Bizot > > > > > > > > I received your e-mail and tried visiting the link; > > > > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > > > > , but it has been out. I would like to know the hydrophobic scale. I > > would > > > > appreciate it if you could tell me the appropriate address. > > > > > > > > Regards > > > > > > > > ********************************** > > > > (Mr.) IKEHATA, Akihisa > > > > Graduate School of Integrated Sciences > > > > Yokohama City University > > > > Science of Supramolecular Systems > > > > Affiliated with RIKEN Yokohama Institute > > > > ikehata_a@tsurumi.yokohama-cu.ac.jp > > > > ********************************** > > > > > > > > ----- Original Message ----- > > > > From: "Herve Bizot" > > > > To: > > > > Sent: Monday, November 24, 2003 8:33 PM > > > > Subject: hydrophobic scale and display of biopolymers surface > > > > > > > > > > > > Dear all, > > > > possibly related to hydroxyls exposure and orientation is there a tool > > to > > > > display and identify what might be improperly called hydrophobic > > surfaces > > > > of polysaccharides ? > > > > I admit I have not gone through most documentation. > > > > > > > > > > > > Salutations Cordiales / Best regards / ;-) > > > > > > > > > > **************************************************************************** > > > > *********************************** > > > > Hervé Bizot / Unité de Physico-chimie des Macromolécules / Inst. Nat. > > > > Recherche Agronomique / > > > > rue de la Géraudière/ BP# 71627 /44316 NANTES Cédex 03 / FRANCE > > > > Tel.: 33 (0)2 40 67 50 00 / FAX.: 33 (0)2 40 67 50 43 or 50 05 / > E-Mail > > : > > > > bizot@nantes.inra.fr > > > > http://www.nantes.inra.fr/public/unites_recherche/upcm/upcm.htm > > > > > > > > > > **************************************************************************** > > > > **************************************. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en X-Virus-Scanned: by KULeuven Antivirus Cluster ++++------+------+------+------+------+------+------+------+------+------+ From: Matheus Froeyen Subject: dials Date: Thu, 11 Dec 2003 11:59:34 +0100 To: rasmol@lists.umass.edu dear all, I attached an old dials box (without leds) to my silicon graphics octane workstation. The confidence tests work fine. However, Rasmol 2.6 or 2.7.2 do not respond to touching the dials. In InsightII (1997) from Acelrys the dials work without problem. Any idea why no reaction in rasmol? Sincerely mathy froeyen ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> <000801c3bb6a$f675f940$0101c80a@gideon> <009301c3bc73$3f425ac0$d72da8c0@HP13792165820> <000c01c3bcd8$a46e3670$0101c80a@gideon> ++++------+------+------+------+------+------+------+------+------+------+ From: Herve Bizot Subject: Re: hydrophobic scale and display of biopolymers surface Date: Thu, 11 Dec 2003 12:40:55 +0100 To: rasmol@lists.umass.edu Dear colleagues, I kept silent but my hope was to identify a method offering some kind of hydrophobic maping surfaces from atomic criteria ( charge, neighbours , extension & shape of hydrophobic patch to account for cooperativity, antitetrahedrality ...) and not only an empirical list for Amino acids as my interest is in polysaccharides . Possibly the question is ill defined . ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> <000801c3bb6a$f675f940$0101c80a@gideon> <009301c3bc73$3f425ac0$d72da8c0@HP13792165820> <000c01c3bcd8$a46e3670$0101c80a@gideon> <5.2.0.9.0.20031211101129.0258a308@nantes.inra.fr> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: hydrophobic scale and display of biopolymers surface Date: Thu, 11 Dec 2003 11:23:58 +0000 (GMT) To: rasmol@lists.umass.edu Cc: bizot@nantes.inra.fr ++ Herve Bizot-- > Dear colleagues, > I kept silent but my hope was to identify a method offering some kind of > hydrophobic maping surfaces from atomic criteria ( charge, neighbours , extension > & shape of hydrophobic patch to account for cooperativity, antitetrahedrality May I ask what this is? Cheers, dan. > ...) and not only an empirical list for Amino acids as my interest is in > polysaccharides . > Possibly the question is ill defined . > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <6.0.0.22.2.20031127150546.01d40b28@staffmail.ed.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: jmol site? Date: Thu, 11 Dec 2003 14:50:24 +0000 (GMT) To: rasmol@lists.umass.edu Hello, I would like to set up a JMOL PDB interface using domain classification of PDB. Ideally I would like to be able to... 1) Get a PDB.. 2) Break down PDB into 'bits' by DALI, SCOP, CATH, TOPS 3) Pick each 'bit' separately (color separately etc.) 4) Generate a list of PDB with same 'bits'. 5) Pick PDB from this list and superimpose. Being able to do this through a web interface would be so cool. I imagine the whole thing as very simple interface, with just a few buttons. I really get lost in those big multi-functional molecular visualization programs. Basically I would like to know if it is easy to hook up Jmol to dynamic database driven web pages and 'modular' algorithms? i.e. Are there any Jmol PHP classes to help do this? Can Jmol subscribe to remote algorithm servers? For example to do the superimposition? Should I be asking these questions elswhere? In my mind Jmol is just web ready rasmol. Sorry if this isn't correct. Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <6.0.0.22.2.20031127150546.01d40b28@staffmail.ed.ac.uk> <53617.193.60.81.207.1071154224.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: jmol site? Date: Thu, 11 Dec 2003 17:09:18 +0100 (CET) To: rasmol@lists.umass.edu > I would like to set up a JMOL PDB interface using domain classification > of PDB. Gulp ... that may be *pushing-the-envelope* for Jmol. But I would love to talk to you about it. > Ideally I would like to be able to... > 1) Get a PDB.. > 2) Break down PDB into 'bits' by DALI, SCOP, CATH, TOPS > 3) Pick each 'bit' separately (color separately etc.) > 4) Generate a list of PDB with same 'bits'. > 5) Pick PDB from this list and superimpose. > > Being able to do this through a web interface would be so cool. Most of these things are beyond my level of understanding, but I get the idea. > Basically I would like to know if it is easy to hook up Jmol to dynamic > database driven web pages and 'modular' algorithms? My answer to this is 'yes' It is easy to hook up Jmol to retrieve models (and scripts) from a database. > i.e. Are there any Jmol PHP classes to help do this? Currently there are no Jmol PHP classes to support this type of work. But PHP would be a very good tool to use. All JmolApplet IO is done with URLs to the web server. So you can use php, Perl, JSP, ... For example, I wrote a small perl script which allows the JmolApplet to load an arbitrary .pdb file. The JmolApplet requests the pdbID from the cgi. The cgi pulls down the .pdb.gz from the PDB and returns it to the JmolApplet. > Can Jmol subscribe to remote algorithm servers? Not sure what you mean by 'subscribe' Jmol can load a model from a URL. If that URL is generated by some remote algorithm, it will work fine. > For example to do the superimposition? To me 'superimposition' sounds like loading several models at the same time. Jmol's current goal is for RasMol/Chime compatibility. It does not currently support loading multiple models at the same time. There have been other requests for this, so it is on the to-do list. > Should I be asking these questions elswhere? It may be more appropriate to have this discussion on jmol-users@lists.sourceforge.net > In my mind Jmol is just web ready rasmol. Well, that is what we *want* Jmol to be ... and I think we are close. But you need to decide whether or not Jmol is *close enough* for your application. The fact is, Jmol is still a bit young and immature. Our current goal is to be funcionally equivalent with Chime. This will allow people to migrate existing Chime applications to Jmol. After reaching parity with Chime, we will look to extend the capabilities. It seems there is a lot of pent-up demand for extended functionality. I encourage all who are interested to take a look at some current JmolApplet demonstrations on: http://jmol.sourceforge.net/preview If you are interested in doing active development with Jmol, including converting existing Chime web applications, then you should participate in the open beta test program at http://jmol.sourceforge.net/betatest Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <6.0.0.22.2.20031127150546.01d40b28@staffmail.ed.ac.uk> <53617.193.60.81.207.1071154224.squirrel@www.mrc-dunn.cam.ac.uk> <35299.212.128.142.25.1071158958.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: jmol site? Date: Thu, 11 Dec 2003 18:11:01 +0100 To: rasmol@lists.umass.edu Miguel Howard wrote: >>I would like to set up a JMOL PDB interface using domain classification >>of PDB. >> >> > >Gulp ... that may be *pushing-the-envelope* for Jmol. > >But I would love to talk to you about it. > > > >>Ideally I would like to be able to... >>1) Get a PDB.. >>2) Break down PDB into 'bits' by DALI, SCOP, CATH, TOPS >> >> only SCOP is supported on http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=yes >>3) Pick each 'bit' separately (color separately etc.) >>4) Generate a list of PDB with same 'bits'. >>5) Pick PDB from this list and superimpose. >> >>Being able to do this through a web interface would be so cool. >> >> > >Most of these things are beyond my level of understanding, but I get the >idea. > > > >>Basically I would like to know if it is easy to hook up Jmol to dynamic >>database driven web pages and 'modular' algorithms? >> >> >My answer to this is 'yes' > >It is easy to hook up Jmol to retrieve models (and scripts) from a database. > > > >>i.e. Are there any Jmol PHP classes to help do this? >> >> > >Currently there are no Jmol PHP classes to support this type of work. But >PHP would be a very good tool to use. > >All JmolApplet IO is done with URLs to the web server. So you can use php, >Perl, JSP, ... > >For example, I wrote a small perl script which allows the JmolApplet to >load an arbitrary .pdb file. The JmolApplet requests the pdbID from the >cgi. The cgi pulls down the .pdb.gz from the PDB and returns it to the >JmolApplet. > > > >>Can Jmol subscribe to remote algorithm servers? >> >> > >Not sure what you mean by 'subscribe' > >Jmol can load a model from a URL. If that URL is generated by some remote >algorithm, it will work fine. > > > >>For example to do the superimposition? >> >> > >To me 'superimposition' sounds like loading several models at the same time. > > please use the term molecule as in RasMol 2.7.2.1 which can load up to 5 separate PDB files which could be manipulated together or separately. Although the term layer may be better, because there is no confusion with chemical meaning of molecule. >Jmol's current goal is for RasMol/Chime compatibility. It does not >currently support loading multiple models at the same time. > >There have been other requests for this, so it is on the to-do list. > > > >>Should I be asking these questions elswhere? >> >> >It may be more appropriate to have this discussion on >jmol-users@lists.sourceforge.net > > > > >>In my mind Jmol is just web ready rasmol. >> >> > >Well, that is what we *want* Jmol to be ... and I think we are close. But >you need to decide whether or not Jmol is *close enough* for your >application. > >The fact is, Jmol is still a bit young and immature. Our current goal is >to be funcionally equivalent with Chime. This will allow people to migrate >existing Chime applications to Jmol. > > you may compare chime and Jmol on http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?CHIME=yes&JMOL=3cro Regards, Jan >After reaching parity with Chime, we will look to extend the capabilities. >It seems there is a lot of pent-up demand for extended functionality. > >I encourage all who are interested to take a look at some current >JmolApplet demonstrations on: > http://jmol.sourceforge.net/preview > >If you are interested in doing active development with Jmol, including >converting existing Chime web applications, then you should participate in >the open beta test program at > http://jmol.sourceforge.net/betatest > > >Miguel > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: jmol site? Date: Thu, 11 Dec 2003 12:24:20 -0500 To: rasmol@lists.umass.edu at 5.09p EDT on 2003 December 11 Thursday Miguel Howard said: > > > Can Jmol subscribe to remote algorithm servers? > > Not sure what you mean by 'subscribe' > > Jmol can load a model from a URL. If that URL is generated by some remote > algorithm, it will work fine. > > > For example to do the superimposition? > > To me 'superimposition' sounds like loading several models at the same time. > > Jmol's current goal is for RasMol/Chime compatibility. It does not > currently support loading multiple models at the same time. > > There have been other requests for this, so it is on the to-do list. > ...unless the algorithm returned a structure file with the superimposed molecules identified as different chains, not models. a number of Web sites do provide this sort of service. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <35299.212.128.142.25.1071158958.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: jmol site? Date: Thu, 11 Dec 2003 18:39:02 +0100 (CET) To: rasmol@lists.umass.edu >> There have been other requests for this, so it is on the to-do list. > ...unless the algorithm returned a structure file with the superimposed > molecules identified as different chains, not models. a number of Web > sites do provide this sort of service. True, that would work just fine. >From Jmol's perspective, they could be either separate chains or separate models ... as long as they are all in the same file. What Jmol can *not* currently do is load more than one file at the same time. And once they are loaded, they cannot be moved/manipulated independently. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Use statistics for my Chime projects Date: Thu, 11 Dec 2003 15:55:42 -0500 To: rasmol@lists.umass.edu After years of not quite completing it, I have finally posted a table summarizing counts of visitors, visits, sessions and downloads for various Chime-based resources I have authored. http://www.umass.edu/microbio/chime/vistats.htm In the past academic year, a new person (unique IP address) visited one of these molecular visualization resources on average every minute (470,000 unique visitors/year, many coming multiple times in the year). On average, 11,600 people (IP addresses) visited each week. Not all visitors have Chime installed or a compatible browser. One out of three of the 105,000 people who visited Protein Explorer last academic year successfully start a session. Each of these visitors starts, on average, almost five sessions. Thus there is an on-line session in Protein Explorer every 4 minutes. A bit less than half of these sessions progress from FirstView to QuickViews. Protein Explorer is downloaded 80 times/day, but I have no estimate of the number of off-line sessions. http://proteinexplorer.org 80% of visitors to PE's FrontDoor page used Internet Explorer, and the remainder, Netscape. 73% of on-line PE sessions are in Internet Explorer. 87% are in Windows, and 13% on Macs. (These stats are live: click the sitemeter at the bottom of PE's FrontDoor page.) Visitors to my most popular tutorial, DNA Structure, exceeded those to Protein Explorer by 1.14-fold (not counting visitors to its Spanish, German and Portuguese translations). Not surprisingly, "DNA Structure" is downloaded at only one-tenth the rate of PE. http://molvis.sdsc.edu/dna/index.htm The World Index of Molecular Visualization Resources was visited every 16 minutes (32,000 times/year, just shy of 90 times/day). http://molvisindex.org The PDB Lite search interface (http://pdblite.org) is being used over 700 times/week (36,000/year). ConSurf (http://consurf.tau.ac.il) colors each residue in a protein by evolutionary conservation, displaying its results in Protein Explorer. Recently, 500-1,000 ConSurf runs are completed successfuly each month (personal communication with Yossi Rosenberg). RasMol remains extremely popular. Version 2.6 has been downloaded from my site between 70,000 and 100,000 times per year (>200 downloads/day) for the past five years, and of course it is available from many other sites, notably http://www.rasmol.org. -Eric Martz University of Massachusetts, Amherst ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <5.2.0.9.2.20031210180218.00a9d140@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Use statistics for my Chime projects Date: Thu, 11 Dec 2003 16:31:54 -0500 To: rasmol@lists.umass.edu For the record, www.rasmol.org does not offer RasMol 2.6. It offers RasMol 2.7, the current release. The best current version is 2.7.2.1. -- HJB At 3:55 PM -0500 12/11/03, Eric Martz wrote: ... > >RasMol remains extremely popular. Version 2.6 has been downloaded >from my site between 70,000 and 100,000 times per year (>200 >downloads/day) for the past five years, and of course it is >available from many other sites, notably http://www.rasmol.org. ... -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <35299.212.128.142.25.1071158958.squirrel@www.howards.org> <35369.212.128.142.25.1071164342.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: jmol site? Date: Thu, 11 Dec 2003 21:19:12 +0000 (GMT) To: rasmol@lists.umass.edu Cc: mth@mth.com ++ Miguel Howard-- >>> There have been other requests for this, so it is on the to-do list. > >> ...unless the algorithm returned a structure file with the superimposed >> molecules identified as different chains, not models. a number of Web sites do >> provide this sort of service. > > True, that would work just fine. I was thinking that the site could be queried with the relevant pair (or more) of molecules, and simply return rotation / translation commands for the viewer in question to perform. Layers sounds like a good term, as it easily lends itself to multi views, turning layers of and on - locking the relative orentation of layers etc. >>From Jmol's perspective, they could be either separate chains or separate > models ... as long as they are all in the same file. > > What Jmol can *not* currently do is load more than one file at the same time. And > once they are loaded, they cannot be moved/manipulated > independently. Will this be tricky? > > > Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20031210180218.00a9d140@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Use statistics for my Chime projects Date: Thu, 11 Dec 2003 21:25:17 +0000 (GMT) To: rasmol@lists.umass.edu Thanks everyone for the feedback. I can parse scop / dali into rasmol style scripts, but I am not sure how to do cath / tops (I haven't looked into it yet), although I am sure it will be easy enough. Ideally I would like to do this for chime / jmol / pymol / et al, but as the scripting languages diversify so it becomes less likely to happen. Thanks all again, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: pdb history [was Re: ssbond questions] Date: Thu, 11 Dec 2003 17:27:05 -0500 To: rasmol@lists.umass.edu at 12.20p EDT on 2003 December 02 Tuesday timothy driscoll said: > > at 10.17a EDT on 2003 December 01 Monday Frances C. Bernstein said: > > > I think that some history might be useful here in explaining bonds > > are represented in PDB entries. > > > [...] > > hi Frances, > > despite having deleted this one for the sake of brevity, I find these > historical explanations extremely helpful. Can you, or someone else, > recommend an authoritative a book on the subject? > am I to intepret the silence to mean there is no such book, or just not one anyone would recommend? ;-) :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: pdb history [was Re: ssbond questions] Date: Thu, 11 Dec 2003 22:16:05 +0000 (GMT) To: rasmol@lists.umass.edu Cc: molvisions@mac.com ++ timothy driscoll-- > at 12.20p EDT on 2003 December 02 Tuesday timothy driscoll said: >> >> at 10.17a EDT on 2003 December 01 Monday Frances C. Bernstein said: >> >> > I think that some history might be useful here in explaining bonds are >> represented in PDB entries. >> > >> [...] >> >> hi Frances, >> >> despite having deleted this one for the sake of brevity, I find these historical >> explanations extremely helpful. Can you, or someone else, recommend an >> authoritative a book on the subject? >> > > am I to intepret the silence to mean there is no such book, or just not one anyone > would recommend? ;-) If you are really desparate here is a link to my MSc project report I wrote with Jong Park. I review what I thought were the major historic events in protein structure classification in the introduction (just a couple of pages). At the time I thought it was quite good, but looking at it now it reads quite strangely! http://interaction.mrc-dunn.cam.ac.uk/Scientists/Dan_Bolser/protein_periodic_table.pdf In addition to Jong I should also thank Richard Harrington for turning this into a pdf for me. All criticism welcome ;) Dan. > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <35299.212.128.142.25.1071158958.squirrel@www.howards.org> <35369.212.128.142.25.1071164342.squirrel@www.howards.org> <34177.80.1.204.145.1071177552.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: jmol site? Date: Fri, 12 Dec 2003 00:14:04 +0100 (CET) To: rasmol@lists.umass.edu > Layers sounds like a good term, as it easily lends itself to multi > views, turning layers of and on - locking the relative orentation of > layers etc. I agree that 'layers' sounds like a good term to use for this kind of functionality. >> What Jmol can *not* currently do is load more than one file at the >> same time. And once they are loaded, they cannot be moved/manipulated >> independently. > > Will this be tricky? I don't think the implementation will be very difficult ... but I also suspect that there will be a few unexpected *surprises*. The big issues will be - specifying the user interface/gesture behavior - understanding the impact on the scripting language - deciding where this fits on the priority list of feature requests Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: pdb history [was Re: ssbond questions] Date: Thu, 11 Dec 2003 19:08:38 -0500 (EST) To: rasmol@lists.umass.edu Dear Tim, There is no such book. You could consult the archive of BNL PDB Newsletters and published articles about the PDB as well as the mmcif and the RCSB PDB pdb-l e-mail archives. Tom Koetzle was head of the PDB from 1973 until 1993 but was not always involved in the format details in the later years. Enrique Abola was involved with the format from 1979 until the PDB left BNL in 1999. I was involved with the format from 1974 until 1998 when I left the PDB. Note that the current PDB format is the second one used by the PDB (original format was based on the Diamond output format) and I was there when the current 80-column format was designed. And, of course, there are a number of PDB people who were active in discussions at various times but no others with the same longevity and long-range perspective. I suspect that I am the only one of the above people still actively following the PDB mailing list and this rasmol list. Some software developers and heavy PDB users also have tracked the PDB format very carefully over the years (e.g. Gerard Kleywegt) and they often make useful contributions to online discussions. Frances Bernstein ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Thu, 11 Dec 2003, timothy driscoll wrote: > at 12.20p EDT on 2003 December 02 Tuesday timothy driscoll said: > > > > at 10.17a EDT on 2003 December 01 Monday Frances C. Bernstein said: > > > > > I think that some history might be useful here in explaining bonds > > > are represented in PDB entries. > > > > > [...] > > > > hi Frances, > > > > despite having deleted this one for the sake of brevity, I find these > > historical explanations extremely helpful. Can you, or someone else, > > recommend an authoritative a book on the subject? > > > > am I to intepret the silence to mean there is no such book, or just not one > anyone would recommend? ;-) > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- protocol="application/pgp-signature"; boundary="86iauDJ7Z6qm7j1O" Content-disposition: inline User-Agent: Mutt/1.4i References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Re: pdb history [was Re: ssbond questions] Date: Fri, 12 Dec 2003 13:35:10 +0100 To: rasmol@lists.umass.edu --86iauDJ7Z6qm7j1O Content-Disposition: inline On Thu, Dec 11, 2003 at 07:08:38PM -0500, Frances C. Bernstein wrote: > I suspect that I am the only one of the above people > still actively following the PDB mailing list and this rasmol > list. Some software developers and heavy PDB users also have > tracked the PDB format very carefully over the years (e.g. > Gerard Kleywegt) and they often make useful contributions > to online discussions. Frances, am I correct in my assumption that mmCIF is now the canonical new format for anything involving high-resolution biomolecules, or are there alternative formats I'm not aware of? -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net --86iauDJ7Z6qm7j1O * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --86iauDJ7Z6qm7j1O-- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: pdb history [was Re: ssbond questions] Date: Fri, 12 Dec 2003 08:58:34 -0500 (EST) To: rasmol@lists.umass.edu Dear Eugen, mmCIF issues should really be answered by the people at the RCSB PDB. On a practical level it appears that many programs are not yet ready to write/read mmCIF. The 80-column PDB format has been in use for close to 30 years and is deeply embedded in code. Reading mmCIF is more difficult and I refer you to the IUCr web pages for information on software packages/routines to help in that process. There is work being done reative to XML and CML but these formats are not in wide use at present relative to macromolecular structures. And, of course, program suites have their own 'internal' formats but generally can output something rather close to the PDB 80-column format. Frances Bernstein ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 12 Dec 2003, Eugen Leitl wrote: > On Thu, Dec 11, 2003 at 07:08:38PM -0500, Frances C. Bernstein wrote: > > > I suspect that I am the only one of the above people > > still actively following the PDB mailing list and this rasmol > > list. Some software developers and heavy PDB users also have > > tracked the PDB format very carefully over the years (e.g. > > Gerard Kleywegt) and they often make useful contributions > > to online discussions. > > Frances, > > am I correct in my assumption that mmCIF is now the > canonical new format for anything involving high-resolution > biomolecules, or are there alternative formats I'm not > aware of? > > -- Eugen* Leitl leitl > ______________________________________________________________ > ICBM: 48.07078, 11.61144 http://www.leitl.org > 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE > http://moleculardevices.org http://nanomachines.net > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <20031212123510.GM13099@leitl.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: pdb history [was Re: ssbond questions] Date: Fri, 12 Dec 2003 13:24:23 +0000 (GMT) To: rasmol@lists.umass.edu Cc: eugen@leitl.org ++ Eugen Leitl-- > On Thu, Dec 11, 2003 at 07:08:38PM -0500, Frances C. Bernstein wrote: > >> I suspect that I am the only one of the above people >> still actively following the PDB mailing list and this rasmol >> list. Some software developers and heavy PDB users also have >> tracked the PDB format very carefully over the years (e.g. >> Gerard Kleywegt) and they often make useful contributions >> to online discussions. > > Frances, > > am I correct in my assumption that mmCIF is now the > canonical new format for anything involving high-resolution > biomolecules, or are there alternative formats I'm not > aware of? Given the restrictions of the PDB format, is there any drive to move away from this format? Can rasmol load mmCIF? Ta > -- Eugen* Leitl leitl > ______________________________________________________________ > ICBM: 48.07078, 11.61144 http://www.leitl.org > 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE > http://moleculardevices.org http://nanomachines.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <20031212123510.GM13099@leitl.org> <35607.193.60.81.207.1071235463.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: pdb history [was Re: ssbond questions] Date: Fri, 12 Dec 2003 15:16:00 +0100 To: rasmol@lists.umass.edu Dan Bolser wrote: >++ Eugen Leitl-- > > >>On Thu, Dec 11, 2003 at 07:08:38PM -0500, Frances C. Bernstein wrote: >> >> >> >>> I suspect that I am the only one of the above people >>>still actively following the PDB mailing list and this rasmol >>>list. Some software developers and heavy PDB users also have >>>tracked the PDB format very carefully over the years (e.g. >>>Gerard Kleywegt) and they often make useful contributions >>>to online discussions. >>> >>> >>Frances, >> >>am I correct in my assumption that mmCIF is now the >>canonical new format for anything involving high-resolution >>biomolecules, or are there alternative formats I'm not >>aware of? >> >> > >Given the restrictions of the PDB format, is there any drive to move away from this >format? > >Can rasmol load mmCIF? > > no, not really. I tried with 1KYZ.cif and only some header information is interpreted, no coordinates show up. Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 16:44:25 +0100 (CET) To: rasmol@lists.umass.edu This question involves group (residue) sequence numbers in .pdb files and whether or not negative sequence numbers are valid. The RasMol documentation says that 'renumber' can be used to assign new numbers to groups. It says that negative numbers are valid. When I read this earlier this year I assumed that this implied that normal/legal .pdb files could have negative residue sequence numbers. The pdb spec says: 23 - 26 Integer resSeq Residue sequence number. ... Integer Right-justified blank-filled integer value. Q: Are negative group sequence numbers found in .pdb files? Q: If so, can someone please send me a PdbID of an example? Q: If so, can someone please send me a PdbID of a file that has both a negative group sequence number *and* an insertion code associated with that negative sequence number? Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 11:01:35 -0500 (EST) To: rasmol@lists.umass.edu Negative residue numbers, as well as 0, are permitted in PDB entries. I know that there are entries that have used them. One might ask why residue numbers are not simply sequential from 1 to n. Because many proteins exist in multiple species with slightly different sequences, the community felt that it was useful to use residue numbering that does an alignment and uses the same residue numbers for 'identical' residues. This leads to numbering gaps and insertions relative to the protein that was originally numbered 1 to n. To follow the community and be able to relate the residue numbering in the entry with the residue numbering in the literature, the PDB allows gaps in residue numbering, insertions (that are handled using the insertion code field), negative numbers, 0, and even residue numbering that runs 'backwards'. This leads to the fact that one cannot use the residue numbers to determine whether all residues that are in the material studied are also in the entry. For that one must do a sequence alignment with the SEQRES records. Frances Bernstein ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 12 Dec 2003, Miguel Howard wrote: > This question involves group (residue) sequence numbers in .pdb files and > whether or not negative sequence numbers are valid. > > > The RasMol documentation says that 'renumber' can be used to assign new > numbers to groups. It says that negative numbers are valid. When I read > this earlier this year I assumed that this implied that normal/legal .pdb > files could have negative residue sequence numbers. > > The pdb spec says: > > 23 - 26 Integer resSeq Residue sequence number. > ... > Integer Right-justified blank-filled integer value. > > > Q: Are negative group sequence numbers found in .pdb files? > > Q: If so, can someone please send me a PdbID of an example? > > Q: If so, can someone please send me a PdbID of a file that has both a > negative group sequence number *and* an insertion code associated with > that negative sequence number? > > > Thanks, > Miguel > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <35873.212.128.142.25.1071243865.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 18:16:02 +0100 (CET) To: rasmol@lists.umass.edu Frances, > Negative residue numbers, as well as 0, are permitted in > PDB entries. I know that there are entries that have used them. Thanks. > the PDB allows gaps > in residue numbering, insertions (that are handled using the > insertion code field), negative numbers, 0, and even residue > numbering that runs 'backwards'. I have seen insertion codes that run backwards, but did not realize that the residue numbers themselves could run backwards. This reminds me of a related insertion-code question. The PDB spec says 27 AChar iCode Code for insertion of residues ... AChar An alphabetic character (A-Z, a-z) Q: Is the normal insertion sequence uppercase A-Z followed by lower case a-z? Q: In practice, are there pdb entries with insertion codes which extend into the lower case letters? Q: Are there pdb entries when need to extend beyond the lower case letters? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 12:16:58 -0500 To: rasmol@lists.umass.edu Cc: Jaime.Prilusky@weizmann.ac.il, henrick@ebi.ac.uk At 12/12/03, Miguel Howard wrote: >Q: Are negative group sequence numbers found in .pdb files? Frances has answered this authoritatively. >Q: If so, can someone please send me a PdbID of an example? I have kept notes on examples of unusual PDB files of many sorts that I've tried to deal with in Protein Explorer. 1AVQ has -1 and 0 in chains A and B. 1BXW has a single chain beginning with 0. 1D5T starts at -2 and skips 0. Some other bizzare cases: 1JDP:B has residue 1000 numbered -1 in chain B, but not in identical chains E,H,K. 1UCY numbers insertions before residue 1 in reverse alphabetical order (1H ... 1A, 1), but insertions after residue 2 in forward alphabetical order. 5HVP (see above) has two copies of the inhibitor both in chain C. It counts up from 1-5, then from 1-5 again in the same chain! >Q: If so, can someone please send me a PdbID of a file that has both a >negative group sequence number *and* an insertion code associated with >that negative sequence number? That's a tall order. But you can easily concoct one yourself for test purposes. I often create single or oligo-atom PDB files for test purposes with a text editor. Some examples are the ones that generate X and Y images in Chime at http://www.umass.edu/microbio/chime/chimehow/chimehow.htm Of course, you can right click on any molecule you are viewing in Chime and save the PDB file to disk. It would be very helpful for developers if one could search the PDB to find examples of these sorts of things. I haven't tried looking for negative sequence numbers with insertion codes. Generally, I have found Jaime Prilusky's OCA browser to be a good alternative when the RCSB search interface doesn't support what you need (often the case). OCA is linked to pdblite.org (easy URL to remember). RCSB has recently revamped their search interface and I don't have much experience with the new version. The problem is that they generally haven't documented the inadequacies of their search interface, or bugs, or when bugs are fixed, or what the capabilities and limitations are. So you have to deduce these by trial and error. One can hope that the new WWPDB partners (www.wwpdb.org) will have more capable and better-documented search interfaces. Jaime Prilusky has been very helpful to us in the past. For example, when we were implementing the human-readable PDB-header control panel in Protein Explorer 2.1 Alpha ("Features" of the PDB file) he set up a non-public search mechanism for us that finds all PDB entries that have or lack a particular header record type. This was invaluable for finding rare examples, and frequencies of usage/occurrence of header record types. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en References: <5.2.0.9.2.20031212114138.02205210@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 13:37:31 -0500 To: rasmol@lists.umass.edu Eric and Miguel, We have a PDB with very weird numbering--negative numbers and "p" designated numbers. http://biology.kenyon.edu/slonc/1DKI.pdb We can't figure out how to write a Chime command to designate the "p" residues separately from the non-"p" residues in the same chain. Any ideas? Thanks, Joan P.S. Any Howard Dean supporters out there, please let's connect. Joan L. Slonczewski Professor of Biology Higley Hall, 202 N. College Drive Kenyon College Gambier, OH 43022 http://biology.kenyon.edu/slonc/slonc.htm slonczewski@kenyon.edu Phone: 740-427-5397 Fax: 740-427-5741 "The Doctor is In" Howard Dean for America: deanforamerica.com http://personal.kenyon.edu/~slonczewski/Dean/knoxmeetup/index.htm Eric Martz wrote: > At 12/12/03, Miguel Howard wrote: > >> Q: Are negative group sequence numbers found in .pdb files? > > > Frances has answered this authoritatively. > >> Q: If so, can someone please send me a PdbID of an example? > > > I have kept notes on examples of unusual PDB files of many sorts that > I've tried to deal with in Protein Explorer. > > 1AVQ has -1 and 0 in chains A and B. > 1BXW has a single chain beginning with 0. > 1D5T starts at -2 and skips 0. > > Some other bizzare cases: > > 1JDP:B has residue 1000 numbered -1 in chain B, but not in identical > chains E,H,K. > > 1UCY numbers insertions before residue 1 in reverse alphabetical order > (1H ... 1A, 1), but insertions after residue 2 in forward alphabetical > order. > > 5HVP (see above) has two copies of the inhibitor both in chain C. It > counts up from 1-5, then from 1-5 again in the same chain! > > >> Q: If so, can someone please send me a PdbID of a file that has both a >> negative group sequence number *and* an insertion code associated with >> that negative sequence number? > > > > That's a tall order. But you can easily concoct one yourself for test > purposes. I often create single or oligo-atom PDB files for test > purposes with a text editor. Some examples are the ones that generate > X and Y images in Chime at > http://www.umass.edu/microbio/chime/chimehow/chimehow.htm > Of course, you can right click on any molecule you are viewing in > Chime and save the PDB file to disk. > > It would be very helpful for developers if one could search the PDB to > find examples of these sorts of things. I haven't tried looking for > negative sequence numbers with insertion codes. Generally, I have > found Jaime Prilusky's OCA browser to be a good alternative when the > RCSB search interface doesn't support what you need (often the case). > OCA is linked to pdblite.org (easy URL to remember). > > RCSB has recently revamped their search interface and I don't have > much experience with the new version. The problem is that they > generally haven't documented the inadequacies of their search > interface, or bugs, or when bugs are fixed, or what the capabilities > and limitations are. So you have to deduce these by trial and error. > > One can hope that the new WWPDB partners (www.wwpdb.org) will have > more capable and better-documented search interfaces. > > Jaime Prilusky has been very helpful to us in the past. For example, > when we were implementing the human-readable PDB-header control panel > in Protein Explorer 2.1 Alpha ("Features" of the PDB file) he set up a > non-public search mechanism for us that finds all PDB entries that > have or lack a particular header record type. This was invaluable for > finding rare examples, and frequencies of usage/occurrence of header > record types. > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20031212114138.02205210@marlin.bio.umass.edu> <3FDA0AEB.9080902@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 20:08:25 +0100 (CET) To: rasmol@lists.umass.edu Joan, (Be advised that I am still a novice at this :-) > We have a PDB with very weird numbering--negative numbers and "p" > designated numbers. > http://biology.kenyon.edu/slonc/1DKI.pdb Those 'P' designations are in the 'insertion code' column. But, based upon my very limited experience, it doesn't look like to me that it is being used in the 'normal' way. > We can't figure out how to write a Chime command to designate the "p" > residues separately from the non-"p" residues in the same chain. Any > ideas? I have never used Chime, but I don't think it supports insertion codes. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- zardecki@rcsb.rutgers.edu X-pair-Authenticated: 209.197.6.81 References: <20031212123510.GM13099@leitl.org> <35607.193.60.81.207.1071235463.squirrel@www.mrc-dunn.cam.ac.uk> <3FD9CDA0.8050301@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: pdb history [was Re: ssbond questions] Date: Fri, 12 Dec 2003 15:08:53 -0500 To: rasmol@lists.umass.edu Cc: jwest@rutchem.rutgers.edu, Helen Berman , Actually, RasMol can load the mmCIF files produced by pdb2cif and, with a minor change, can load the mmCIF extensions files produced now by the PDB. Frances Bernstein just found the problem that had been preventing loading of the mmCIF extensions files by RasMol. The new extensions files use the somewhat unusual atom name 'O''' for OXT atoms, and that name is breaking the parser from CBFlib used by RasMol. There are 4 apostrophes in the name -- two as quote marks and two in the name itself As a temporary fix, until we can release a fix for the parser in RasMol, we would suggest changing the name 'O''' to "O''" with a text editor before displaying with RasMol. If you use ex, the command would be: 1,$s/'O'''/"O''"/g Please note that the name 'O''' as used by the RCSB is valid according to the CIF syntax rules. Our apologies for not spotting the error in the parser sooner, and our thanks to Frances Bernstein for finding this. -- Herbert At 3:16 PM +0100 12/12/03, Jan Reichert wrote: >Dan Bolser wrote: > >>++ Eugen Leitl-- >> >>>On Thu, Dec 11, 2003 at 07:08:38PM -0500, Frances C. Bernstein wrote: >>> >>> >>> >>>> I suspect that I am the only one of the above people >>>>still actively following the PDB mailing list and this rasmol >>>>list. Some software developers and heavy PDB users also have >>>>tracked the PDB format very carefully over the years (e.g. >>>>Gerard Kleywegt) and they often make useful contributions >>>>to online discussions. >>>> >>>> >>>Frances, >>> >>>am I correct in my assumption that mmCIF is now the >>>canonical new format for anything involving high-resolution >>>biomolecules, or are there alternative formats I'm not >>>aware of? >>> >>> >> >>Given the restrictions of the PDB format, is there any drive to >>move away from this >>format? >> >>Can rasmol load mmCIF? >> >no, not really. I tried with 1KYZ.cif and only some header >information is interpreted, no coordinates show up. >Regards, Jan > > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 17:26:01 -0500 (EST) To: rasmol@lists.umass.edu I can only speak to the entries that were processed while the PDB was at BNL. We never used lower-case letters. For information about entries processed by RCSB you will have to contact them to find out if they have ever used lower-case letters anywhere in the entries that they have processed. Frances ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 12 Dec 2003, Miguel Howard wrote: > Frances, > > > Negative residue numbers, as well as 0, are permitted in > > PDB entries. I know that there are entries that have used them. > > Thanks. > > > the PDB allows gaps > > in residue numbering, insertions (that are handled using the > > insertion code field), negative numbers, 0, and even residue > > numbering that runs 'backwards'. > > I have seen insertion codes that run backwards, but did not realize that > the residue numbers themselves could run backwards. > > > This reminds me of a related insertion-code question. The PDB spec says > > 27 AChar iCode Code for insertion of residues > ... > AChar An alphabetic character (A-Z, a-z) > > Q: Is the normal insertion sequence uppercase A-Z followed by lower case a-z? > > Q: In practice, are there pdb entries with insertion codes which extend > into the lower case letters? > > Q: Are there pdb entries when need to extend beyond the lower case letters? > > > Miguel > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 17:35:17 -0500 (EST) To: rasmol@lists.umass.edu The molecule presented in this entry apparently is a zymogen (based on COMPND) and I would assume that the residues with P in the insertion code column are the residues that are cleaved off to make the biologically active molecule and that P means 'precurser'; i.e. that they are only present in the precurser. Frances P.S. I have not checked the literature or sequence databases in formulating the above answer. ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 12 Dec 2003, Miguel Howard wrote: > Joan, > > (Be advised that I am still a novice at this :-) > > > We have a PDB with very weird numbering--negative numbers and "p" > > designated numbers. > > http://biology.kenyon.edu/slonc/1DKI.pdb > > Those 'P' designations are in the 'insertion code' column. > > But, based upon my very limited experience, it doesn't look like to me > that it is being used in the 'normal' way. > > > We can't figure out how to write a Chime command to designate the "p" > > residues separately from the non-"p" residues in the same chain. Any > > ideas? > > I have never used Chime, but I don't think it supports insertion codes. > > > Miguel > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: negative group sequence numbers in .pdb? Date: Fri, 12 Dec 2003 23:48:18 +0100 (CET) To: rasmol@lists.umass.edu Frances, > I can only speak to the entries that were processed > while the PDB was at BNL. We never used lower-case letters. > For information about entries processed by RCSB you will > have to contact them to find out if they have ever used > lower-case letters anywhere in the entries that they have > processed. Will do. Thanks, Miguel -------------------------------------------------- Miguel Howard miguel@howards.org c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Please Tell Me If You Teach With Protein Explorer Date: Fri, 12 Dec 2003 17:51:47 -0500 To: rasmol@lists.umass.edu To All Educators Who Are Using Protein Explorer in Classes: I am reporting to NSF. If you have used PE in your class, please drop me an email. NSF cares mostly about people in the USA, but I'm happy to hear from educators elsewhere. Please tell me -name of class -how many students -roughly how many hours of class time PE was used -used only in lecture, or also for hands-on student assignments -your name -your institution, city, state As the semester wraps up, please consider handing out the short one-page Student Assessment of Learning Gains (SALG) form available at http://molvis.sdsc.edu/protexpl/evalppr.htm This will only take about 5 minutes of class time and the results will be very useful to us. Thanks, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <5.2.0.9.2.20031212173822.00ab9ec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Fri, 12 Dec 2003 18:17:14 -0500 To: rasmol@lists.umass.edu My class at James Madison University is called ISAT 454: Computer Applications in Biotechnology. One of the assignments is to do a software review and Protein Explorer is one of the topics for this review. Cindy Klevickis Eric Martz wrote: > To All Educators Who Are Using Protein Explorer in Classes: > > I am reporting to NSF. If you have used PE in your class, please drop > me an email. NSF cares mostly about people in the USA, but I'm happy > to hear from educators elsewhere. > > Please tell me > > -name of class > -how many students > -roughly how many hours of class time PE was used > -used only in lecture, or also for hands-on student assignments > > -your name > -your institution, city, state > > As the semester wraps up, please consider handing out the short > one-page Student Assessment of Learning Gains (SALG) form available at > http://molvis.sdsc.edu/protexpl/evalppr.htm > > This will only take about 5 minutes of class time and the results will be > very useful to us. > > Thanks, -Eric Martz > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Graphical representations of aromatic bonds Date: Sat, 13 Dec 2003 12:24:38 +0100 (CET) To: rasmol@lists.umass.edu, tmanz@purdue.edu, jmol-users@lists.sourceforge.net I am in the process of adding support for aromatic bonds in Jmol. These questions are about graphical representations for aromatic bonds. I believe that the normal way to represent aromatic bonds is to have a solid line and a dashed/broken line. With this representation, the dashed line/cylinder is on the *inside* of the ring. Q: Does this kind of representation have a name? Q: If a bond participates in more than one aromatic ring, is there a 'correct' side to put the dotted line on? The other representation I have seen is single solid lines with a circle in the center. Q: Does this kind of representation have a name? I have been told that this format is 'less acceptable' to some publications and perhaps standards-organizations. Perhaps because it gives wrong impression for bonds that participate in more than one aromatic ring. Q: Is it true that this graphical rendering is less acceptable to publishers/international standards organizations? Q: For the purposes of Jmol, do we care? Both of these representations require me to calculate the 'inside' of the ring. In my search for a simple solution ... Q: Is there an acceptable graphical representation for aromatic bonds that does not require me to calculate the inside of the ring? Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Roberts, Rebecca" Subject: RE: Please Tell Me If You Teach With Protein Explorer Date: Sat, 13 Dec 2003 08:49:26 -0500 To: "'rasmol@lists.umass.edu'" Hi Eric, Glad to hear that NSF is interested! Here's the information - Structural Biology (Bio/BCMB429) 4-5 students 20 hours both lecture and lab hands-on assignments Rebecca Roberts Collegeville PA Biochemistry 15 students 6 hours both lecture and hands-on assignemtns Rebecca Roberts Collegeville PA Have a wonderful holiday! Rebecca -----Original Message----- Sent: Friday, December 12, 2003 5:52 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Please Tell Me If You Teach With Protein Explorer To: rasmol@lists.umass.edu To All Educators Who Are Using Protein Explorer in Classes: I am reporting to NSF. If you have used PE in your class, please drop me an email. NSF cares mostly about people in the USA, but I'm happy to hear from educators elsewhere. Please tell me -name of class -how many students -roughly how many hours of class time PE was used -used only in lecture, or also for hands-on student assignments -your name -your institution, city, state As the semester wraps up, please consider handing out the short one-page Student Assessment of Learning Gains (SALG) form available at http://molvis.sdsc.edu/protexpl/evalppr.htm This will only take about 5 minutes of class time and the results will be very useful to us. Thanks, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: ca X-Spam-Status: No, hits=-5.0 required=5.0 tests=ORIGEN_XTEC autolearn=no version=2.60 X-Spam-Checker-Version: SpamAssassin 2.60 (1.212-2003-09-23-exp) on gregal.xtec.es X-Virus-Scanned: TAMIZ 2.3 + McAfee en gregal.xtec.es X-XTEC-MailScanner: Sembla que estigui net X-XTEC-MailScanner-SpamCheck: no es spam, SpamAssassin (puntuaci*n=0, requerido 5) References: <002c01c3bd3f$018ccd60$545346c8@123> <3FD4B98E.27B3D28C@pie.xtec.es> <000101c3bded$12a66760$f85246c8@123> ++++------+------+------+------+------+------+------+------+------+------+ From: Antonio Parra Subject: Re: Compiling / DDE linking Date: Sat, 13 Dec 2003 20:46:23 +0100 To: rasmol@lists.umass.edu > I have the VB app, which has a WebBrowser control navigating at > URL = my molecule. I did it, and it works. But then, how do I do DDE with > the chime object inside the WebBrowser control? I'm afraid that DDE can only be done between windows, but not to a plug-in inside the window. Anyway, Chime objects can be easily controlled with html code placed in the host page. At the bottom of Erik's web page "Chime Resources" http://www.umass.edu/microbio/chime/ you'll find a section named "How to Create Chime Web Pages". There are several interesting links. -- Antonio Parra http://www.xtec.es/~aparra1/index.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6487.1 Thread-Topic: Please Tell Me If You Teach With Protein Explorer Thread-Index: AcPBBCbqRk758ZZ+T267t+X147v1qgBSHaZ/ content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-PMX-Version: 4.1.0.84332 ++++------+------+------+------+------+------+------+------+------+------+ From: "Miller, Judith E." Subject: RE: Please Tell Me If You Teach With Protein Explorer Date: Sun, 14 Dec 2003 09:22:16 -0500 To: rasmol@lists.umass.edu Hi, Eric, BB1030 Introduction to Biological Macromolecules (an introductory bio course for majors) 70 students The whole class did the one-hour tour, in class (conference sections of 25), working in pairs in a computer lab. Then they had an out of class group project in which each group of 4-5 students had to pick a protein and explain the relationship between its structure and its function, using information they gleaned from PE about that molecule, and using function information that they gleaned from other sources. I'd be happy to send a copy of the assignment if you (or anyone) would like. The student groups each did an 8-10 minute Ppt presentation on their molecule, and also handed in a paper about it, both of which made extensive use of images derived from PE. The course is already over (we have 7 week terms) so it's too late to use the learning gains instrument, sorry. I'm very grateful for your ongoing assistance over the years. The protein structure projects, using RasMol and PE, have always been quite successful in my view. Judith E. Miller Worcester Polytechnic Institute, Worcester MA -----Original Message----- Sent: Fri 12/12/2003 5:51 PM To All Educators Who Are Using Protein Explorer in Classes: From: owner-rasmol@lists.umass.edu on behalf of Eric Martz Subject: Please Tell Me If You Teach With Protein Explorer To: rasmol@lists.umass.edu Cc: I am reporting to NSF. If you have used PE in your class, please drop me an email. NSF cares mostly about people in the USA, but I'm happy to hear from educators elsewhere. Please tell me -name of class -how many students -roughly how many hours of class time PE was used -used only in lecture, or also for hands-on student assignments -your name -your institution, city, state As the semester wraps up, please consider handing out the short one-page Student Assessment of Learning Gains (SALG) form available at http://molvis.sdsc.edu/protexpl/evalppr.htm This will only take about 5 minutes of class time and the results will be very useful to us. Thanks, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en References: <5.2.0.9.2.20031212173822.00ab9ec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Sun, 14 Dec 2003 17:06:46 +0200 To: rasmol@lists.umass.edu Hi Eric, 200 students Teaching bioinformatics at the TafniTech - Open University School for Management of Technologies, Information & Computers. 7 different courses were given. 170 students received a 1-2 hour demonstration (out of a 60 hour 'introduction to bionformatics course) with specific case studies discussed. 30 students received, as part of a 200-hour bioinformatics course, a 2-hour demo, a 4-hour hands-on in class, and an ~8-hour homework assignment. At the end of the course, several groups decided to use PE for the final project. The use of PE and case-studies for teaching was discussed in the latest ISMB Workshop on Education as part of a presentation on bionfo teaching in Israel: http://surya.bic.nus.edu.sg/web03/abstracts/samish.html Thanks for supplying us with this great freeware. Best regards, Ilan ~~~~~~~~~~~~~~~~~ Ilan Samish Department of Plant Sciences Weizmann Institute of Science Rehovot, Israel Lab: 972 8 9344300 Cell: 972 53 321150 Fax: 972 8 9344181 ilan.samish@weizmann.ac.il http://bioinformatics.weizmann.ac.il/~samish/ ================================= Join us at the 1st Structural Bioinformatics Special Interest Group; Satellite meeting of the ISMB conference. http://3dsig.weizmann.ac.il/ Eric Martz wrote: > To All Educators Who Are Using Protein Explorer in Classes: > > I am reporting to NSF. If you have used PE in your class, please drop > me an email. NSF cares mostly about people in the USA, but I'm happy > to hear from educators elsewhere. > > Please tell me > > -name of class > -how many students > -roughly how many hours of class time PE was used > -used only in lecture, or also for hands-on student assignments > > -your name > -your institution, city, state > > As the semester wraps up, please consider handing out the short > one-page Student Assessment of Learning Gains (SALG) form available at > http://molvis.sdsc.edu/protexpl/evalppr.htm > > This will only take about 5 minutes of class time and the results will be > very useful to us. > > Thanks, -Eric Martz > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <5.2.0.9.2.20031210180218.00a9d140@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Use statistics for my Chime projects Date: Sun, 14 Dec 2003 13:10:20 -0500 To: rasmol@lists.umass.edu At 3:55 PM -0500 12/11/03, Eric Martz wrote: ... > >RasMol remains extremely popular. Version 2.6 has been downloaded >from my site between 70,000 and 100,000 times per year (>200 >downloads/day) for the past five years, and of course it is >available from many other sites, notably http://www.rasmol.org. ... We will do complete statistics on RasMol downloads early in 2004, but working from the stats for downloads just from the primary site, the 2.7 series accounts for approximately 120,000 downloads in the past year, 57% for windows, 12% mac and 31% other. This does not include downloads from the ARCiB site or the IUCr mirrors. This also does not include the 73,000 downloads in 2003 of the obsolete 2.6 series reported by Eric Martz. It seems likely that by the end of 2003, there will have been well over 200,000 RasMol downloads for 2003, with more than 60% being from the 2.7 series. -- Herbert -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <5.2.0.9.0.20031124122453.02a9d540@nantes.inra.fr> <002c01c3b558$36f87d30$d72da8c0@HP13792165820> <000801c3bb6a$f675f940$0101c80a@gideon> <009301c3bc73$3f425ac0$d72da8c0@HP13792165820> <000c01c3bcd8$a46e3670$0101c80a@gideon> <5.2.0.9.0.20031211101129.0258a308@nantes.inra.fr> ++++------+------+------+------+------+------+------+------+------+------+ From: IKEHATA Akihisa Subject: Re: hydrophobic scale and display of biopolymers surface Date: Mon, 15 Dec 2003 13:37:11 +0900 To: rasmol@lists.umass.edu Dear Friends I am also thinking about the polysaccharides, and prediction of protein structure from the hydrophobicity and other factors of the atoms. If you have some interests, please send me e-mail. The address is following. Best regards ********************************** (Mr.) IKEHATA, Akihisa Division of Structural Bioinformatics Graduate School of Integrated Sciences Yokohama City University Science of Supramolecular Systems Affiliated with RIKEN Yokohama Institute ikehata_a@tsurumi.yokohama-cu.ac.jp *********************************** ----- Original Message ----- Sent: Thursday, December 11, 2003 8:40 PM From: "Herve Bizot" Subject: Re: hydrophobic scale and display of biopolymers surface To: > Dear colleagues, > I kept silent but my hope was to identify a method offering some kind of > hydrophobic maping surfaces from atomic criteria ( charge, neighbours , > extension & shape of hydrophobic patch to account for cooperativity, > antitetrahedrality ...) and not only an empirical list for Amino acids as > my interest is in polysaccharides . > Possibly the question is ill defined . > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_GFQpvtkagVdEyZKSeymvjQ)" ++++------+------+------+------+------+------+------+------+------+------+ From: Ira Ropson Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Mon, 15 Dec 2003 08:04:27 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_GFQpvtkagVdEyZKSeymvjQ) On Friday, December 12, 2003, at 05:51 PM, Eric Martz wrote: > To All Educators Who Are Using Protein Explorer in Classes: > > I am reporting to NSF. If you have used PE in your class, please drop > me an email. NSF cares mostly about people in the USA, but I'm happy > to hear from educators elsewhere. > > Please tell me > > -name of class Biochemistry > -how many students 50 > -roughly how many hours of class time PE was used 3 hours > -used only in lecture, or also for hands-on student assignments Lecture only > > -your name Ira Ropson > -your institution, city, state Penn State University, Hershey, PA > > As the semester wraps up, please consider handing out the short > one-page Student Assessment of Learning Gains (SALG) form available at > http://molvis.sdsc.edu/protexpl/evalppr.htm > > This will only take about 5 minutes of class time and the results will > be > very useful to us. > > Thanks, -Eric Martz > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: > http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > > Ira Ropson, Associate Professor Department of Biochemistry and Molecular Biology 500 University Drive Penn State University Hershey, PA 17033 Office: (717)531-4064 Fax: (717)531-7072 email: iropson@psu.edu http://fred.hmc.psu.edu/faculty/iropson This message (including any attachments) contains information intended for a specific individual(s) and purpose that may be privileged, confidential or otherwise protected from disclosure pursuant to applicable law. Any inappropriate use, distribution or copying of the message is strictly prohibited and may subject you to criminal or civil penalty. If you have received this transmission in error, please reply to the sender indicating this error and delete the transmission from your system immediately. --Boundary_(ID_GFQpvtkagVdEyZKSeymvjQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_GFQpvtkagVdEyZKSeymvjQ)-- X-RAVMilter-Version: 8.4.3(snapshot 20030212) (nott.union.edu) References: <5.2.0.9.2.20031212173822.00ab9ec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Kristin Fox Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Mon, 15 Dec 2003 08:53:11 -0500 To: rasmol@lists.umass.edu Eric, I am not sure if you are referring to Fall classes only. I have in the past and will use PE in a winter term class. I plan to do the SALG after this year's class. Biochemistry: Structure and Catalysis 24 students 3 hours lecture/6 hours by students used in lecture and for student assignments Kristin M. Fox Union College, Schenectady, NY >To All Educators Who Are Using Protein Explorer in Classes: > >I am reporting to NSF. If you have used PE in your class, please drop >me an email. NSF cares mostly about people in the USA, but I'm happy >to hear from educators elsewhere. > >Please tell me > >-name of class >-how many students >-roughly how many hours of class time PE was used >-used only in lecture, or also for hands-on student assignments > >-your name >-your institution, city, state > >As the semester wraps up, please consider handing out the short >one-page Student Assessment of Learning Gains (SALG) form available at >http://molvis.sdsc.edu/protexpl/evalppr.htm > >This will only take about 5 minutes of class time and the results will be >very useful to us. > >Thanks, -Eric Martz > > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor (Immunology), Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > -- Kristin M. Fox Phone: (518)388-6250 Associate Professor of Chemistry FAX: (518)388-6795 Director of Biochemistry Email: foxk@union.edu Union College 807 Union Street Schenectady, NY 12308 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Proposed insertion code syntax Date: Mon, 15 Dec 2003 20:41:40 +0100 (CET) To: rasmol@lists.umass.edu Request For Comments: Proposed insertion code syntax ==================================================== The Jmol project is proposing a syntax extension to the Atom Expression component of the RasMol scripting language. We are requesting feedback from the user community to ensure that this syntax extension: - does not conflict with other existing or future implementations of the RasMol scripting language - does not break existing scripts - meets the needs of the user community Summary ======= The Jmol Project proposes using the ^ (caret) character followed by a single case-sensitive character as the syntax for identifying insertion codes: select 1^A select 1^Z-1^A select 0^B select -1^A--2^Z Detail ====== The PDB File Format Specification identifies groups (residues) by a sequence number and an optional insertion code. The sequence number is a signed integer value. The insertion code is a single character field. The insertion code field is usually a ' ' (space) character. However, the specification indicates that it may also be in the ranges A-Z,a-z. The combination of a 'sequence number' and the 'insertion code' forms a unique group identifier within a chain. In this document we will refer to the combined 'sequence number' + 'insertion code' as a *sequence code*. Sequence codes are considered unique identifiers for groups. No assumptions are made about sequence code ordering. The RasMol scripting language supports integer group number specifications in atom expressions. However, there is no syntatical support for insertion codes. Therefore, a full/unique sequence code cannot be specified. We need to extend the atom expression syntax to allow unique specification of sequence codes. Potential conflict with chain specification ------------------------------------------- The natural extension to the atom expression language would be to allow the addition of an alpha character after an integer value ... as in: select 1A However, the current RasMol parser allows this 'relaxed' syntax as an alternate form for the more formal chain specification syntax select 1:A Therefore, we must reject this syntax in order to maintain compatibility with existing RasMol/Chime scripts. We propose using the ^ caret character followed by a single case-sensitive character as the insertion code specification. This will allow full specification of a unique sequence code ... as in: select 1^A This syntax would (of course) be allowed in all contexts where a group number specification is currently accepted, including range specifications: select 1^A-99^Z And could (of course) be combined with other expression specifications: select [HIS]84^D:A.CA/1 Optional ^ ---------- If the ^ (caret) and insertion code are missing then it is assumed that the sequence code consists of sequence number followed by the ' ' (space) insertion code No whitespace ------------- The ^ (caret) and insertion code specification must immediately follow the integer sequence number value. No white space characters are allowed either before or after the ^ (caret). Single character A-Z,a-z ------------------------ The insertion code specification must be a single character in the range A-Z or a-z. Note that the insertion code with value ' ' cannot be specified with a ^ (caret) followed by a ' ' (space) character. Instead, the ^ (caret) should be dropped. Case sensitivity ---------------- The PDB format specification indicates that lower case letters are acceptable (although probably none exist in current .pdb files). Therefore, sequence codes must be specified with a single case-sensitive character. select 1^A does *not* select the same residue as select 1^a No wildcards ------------ The wildcard character is not accepted in this context. No assumptions can be made about collating sequence of sequence codes, so wildcards are not appropriate. The range specification should be used instead. Feedback appreciated ==================== If you have read this far, you must have *some* thoughts :-) Please post feedback to rasmol@lists.umass.edu -------------------------------------------------- Miguel Howard miguel@howards.org c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- -------------------------------------------------- Miguel Howard miguel@howards.org c/Peña Primera 11-13 esc dcha 6B 37002 Salamanca España Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from 8bit to quoted-printable by mail.mrc-dunn.cam.ac.uk id hBFK44R30334 Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <40268.80.58.16.235.1071517300.squirrel@www.howards.org> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id hBFK0hh24154 ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Proposed insertion code syntax Date: Mon, 15 Dec 2003 19:23:08 +0000 (GMT) To: rasmol@lists.umass.edu Cc: mth@mth.com Who uses insert codes in this modern day and age? I mean for practical purposes, rather than for structure submission / historical consistency? I would *happily* do away with them for all time, but then again they do say ignorance is bliss. ++ Miguel Howard-- > Request For Comments: Proposed insertion code syntax > ==================================================The Jmol project is proposing a > syntax extension to the Atom Expression component of the RasMol scripting > language. > > We are requesting feedback from the user community to ensure that this syntax > extension: > - does not conflict with other existing or future > implementations of the RasMol scripting language > - does not break existing scripts > - meets the needs of the user community > > > Summary > =====The Jmol Project proposes using the ^ (caret) character followed by a single > case-sensitive character as the syntax for identifying insertion codes: > > select 1^A > select 1^Z-1^A > select 0^B > select -1^A--2^Z > > > Detail > =====The PDB File Format Specification identifies groups (residues) by a sequence > number and an optional insertion code. The sequence number is a signed integer > value. The insertion code is a single character field. The insertion code field is > usually a ' ' (space) character. However, the specification indicates that it may > also be in the ranges A-Z,a-z. > > The combination of a 'sequence number' and the 'insertion code' forms a unique > group identifier within a chain. In this document we will refer to the combined > 'sequence number' + 'insertion code' as a *sequence code*. Sequence codes are > considered unique identifiers for groups. No assumptions are made about sequence > code ordering. > > The RasMol scripting language supports integer group number > specifications in atom expressions. However, there is no syntatical support for > insertion codes. Therefore, a full/unique sequence code cannot be specified. > > We need to extend the atom expression syntax to allow unique specification of > sequence codes. > > > Potential conflict with chain specification > ------------------------------------------- > The natural extension to the atom expression language would be to allow the > addition of an alpha character after an integer value ... as in: > select 1A > > However, the current RasMol parser allows this 'relaxed' syntax as an alternate > form for the more formal chain specification syntax > select 1:A > > Therefore, we must reject this syntax in order to maintain compatibility with > existing RasMol/Chime scripts. > > We propose using the ^ caret character followed by a single > case-sensitive character as the insertion code specification. This will allow full > specification of a unique sequence code ... as in: > select 1^A > > This syntax would (of course) be allowed in all contexts where a group number > specification is currently accepted, including range > specifications: > select 1^A-99^Z > > And could (of course) be combined with other expression specifications: > select [HIS]84^D:A.CA/1 > > > Optional ^ > ---------- > If the ^ (caret) and insertion code are missing then it is assumed that the > sequence code consists of sequence number followed by the ' ' > (space) insertion code > > No whitespace > ------------- > The ^ (caret) and insertion code specification must immediately follow the integer > sequence number value. No white space characters are allowed either before or > after the ^ (caret). > > Single character A-Z,a-z > ------------------------ > The insertion code specification must be a single character in the range A-Z or > a-z. Note that the insertion code with value ' ' cannot be > specified with a ^ (caret) followed by a ' ' (space) character. Instead, the ^ > (caret) should be dropped. > > Case sensitivity > ---------------- > The PDB format specification indicates that lower case letters are acceptable > (although probably none exist in current .pdb files). > Therefore, sequence codes must be specified with a single case-sensitive > character. > select 1^A > does *not* select the same residue as > select 1^a > > No wildcards > ------------ > The wildcard character is not accepted in this context. No assumptions can be made > about collating sequence of sequence codes, so wildcards are not appropriate. The > range specification should be used instead. > > > Feedback appreciated > ===================If you have read this far, you must have *some* thoughts :-) > > Please post feedback to rasmol@lists.umass.edu > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US home 011 34 923 27 10 82 12:00 > noon Eastern US cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US home 011 34 923 27 10 82 12:00 > noon Eastern US cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > ----------------------------------------------------------------rasmol-+ > > To change your address, unsubscribe, view previous messages/history, receive > messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ----------------------------------------------------------------rasmol-- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: fcb@epsilon.pair.com X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id hBFK3gh24376 ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: Proposed insertion code syntax Date: Mon, 15 Dec 2003 15:02:04 -0500 (EST) To: rasmol@lists.umass.edu It would be prudent for someone to check all entries to make sure that all insertion codes are, in fact, alphabetic. I would not be surprised if a numeric character has been used as an insertion code in one or more entries although the format document says that it must be alphabetic. If my suspicions are correct, then a policy decision must be made whether the format description should be changed or whether those entries must be revised. Frances ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Mon, 15 Dec 2003, Miguel Howard wrote: > Request For Comments: Proposed insertion code syntax > ==================================================== > > The Jmol project is proposing a syntax extension to the Atom Expression > component of the RasMol scripting language. > > We are requesting feedback from the user community to ensure that this > syntax extension: > - does not conflict with other existing or future > implementations of the RasMol scripting language > - does not break existing scripts > - meets the needs of the user community > > > Summary > ======= > > The Jmol Project proposes using the ^ (caret) character followed by a > single case-sensitive character as the syntax for identifying insertion > codes: > > select 1^A > select 1^Z-1^A > select 0^B > select -1^A--2^Z > > > Detail > ====== > The PDB File Format Specification identifies groups (residues) by a > sequence number and an optional insertion code. The sequence number is a > signed integer value. The insertion code is a single character field. > The insertion code field is usually a ' ' (space) character. However, > the specification indicates that it may also be in the ranges A-Z,a-z. > > The combination of a 'sequence number' and the 'insertion code' forms a > unique group identifier within a chain. In this document we will refer > to the combined 'sequence number' + 'insertion code' as a *sequence > code*. Sequence codes are considered unique identifiers for groups. No > assumptions are made about sequence code ordering. > > The RasMol scripting language supports integer group number > specifications in atom expressions. However, there is no syntatical > support for insertion codes. Therefore, a full/unique sequence code > cannot be specified. > > We need to extend the atom expression syntax to allow unique specification > of sequence codes. > > > Potential conflict with chain specification > ------------------------------------------- > The natural extension to the atom expression language would be to allow > the addition of an alpha character after an integer value ... as in: > select 1A > > However, the current RasMol parser allows this 'relaxed' syntax as an > alternate form for the more formal chain specification syntax > select 1:A > > Therefore, we must reject this syntax in order to maintain compatibility > with existing RasMol/Chime scripts. > > We propose using the ^ caret character followed by a single > case-sensitive character as the insertion code specification. This will > allow full specification of a unique sequence code ... as in: > select 1^A > > This syntax would (of course) be allowed in all contexts where a group > number specification is currently accepted, including range > specifications: > select 1^A-99^Z > > And could (of course) be combined with other expression specifications: > select [HIS]84^D:A.CA/1 > > > Optional ^ > ---------- > If the ^ (caret) and insertion code are missing then it is assumed that > the sequence code consists of sequence number followed by the ' ' > (space) insertion code > > No whitespace > ------------- > The ^ (caret) and insertion code specification must immediately follow > the integer sequence number value. No white space characters are allowed > either before or after the ^ (caret). > > Single character A-Z,a-z > ------------------------ > The insertion code specification must be a single character in the range > A-Z or a-z. Note that the insertion code with value ' ' cannot be > specified with a ^ (caret) followed by a ' ' (space) character. Instead, > the ^ (caret) should be dropped. > > Case sensitivity > ---------------- > The PDB format specification indicates that lower case letters are > acceptable (although probably none exist in current .pdb files). > Therefore, sequence codes must be specified with a single case-sensitive > character. > select 1^A > does *not* select the same residue as > select 1^a > > No wildcards > ------------ > The wildcard character is not accepted in this context. No assumptions > can be made about collating sequence of sequence codes, so wildcards are > not appropriate. The range specification should be used instead. > > > Feedback appreciated > ==================== > If you have read this far, you must have *some* thoughts :-) > > Please post feedback to rasmol@lists.umass.edu > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id hBFKBSh24938 ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Proposed insertion code syntax Date: Mon, 15 Dec 2003 14:10:48 -0600 (CST) To: rasmol@lists.umass.edu Hi, This is isn't my area at all so I really have no clue :-). But ^ is a poor choice. The symbol ^ is used in regular expressions and regular expressions should be present (if they are not already) as an option to select residues. Regards Bruce On Mon, 15 Dec 2003, Miguel Howard wrote: > Request For Comments: Proposed insertion code syntax > ==================================================== > > The Jmol project is proposing a syntax extension to the Atom Expression > component of the RasMol scripting language. > > We are requesting feedback from the user community to ensure that this > syntax extension: > - does not conflict with other existing or future > implementations of the RasMol scripting language > - does not break existing scripts > - meets the needs of the user community > > > Summary > ======= > > The Jmol Project proposes using the ^ (caret) character followed by a > single case-sensitive character as the syntax for identifying insertion > codes: > > select 1^A > select 1^Z-1^A > select 0^B > select -1^A--2^Z > > > Detail > ====== > The PDB File Format Specification identifies groups (residues) by a > sequence number and an optional insertion code. The sequence number is a > signed integer value. The insertion code is a single character field. > The insertion code field is usually a ' ' (space) character. However, > the specification indicates that it may also be in the ranges A-Z,a-z. > > The combination of a 'sequence number' and the 'insertion code' forms a > unique group identifier within a chain. In this document we will refer > to the combined 'sequence number' + 'insertion code' as a *sequence > code*. Sequence codes are considered unique identifiers for groups. No > assumptions are made about sequence code ordering. > > The RasMol scripting language supports integer group number > specifications in atom expressions. However, there is no syntatical > support for insertion codes. Therefore, a full/unique sequence code > cannot be specified. > > We need to extend the atom expression syntax to allow unique specification > of sequence codes. > > > Potential conflict with chain specification > ------------------------------------------- > The natural extension to the atom expression language would be to allow > the addition of an alpha character after an integer value ... as in: > select 1A > > However, the current RasMol parser allows this 'relaxed' syntax as an > alternate form for the more formal chain specification syntax > select 1:A > > Therefore, we must reject this syntax in order to maintain compatibility > with existing RasMol/Chime scripts. > > We propose using the ^ caret character followed by a single > case-sensitive character as the insertion code specification. This will > allow full specification of a unique sequence code ... as in: > select 1^A > > This syntax would (of course) be allowed in all contexts where a group > number specification is currently accepted, including range > specifications: > select 1^A-99^Z > > And could (of course) be combined with other expression specifications: > select [HIS]84^D:A.CA/1 > > > Optional ^ > ---------- > If the ^ (caret) and insertion code are missing then it is assumed that > the sequence code consists of sequence number followed by the ' ' > (space) insertion code > > No whitespace > ------------- > The ^ (caret) and insertion code specification must immediately follow > the integer sequence number value. No white space characters are allowed > either before or after the ^ (caret). > > Single character A-Z,a-z > ------------------------ > The insertion code specification must be a single character in the range > A-Z or a-z. Note that the insertion code with value ' ' cannot be > specified with a ^ (caret) followed by a ' ' (space) character. Instead, > the ^ (caret) should be dropped. > > Case sensitivity > ---------------- > The PDB format specification indicates that lower case letters are > acceptable (although probably none exist in current .pdb files). > Therefore, sequence codes must be specified with a single case-sensitive > character. > select 1^A > does *not* select the same residue as > select 1^a > > No wildcards > ------------ > The wildcard character is not accepted in this context. No assumptions > can be made about collating sequence of sequence codes, so wildcards are > not appropriate. The range specification should be used instead. > > > Feedback appreciated > ==================== > If you have read this far, you must have *some* thoughts :-) > > Please post feedback to rasmol@lists.umass.edu > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > -------------------------------------------------- > Miguel Howard miguel@howards.org > c/Peña Primera 11-13 esc dcha 6B > 37002 Salamanca > España Spain > -------------------------------------------------- > telefono casa 923 27 10 82 movil 650 52 54 58 > -------------------------------------------------- > To call from the US dial 9:00 am Pacific US = > home 011 34 923 27 10 82 12:00 noon Eastern US = > cell 011 34 650 52 54 58 6:00 pm Spain > -------------------------------------------------- > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Proposed insertion code syntax Date: Mon, 15 Dec 2003 18:26:42 -0500 To: rasmol@lists.umass.edu at 2.10p EDT on 2003 December 15 Monday southey@ux1.cso.uiuc.edu said: > Hi, > > This is isn't my area at all so I really have no clue :-). But ^ is a poor > choice. The symbol ^ is used in regular expressions and regular > expressions should be present (if they are not already) as an option to > select residues. > > Regards > Bruce > > hi Bruce, I knew someone was going to bring that up. ;-) I supported using the carat knowing it is useful in regex; unfortunately, so were all of the options. to make matters worse, many of the others were integral perl symbols as well, which I thought made them even less desirable. also, the carat implies an editor's insertion point, which makes it somewhat memorable as an indicator of insertion codes. hopefully, grep expressions can escape the carat if you need to search by insertion code. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > On Mon, 15 Dec 2003, Miguel Howard wrote: > > > Request For Comments: Proposed insertion code syntax > > ==================================================== > > > > The Jmol project is proposing a syntax extension to the Atom Expression > > component of the RasMol scripting language. > > > > We are requesting feedback from the user community to ensure that this > > syntax extension: > > - does not conflict with other existing or future > > implementations of the RasMol scripting language > > - does not break existing scripts > > - meets the needs of the user community > > > > > > Summary > > ======= > > > > The Jmol Project proposes using the ^ (caret) character followed by a > > single case-sensitive character as the syntax for identifying insertion > > codes: > > > > select 1^A > > select 1^Z-1^A > > select 0^B > > select -1^A--2^Z > > > > > > Detail > > ====== > > The PDB File Format Specification identifies groups (residues) by a > > sequence number and an optional insertion code. The sequence number is a > > signed integer value. The insertion code is a single character field. > > The insertion code field is usually a ' ' (space) character. However, > > the specification indicates that it may also be in the ranges A-Z,a-z. > > > > The combination of a 'sequence number' and the 'insertion code' forms a > > unique group identifier within a chain. In this document we will refer > > to the combined 'sequence number' + 'insertion code' as a *sequence > > code*. Sequence codes are considered unique identifiers for groups. No > > assumptions are made about sequence code ordering. > > > > The RasMol scripting language supports integer group number > > specifications in atom expressions. However, there is no syntatical > > support for insertion codes. Therefore, a full/unique sequence code > > cannot be specified. > > > > We need to extend the atom expression syntax to allow unique specification > > of sequence codes. > > > > > > Potential conflict with chain specification > > ------------------------------------------- > > The natural extension to the atom expression language would be to allow > > the addition of an alpha character after an integer value ... as in: > > select 1A > > > > However, the current RasMol parser allows this 'relaxed' syntax as an > > alternate form for the more formal chain specification syntax > > select 1:A > > > > Therefore, we must reject this syntax in order to maintain compatibility > > with existing RasMol/Chime scripts. > > > > We propose using the ^ caret character followed by a single > > case-sensitive character as the insertion code specification. This will > > allow full specification of a unique sequence code ... as in: > > select 1^A > > > > This syntax would (of course) be allowed in all contexts where a group > > number specification is currently accepted, including range > > specifications: > > select 1^A-99^Z > > > > And could (of course) be combined with other expression specifications: > > select [HIS]84^D:A.CA/1 > > > > > > Optional ^ > > ---------- > > If the ^ (caret) and insertion code are missing then it is assumed that > > the sequence code consists of sequence number followed by the ' ' > > (space) insertion code > > > > No whitespace > > ------------- > > The ^ (caret) and insertion code specification must immediately follow > > the integer sequence number value. No white space characters are allowed > > either before or after the ^ (caret). > > > > Single character A-Z,a-z > > ------------------------ > > The insertion code specification must be a single character in the range > > A-Z or a-z. Note that the insertion code with value ' ' cannot be > > specified with a ^ (caret) followed by a ' ' (space) character. Instead, > > the ^ (caret) should be dropped. > > > > Case sensitivity > > ---------------- > > The PDB format specification indicates that lower case letters are > > acceptable (although probably none exist in current .pdb files). > > Therefore, sequence codes must be specified with a single case-sensitive > > character. > > select 1^A > > does *not* select the same residue as > > select 1^a > > > > No wildcards > > ------------ > > The wildcard character is not accepted in this context. No assumptions > > can be made about collating sequence of sequence codes, so wildcards are > > not appropriate. The range specification should be used instead. > > > > > > Feedback appreciated > > ==================== > > If you have read this far, you must have *some* thoughts :-) > > > > Please post feedback to rasmol@lists.umass.edu > > > > > > -------------------------------------------------- > > Miguel Howard miguel@howards.org > > c/PeÃ’a Primera 11-13 esc dcha 6B > > 37002 Salamanca > > EspaÃ’a Spain > > -------------------------------------------------- > > telefono casa 923 27 10 82 movil 650 52 54 58 > > -------------------------------------------------- > > To call from the US dial 9:00 am Pacific US = > > home 011 34 923 27 10 82 12:00 noon Eastern US = > > cell 011 34 650 52 54 58 6:00 pm Spain > > -------------------------------------------------- > > > > > > -------------------------------------------------- > > Miguel Howard miguel@howards.org > > c/PeÃ’a Primera 11-13 esc dcha 6B > > 37002 Salamanca > > EspaÃ’a Spain > > -------------------------------------------------- > > telefono casa 923 27 10 82 movil 650 52 54 58 > > -------------------------------------------------- > > To call from the US dial 9:00 am Pacific US = > > home 011 34 923 27 10 82 12:00 noon Eastern US = > > cell 011 34 650 52 54 58 6:00 pm Spain > > -------------------------------------------------- > > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Proposed insertion code syntax Date: Mon, 15 Dec 2003 23:11:06 -0500 To: rasmol@lists.umass.edu I would suggest we use the residue number and insertion code as written in the entry, as in > select 1A > select 1Z-1A > select 0B > select -1A--2Z When residues in a particular chain are required, a colon would be used, as is now required for numeric chain identifiers. This would create an incompatibility with the existing script language. We could resolve that by providing a mode switch: icode on icode off When icodes are enabled, a trailing letter on a residue number would be an insertion code. When icodes are disabled, a trailing letter on a residue number could be interpreted as a chain identifier as at present. I know this is not a neat solution, but it allows existing scripts to run as intended, while allowing new scripts to be written that can be sensitive to insertion codes, without the need for yet another cryptic flag character. -- Herbert At 2:10 PM -0600 12/15/03, southey@ux1.cso.uiuc.edu wrote: >Hi, > >This is isn't my area at all so I really have no clue :-). But ^ is a poor >choice. The symbol ^ is used in regular expressions and regular >expressions should be present (if they are not already) as an option to >select residues. > >Regards >Bruce > > >On Mon, 15 Dec 2003, Miguel Howard wrote: > >> Request For Comments: Proposed insertion code syntax >> ==================================================== >> >> The Jmol project is proposing a syntax extension to the Atom Expression >> component of the RasMol scripting language. >> >> We are requesting feedback from the user community to ensure that this >> syntax extension: >> - does not conflict with other existing or future >> implementations of the RasMol scripting language >> - does not break existing scripts >> - meets the needs of the user community >> >> >> Summary >> ======= >> >> The Jmol Project proposes using the ^ (caret) character followed by a >> single case-sensitive character as the syntax for identifying insertion >> codes: >> > > select 1^A >> select 1^Z-1^A >> select 0^B >> select -1^A--2^Z > > >> >> Detail >> ====== >> The PDB File Format Specification identifies groups (residues) by a >> sequence number and an optional insertion code. The sequence number is a >> signed integer value. The insertion code is a single character field. >> The insertion code field is usually a ' ' (space) character. However, >> the specification indicates that it may also be in the ranges A-Z,a-z. >> >> The combination of a 'sequence number' and the 'insertion code' forms a >> unique group identifier within a chain. In this document we will refer >> to the combined 'sequence number' + 'insertion code' as a *sequence >> code*. Sequence codes are considered unique identifiers for groups. No >> assumptions are made about sequence code ordering. >> >> The RasMol scripting language supports integer group number >> specifications in atom expressions. However, there is no syntatical >> support for insertion codes. Therefore, a full/unique sequence code >> cannot be specified. >> >> We need to extend the atom expression syntax to allow unique specification >> of sequence codes. >> >> >> Potential conflict with chain specification >> ------------------------------------------- >> The natural extension to the atom expression language would be to allow >> the addition of an alpha character after an integer value ... as in: >> select 1A >> >> However, the current RasMol parser allows this 'relaxed' syntax as an > > alternate form for the more formal chain specification syntax > > select 1:A > > > > Therefore, we must reject this syntax in order to maintain compatibility > > with existing RasMol/Chime scripts. >> >> We propose using the ^ caret character followed by a single >> case-sensitive character as the insertion code specification. This will >> allow full specification of a unique sequence code ... as in: >> select 1^A >> >> This syntax would (of course) be allowed in all contexts where a group >> number specification is currently accepted, including range > > specifications: >> select 1^A-99^Z >> >> And could (of course) be combined with other expression specifications: >> select [HIS]84^D:A.CA/1 >> >> >> Optional ^ >> ---------- >> If the ^ (caret) and insertion code are missing then it is assumed that >> the sequence code consists of sequence number followed by the ' ' >> (space) insertion code >> >> No whitespace >> ------------- >> The ^ (caret) and insertion code specification must immediately follow >> the integer sequence number value. No white space characters are allowed >> either before or after the ^ (caret). >> >> Single character A-Z,a-z >> ------------------------ >> The insertion code specification must be a single character in the range >> A-Z or a-z. Note that the insertion code with value ' ' cannot be >> specified with a ^ (caret) followed by a ' ' (space) character. Instead, >> the ^ (caret) should be dropped. >> >> Case sensitivity >> ---------------- >> The PDB format specification indicates that lower case letters are >> acceptable (although probably none exist in current .pdb files). >> Therefore, sequence codes must be specified with a single case-sensitive >> character. >> select 1^A >> does *not* select the same residue as >> select 1^a >> >> No wildcards >> ------------ >> The wildcard character is not accepted in this context. No assumptions >> can be made about collating sequence of sequence codes, so wildcards are >> not appropriate. The range specification should be used instead. >> >> >> Feedback appreciated >> ==================== >> If you have read this far, you must have *some* thoughts :-) >> >> Please post feedback to rasmol@lists.umass.edu >> >> >> -------------------------------------------------- >> Miguel Howard miguel@howards.org >> c/PeÒa Primera 11-13 esc dcha 6B >> 37002 Salamanca >> EspaÒa Spain >> -------------------------------------------------- >> telefono casa 923 27 10 82 movil 650 52 54 58 >> -------------------------------------------------- >> To call from the US dial 9:00 am Pacific US = >> home 011 34 923 27 10 82 12:00 noon Eastern US = >> cell 011 34 650 52 54 58 6:00 pm Spain >> -------------------------------------------------- >> >> >> -------------------------------------------------- >> Miguel Howard miguel@howards.org >> c/PeÒa Primera 11-13 esc dcha 6B >> 37002 Salamanca >> EspaÒa Spain >> -------------------------------------------------- >> telefono casa 923 27 10 82 movil 650 52 54 58 >> -------------------------------------------------- >> To call from the US dial 9:00 am Pacific US = >> home 011 34 923 27 10 82 12:00 noon Eastern US = >> cell 011 34 650 52 54 58 6:00 pm Spain >> -------------------------------------------------- >> >> >> > > > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Proposed insertion code syntax Date: Mon, 15 Dec 2003 22:44:51 -0800 To: rasmol@lists.umass.edu > icode on > icode off Still never ending storing. Why not introducing a magic tag to make sure that a script file is a rasmol script and a versioning system to solve the problem of keyword evolution once for all. RasTop uses the magic word #!rasmol at the begining of a script. This tag was already found in many scripts. We could have something like: #!rasmol -version 3.0 at start to indicate that a file is a rasmol script and it is using the keywords version 3.0. By default, absence of tag indicates scripting such as in the 2.7.1 series. This may sound a bit heavy on the scripting side, but it simplifies a lot of issues. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en X-AntiVirus: checked by Vexira MailArmor (version: 2.0.1.16; VAE: 6.23.0.1; VDF: 6.23.0.2; host: postbode02.zonnet.nl) References: <5.2.0.9.2.20031212173822.00ab9ec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Anton Feenstra Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Tue, 16 Dec 2003 08:44:28 +0100 To: rasmol@lists.umass.edu Eric Martz wrote: > To All Educators Who Are Using Protein Explorer in Classes: > > I am reporting to NSF. If you have used PE in your class, please drop > me an email. NSF cares mostly about people in the USA, but I'm happy > to hear from educators elsewhere. Would I be to much of a nitpicker if I took this opportunity to mention that, after playing around myself with PE, I reverted back to rasmol for my students to use? This was in the context of a 3rd year biochemistry course 'Structural Biology' and intended to let them get some 'hands-on' experience with protein structures. The main reason against using PE was the number of not directly relevant options; all features of protein structures I wanted to illustrate, I found could be readily shown using the simple menu options of rasmol. Please note I do not mean this as a ruse against PE, IMHO it is a good successor to rasmol, but it simply did not fit the objectives of this particular course as well as simple plain rasmol did. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra@chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <40268.80.58.16.235.1071517300.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 09:40:22 +0100 (CET) To: rasmol@lists.umass.edu > It would be prudent for someone to check all entries > to make sure that all insertion codes are, in fact, alphabetic. That sounds like a good idea. Unfortunately, I don't have a mirror nor a tool set/test harness set up for doing this kind of work. If someone has an environment set up and could collect some simple statistics about insertion codes it would be helpful. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 10:43:17 +0100 To: rasmol@lists.umass.edu Herbert J. Bernstein wrote: > I would suggest we use the residue number and insertion code > as written in the entry, as in > >> select 1A >> select 1Z-1A >> select 0B >> select -1A--2Z > I agree, changing old scripts with $expression=~s/(\d+)([a-z])(?!\])\b/$1:$2/ig would be easy > > When residues in a particular chain are required, a colon would be > used, as is now required for numeric chain identifiers. This would > create an incompatibility with the existing script language. We could > resolve that by providing a mode switch: > > icode on > icode off good idea, and alternatively a new implementation of the version parameter as Philippe suggested would be nice, because this is the header of the script. (stop execution of RasMol if the value of the version parameter is less than the value given). > > When icodes are enabled, a trailing letter on a residue number would > be an insertion code. When icodes are disabled, a trailing letter on > a residue number could be interpreted as a chain identifier as at > present. > > I know this is not a neat solution, but it allows existing scripts to run > as intended, while allowing new scripts to be written that can be > sensitive to insertion codes, without the need for yet another cryptic > flag character. > > -- Herbert > > > At 2:10 PM -0600 12/15/03, southey@ux1.cso.uiuc.edu wrote: > >> Hi, >> >> This is isn't my area at all so I really have no clue :-). But ^ is a >> poor >> choice. The symbol ^ is used in regular expressions and regular >> expressions should be present (if they are not already) as an option to >> select residues. >> >> Regards >> Bruce >> >> >> On Mon, 15 Dec 2003, Miguel Howard wrote: >> >>> Request For Comments: Proposed insertion code syntax >>> ==================================================== >>> >>> The Jmol project is proposing a syntax extension to the Atom >>> Expression >>> component of the RasMol scripting language. >>> >>> We are requesting feedback from the user community to ensure that this >>> syntax extension: >>> - does not conflict with other existing or future >>> implementations of the RasMol scripting language >>> - does not break existing scripts >>> - meets the needs of the user community >>> >>> >>> Summary >>> ======= >>> >>> The Jmol Project proposes using the ^ (caret) character followed by a >>> single case-sensitive character as the syntax for identifying >>> insertion >>> codes: >>> >> > select 1^A >> >>> select 1^Z-1^A >>> select 0^B >>> select -1^A--2^Z >> >> > >> >>> >>> Detail >>> ====== >>> The PDB File Format Specification identifies groups (residues) by a >>> sequence number and an optional insertion code. The sequence number >>> is a >>> signed integer value. The insertion code is a single character field. >>> The insertion code field is usually a ' ' (space) character. However, >>> the specification indicates that it may also be in the ranges A-Z,a-z. >>> >>> The combination of a 'sequence number' and the 'insertion code' >>> forms a >>> unique group identifier within a chain. In this document we will refer >>> to the combined 'sequence number' + 'insertion code' as a *sequence >>> code*. Sequence codes are considered unique identifiers for groups. No >>> assumptions are made about sequence code ordering. >>> >>> The RasMol scripting language supports integer group number >>> specifications in atom expressions. However, there is no syntatical >>> support for insertion codes. Therefore, a full/unique sequence code >>> cannot be specified. >>> >>> We need to extend the atom expression syntax to allow unique >>> specification >>> of sequence codes. >>> >>> >>> Potential conflict with chain specification >>> ------------------------------------------- >>> The natural extension to the atom expression language would be to >>> allow >>> the addition of an alpha character after an integer value ... as in: >>> select 1A >>> >>> However, the current RasMol parser allows this 'relaxed' syntax as an >> >> > alternate form for the more formal chain specification syntax >> > select 1:A >> > >> > Therefore, we must reject this syntax in order to maintain >> compatibility >> > with existing RasMol/Chime scripts. >> >>> >>> We propose using the ^ caret character followed by a single >>> case-sensitive character as the insertion code specification. This >>> will >>> allow full specification of a unique sequence code ... as in: >>> select 1^A >>> >>> This syntax would (of course) be allowed in all contexts where a group >>> number specification is currently accepted, including range >> >> > specifications: >> >>> select 1^A-99^Z >>> >>> And could (of course) be combined with other expression >>> specifications: >>> select [HIS]84^D:A.CA/1 >>> >>> >>> Optional ^ >>> ---------- >>> If the ^ (caret) and insertion code are missing then it is assumed >>> that >>> the sequence code consists of sequence number followed by the ' ' >>> (space) insertion code >>> >>> No whitespace >>> ------------- >>> The ^ (caret) and insertion code specification must immediately follow >>> the integer sequence number value. No white space characters are >>> allowed >>> either before or after the ^ (caret). >>> >>> Single character A-Z,a-z >>> ------------------------ >>> The insertion code specification must be a single character in the >>> range >>> A-Z or a-z. Note that the insertion code with value ' ' cannot be >>> specified with a ^ (caret) followed by a ' ' (space) character. >>> Instead, >>> the ^ (caret) should be dropped. >>> >>> Case sensitivity >>> ---------------- >>> The PDB format specification indicates that lower case letters are >>> acceptable (although probably none exist in current .pdb files). >>> Therefore, sequence codes must be specified with a single >>> case-sensitive >>> character. >>> select 1^A >>> does *not* select the same residue as >>> select 1^a >>> >>> No wildcards >>> ------------ >>> The wildcard character is not accepted in this context. No assumptions >>> can be made about collating sequence of sequence codes, so >>> wildcards are >>> not appropriate. The range specification should be used instead. >> I would like to have wildcards. Regards, Jan >>> >>> >>> Feedback appreciated >>> ==================== >>> If you have read this far, you must have *some* thoughts :-) >>> >>> Please post feedback to rasmol@lists.umass.edu >>> >>> >>> -------------------------------------------------- >>> Miguel Howard miguel@howards.org >>> c/PeÒa Primera 11-13 esc dcha 6B >>> 37002 Salamanca >>> EspaÒa Spain >>> -------------------------------------------------- >>> telefono casa 923 27 10 82 movil 650 52 54 58 >>> -------------------------------------------------- >>> To call from the US dial 9:00 am Pacific US = >>> home 011 34 923 27 10 82 12:00 noon Eastern US = >>> cell 011 34 650 52 54 58 6:00 pm Spain >>> -------------------------------------------------- >>> >>> >>> -------------------------------------------------- >>> Miguel Howard miguel@howards.org >>> c/PeÒa Primera 11-13 esc dcha 6B >>> 37002 Salamanca >>> EspaÒa Spain >>> -------------------------------------------------- >>> telefono casa 923 27 10 82 movil 650 52 54 58 >>> -------------------------------------------------- >>> To call from the US dial 9:00 am Pacific US = >>> home 011 34 923 27 10 82 12:00 noon Eastern US = >>> cell 011 34 650 52 54 58 6:00 pm Spain >>> -------------------------------------------------- >>> >>> >>> >> >> >> > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 04:55:14 -0500 To: rasmol@lists.umass.edu at 11.11p EDT on 2003 December 15 Monday Herbert J. Bernstein said: > I would suggest we use the residue number and insertion code > as written in the entry, as in > > > select 1A > > select 1Z-1A > > select 0B > > select -1A--2Z > > When residues in a particular chain are required, a colon would be > used, as is now required for numeric chain identifiers. This would > create an incompatibility with the existing script language. We could > resolve that by providing a mode switch: > > icode on > icode off > I think this is a decent alternative to using the carat, but I still prefer the carat. for example, what if I call a script from within a script, and the internally-called script uses the "loose" chain syntax while the external script uses an icode reference? icode on select (1b-57) and :a script selectmystuff.spt # has one command: select 40-50a,40-50b color cpk spacefill this probably seems esoteric, but I have done this on occasion to globalize definitions or selected sets. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 07:03:58 -0500 (EST) To: rasmol@lists.umass.edu If we reset the icode mode (or the suggested rasmiol version) at the start of each script load, we should avoid the problem Timothy raises. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 16 Dec 2003, timothy driscoll wrote: > at 11.11p EDT on 2003 December 15 Monday Herbert J. Bernstein said: > > > I would suggest we use the residue number and insertion code > > as written in the entry, as in > > > > > select 1A > > > select 1Z-1A > > > select 0B > > > select -1A--2Z > > > > When residues in a particular chain are required, a colon would be > > used, as is now required for numeric chain identifiers. This would > > create an incompatibility with the existing script language. We could > > resolve that by providing a mode switch: > > > > icode on > > icode off > > > > I think this is a decent alternative to using the carat, but I still prefer > the carat. for example, what if I call a script from within a script, and > the internally-called script uses the "loose" chain syntax while the external > script uses an icode reference? > > icode on > select (1b-57) and :a > > script selectmystuff.spt > # has one command: select 40-50a,40-50b > > color cpk > spacefill > > this probably seems esoteric, but I have done this on occasion to globalize > definitions or selected sets. > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.0.9.2.20031212173822.00ab9ec0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Tue, 16 Dec 2003 10:23:34 -0500 To: rasmol@lists.umass.edu Thanks, Ilan. It is very impressive to know what you are doing! We have a script recorder within PE close to release (spring 2004). It enables an "un-do" button. We are evaluating Jmol (open source, java applet, all browsers, all platforms) as a replacement for Chime in PE. I will be retired from teaching immunology at UMass in January, 2004, so will have much more time for PE! Warm regards, -Eric At 12/14/03, you wrote: >Hi Eric, > >200 students > >Teaching bioinformatics at the TafniTech - Open University School for >Management of Technologies, Information & Computers. > >7 different courses were given. 170 students received a 1-2 hour >demonstration (out of a 60 hour 'introduction to bionformatics course) >with specific case studies discussed. 30 students received, as part of a >200-hour bioinformatics course, a 2-hour demo, a 4-hour hands-on in class, >and an ~8-hour homework assignment. At the end of the course, several >groups decided to use PE for the final project. > >The use of PE and case-studies for teaching was discussed in the latest >ISMB Workshop on Education as part of a presentation on bionfo teaching in >Israel: http://surya.bic.nus.edu.sg/web03/abstracts/samish.html > >Thanks for supplying us with this great freeware. > >Best regards, > >Ilan > >~~~~~~~~~~~~~~~~~ >Ilan Samish >Department of Plant Sciences >Weizmann Institute of Science >Rehovot, Israel >Lab: 972 8 9344300 >Cell: 972 53 321150 >Fax: 972 8 9344181 >ilan.samish@weizmann.ac.il >http://bioinformatics.weizmann.ac.il/~samish/ >================================= >Join us at the 1st Structural Bioinformatics Special Interest Group; >Satellite meeting of the ISMB conference. >http://3dsig.weizmann.ac.il/ > > > > >Eric Martz wrote: > >>To All Educators Who Are Using Protein Explorer in Classes: >> >>I am reporting to NSF. If you have used PE in your class, please drop >>me an email. NSF cares mostly about people in the USA, but I'm happy >>to hear from educators elsewhere. >> >>Please tell me >> >>-name of class >>-how many students >>-roughly how many hours of class time PE was used >>-used only in lecture, or also for hands-on student assignments >> >>-your name >>-your institution, city, state >> >>As the semester wraps up, please consider handing out the short >>one-page Student Assessment of Learning Gains (SALG) form available at >>http://molvis.sdsc.edu/protexpl/evalppr.htm >> >>This will only take about 5 minutes of class time and the results will be >>very useful to us. >> >>Thanks, -Eric Martz >> >> >> >>/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >>Protein Explorer - 3D Visualization: http://proteinexplorer.org >>Workshops: http://www.umass.edu/molvis/workshop >>World Index of Molecular Visualization Resources: http://molvisindex.org >>ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >>Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >>PDB Lite Macromolecule Finder: http://pdblite.org >>Molecular Visualization EMail List: >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >>Eric Martz, Professor (Immunology), Dept Microbiology >>U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 >> http://www.umass.edu/molvis/martz >>- - - - - - - - - - - - - - - - - - - - - - - - - - - */ >> >> > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 08:31:17 -0700 (MST) To: rasmol@lists.umass.edu On Tue, 16 Dec 2003, timothy driscoll wrote: > > I would suggest we use the residue number and insertion code > > as written in the entry, as in > > > > > select 1A > > > select 1Z-1A > > > select 0B > > > select -1A--2Z > > > > When residues in a particular chain are required, a colon would be > > used, as is now required for numeric chain identifiers. This would > > create an incompatibility with the existing script language. We could > > resolve that by providing a mode switch: > > > > icode on > > icode off > > > > I think this is a decent alternative to using the carat, but I still > prefer the carat. Only my 2 cents, but I also prefer the introduction of the caret as an insertion code prefix. Primarily both for backward compatability with the existing RasMol selection syntax, but also because the more commonly occuring expressions are easier to write. When deciding the semantics of "select 5a", its important to remember that the need to specify a chain is far more likely than to specify an insertion code, from the perspective of a user or student. Yes "select 5:a" is also the same, but the colon was introduced to avoid ambiguity with chain digits which are also rare. Much like the square brackets in "select [asp]" can be omitted if the residue name doesn't contain digits. The rule of thumb should be that the common cases are easy to remember. I even like the mnemonic of "^" as an editor's insertion point. The additional advantage of a "^" prefix, is that it can also handle the possibility of numeric insertion codes, which as Frances points out aren't intended to be part of the PDB file format, but which unfortunately have become a feature of the PDB-like files we have to deal with. The need for numeric chains and insertion codes, therefore requires both ":" and "^". Which is the default and can then be omitted for alphabetic values, seems to be an easy decision based upon frequency and compatability. Roger -- Roger Sayle, E-mail: roger@eyesopen.com OpenEye Scientific Software, WWW: http://www.eyesopen.com/ Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <40268.80.58.16.235.1071517300.squirrel@www.howards.org> <33301.212.128.142.25.1071564022.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 15:47:59 +0000 (GMT) To: rasmol@lists.umass.edu Cc: mth@mth.com ++ Miguel Howard-- > >> It would be prudent for someone to check all entries >> to make sure that all insertion codes are, in fact, alphabetic. > > That sounds like a good idea. > > Unfortunately, I don't have a mirror nor a tool set/test harness set up for doing > this kind of work. > > If someone has an environment set up and could collect some simple statistics > about insertion codes it would be helpful. I am back to squair one in this regard, I was waiting for the MSD RDB PDB (if that makes sense) but now I am building my own again... > > Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: Proposed insertion code syntax Date: Tue, 16 Dec 2003 08:30:23 -0800 To: rasmol@lists.umass.edu > I think this is a decent alternative to using the carat, but I still prefer > the carat. Do we really need the caret? Extra semi-colons should be able to remove any ambiguities. Compare the following examples, it is pretty self-explanatory: select 1A select 1:A select 1A: select 1A:A select 1A:-1Z: Philippe ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gerry Prody Subject: Re: Please Tell Me If You Teach With Protein Explorer Date: Tue, 16 Dec 2003 12:18:51 -0800 To: rasmol@lists.umass.edu I use it for Biochem (Chem 471) At 05:51 PM 12/12/2003 -0500, you wrote: >To All Educators Who Are Using Protein Explorer in Classes: > >I am reporting to NSF. If you have used PE in your class, please drop >me an email. NSF cares mostly about people in the USA, but I'm happy >to hear from educators elsewhere. > >Please tell me > >-name of class >-how many students >-roughly how many hours of class time PE was used >-used only in lecture, or also for hands-on student assignments > >-your name >-your institution, city, state > >As the semester wraps up, please consider handing out the short >one-page Student Assessment of Learning Gains (SALG) form available at >http://molvis.sdsc.edu/protexpl/evalppr.htm > >This will only take about 5 minutes of class time and the results will be >very useful to us. > >Thanks, -Eric Martz > > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor (Immunology), Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > Gerry A. Prody Associate Professor of Chemistry Western Washington University Bellingham, WA 98225-9150 360 650 3156 360 650 2826 fax ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- CHMINF-L@LISTSERV.INDIANA.EDU X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: VEGA1.5.1 release Date: Wed, 17 Dec 2003 09:33:20 +0100 To: rasmol@lists.umass.edu, pdb-l@rcsb.org, chemweb@ic.ac.uk, Dear all, We are proud to announce the release of VEGA1.5.1 release that is freely downloadable at www.ddl.unimi.it. Among the several new functions we would like to focus your attention on the capability to add the hydrogens, on the complete 3D molecular editor with fragment libraries and on the database engine. New features: - Chem3D loader. - Accelrys archive file (.arc) support in the trajectory analysis. - Capability to add the hydrogens. - RMSD calculation in the trajectory analysis. - CHARMM lipid and GRID force field templates. - POPC lipid bilayer cluster in crystal and solid phase. New OpenGL features: - ESCHER NG and ESCHER NG Plugin: protein-protein and DNA-protein docking system. - Database engine for directory, sdf and zip files. - Complete 3D molecular editor with fragment libraries. - Multiple workspaces. - Remove residue/s dialog box. - Molecule place dialog box. - Fix/merge molecules. - Multiple Mini Editor and Graph Editor windows. - Now the centroids can be updated dynamically or kept fixed. - The residue renumbering is now available for all atoms and for the selected atoms only. Best regards Giulio Vistoli & Alessandro Pedretti ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- CHMINF-L@LISTSERV.INDIANA.EDU X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Escher NG 1.0 release Date: Wed, 17 Dec 2003 09:34:15 +0100 To: rasmol@lists.umass.edu, pdb-l@rcsb.org, chemweb@ic.ac.uk, Dear all, We are proud to announce the release of Escher NG 1.0, freely downloadable at www.ddl.unimi.it ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich. The new release, with a reengineered code, includes some new features: - Protein-protein and DNA-protein docking capability. - Fast surface calculation based on the NSC algorithm. No external software are required. - Only two PDB files are required as input. - Parallel code. ESCHER NG is one of the first docking software that take full advantages of the multiprocessor hardware. Tested on two processor systems, ESCHER runs about 1.8 time faster than an equivalent single processor workstations (same CPU and same clock). These performances can be increased optimizing the code that was not originally developed to the parallel execution. ESCHER NG can run also on single processor systems in sequential mode. - Language localization. The Win32 version is included in the latest VEGA OpenGL package and in the full package we can find the source code and the executables for Win32, Irix6.2, Linux, AmigaOS. Best regards Giulio Vistoli and Alessandro Pedretti ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de, en-us, en References: <000901c3c3f1$e81dd630$fb07cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: Proposed insertion code syntax Date: Wed, 17 Dec 2003 10:13:08 +0100 To: rasmol@lists.umass.edu Philippe wrote: >>I think this is a decent alternative to using the carat, but I still >> >> >prefer > > >>the carat. >> >> > >Do we really need the caret? Extra semi-colons should be able to remove any >ambiguities. Compare the following examples, it is pretty self-explanatory: > >select 1A >select 1:A >select 1A: >select 1A:A >select 1A:-1Z: > >Philippe > > good idea, but in the current PDB there are some files with digit insertion codes 1bit 5tra 1g0u 1hzp I have asked RCSB whether they will alter the above files, and some format violations (no insertion codes, part of the residue number) in: 1bn9 1c5n 1gp8 2gp8 Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Proposed insertion code syntax Date: Thu, 18 Dec 2003 04:33:00 -0500 To: rasmol@lists.umass.edu, LIST Jmol users at 10.13a EDT on 2003 December 17 Wednesday Jan Reichert said: > Philippe wrote: > > > > >Do we really need the caret? Extra semi-colons should be able to > >remove any ambiguities. Compare the following examples, it is pretty > >self-explanatory: > > > >select 1A > >select 1:A > >select 1A: > >select 1A:A > >select 1A:-1Z: > > > >Philippe > > > > > good idea, but in the current PDB there are some files with digit > insertion codes > 1bit > 5tra > 1g0u > 1hzp > I have asked RCSB whether they will alter the above files, > good morning, since I am leaving on vacation for the holidays tomorrow, and I was partly responsible for starting this thread, I thought I would sum up my position and make a graceful exit. how graceful is debatable, of course. my opinion is that insertion codes are best indicated in scripts by preceding them with an identifier (ostensibly, the symbol ^). this identifier: - allows immediate visual recognition; - does not conflict with the existing (though undocumented) chain selection; - can handle numeric insertion codes in those instances where they arise. using extra colons is an unnecessary kludge, and much less visually intuitive than ^. for example, the extra mental processing step required to decipher the above list is not onerous, even at this hour, but hardly intuitive. and it becomes progressively harder in complex select commands. I believe the use of chains does, and will continue to far outweigh the use of insertion codes in scripting, and so the alternative syntax for chain selection should be supported. for all these reasons, I still suggest using ^ to indicate insertion codes, and maintaining the alternative chain selection syntax without modification. I think it is the best way to address all of the relevant issues. whether or not ^ is the most natural syntax to use for insertion codes; well, for some people it is, maybe not for others, and maybe some don't have a preference. in any case, I don't believe this should be the deciding factor that trumps ease of implementation, visual recognition, and avoiding conflict with existing conventions. happy holidays! :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: Proposed insertion code syntax Date: Thu, 18 Dec 2003 12:11:29 +0100 (CET) To: jmol-users@lists.sourceforge.net, rasmol@lists.umass.edu > since I am leaving on vacation for the holidays tomorrow, and I was > partly responsible for starting this thread, I thought I would sum up > my position and make a graceful exit. Since I am *primarily* responsible and since I am also going to be travelling ... I should do the same :-) I have not posted anything the last couple of days. In part because I have been busy and in large part because I don't have any vested interest one way or the other. I have never written any real RasMol scripts; I don't know what the usual coding standards are and I personally don't have any legacy scripts to support. Here are my thoughts and observations on various postings that were made: ^ conflicts with regular expressions ------------------------------------ This is not an issue. If there were some need to introduce regular expression pattern matching into the scripting language, then we would do so in an unambiguous context. icode on/off ------------ When I first read this proposal I was attracted to it. Because to me the expressions look much cleaner when the insertion code immediately follows the sequence number. (My initial implementation in Jmol operated in this way, and I was quite distressed when someone pointed out that this conflicted with the relaxed/non-colon chain specification syntax.) However, I don't like the idea of having this piece of 'state' as a 'mode setting' in the background. When reading an expression, it is another piece of state that one has to remember ... or forget. It would be better if the expression evaluation behavior was more context-free. The issue of 'subroutines' could certainly be addressed by putting the icode setting at the top of each file, but it is something else that would have to be done. #! version number header ------------------------ I don't think this is appropriate at this time. It implies that there will be other scripting language enhancements. I am not willing to start that discussion until Jmol is released and has 99.44% compatibility with existing Chime scripts. Roger Sayle's 2 cents --------------------- RAS indicated his preference for the ^ syntax. For me, that carries a lot of weight. Tim Driscoll's opinion ---------------------- Tim is actively helping me with Jmol ... *that* carries more weight that Roger :-) Numeric insertion codes ----------------------- This is *the* deciding factor. The fact is, there are entries in the PDB that have numeric insertion codes. (As a software engineer, my favorite is 1BIT :-) Therefore, some escape character is needed to separate the sequence number from the insertion code. I was not aware that these numeric insertion codes existed when I posted the request-for-comments ... the PDB File Format Spec says "A-Z,a-z". I must admit that I have had some second thoughts about having raised this issue. In hindsight, I wonder whether or not I should have stayed away from the 'insertion code' issue. The current goal for Jmol is RasMol/Chime compatibility ... to provide an upgrade path for existing Chime web applications. I chose to bring up the insertion code issue because it was easy for me to fix in the Jmol code and because someone asked me for it. And I thought that the syntax extension would be a good thing to put before the community. But the discussion on this topic has uncovered the fact that we have no formal mechanism to resolve differences of opinion and reach closure on an issue. In summary, I posted a "Request For Comments" and I received some very good and thoughtful comments ... but now I'm not sure what to do. I have the responsibility to follow up on what I started. I suppose that I need to post a final 'ruling', but that seems rather harsh and I'm not particularly comfortable doing it. So I'll put it off and do it next week :-) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Happy Holidays (and hope you're still here afterwards ...) Date: Thu, 18 Dec 2003 14:13:38 -0500 To: rasmol@lists.umass.edu Dear Subscribers to the Molecular Visualization Freeware ("RasMol") EMail List: Here's wishing you holiday greetings and a peaceful, healthy, and very happy new year! However, here is a little friendly word of advice. If you expect your email to go over quota during the holidays, expect to be unsubscribed from this list when you "get back". Alternatively, you can unsubscribe now, and re-subscribe when your email is under control again. To unsubscribe, send email to listproc@lists.umass.edu with only this one line in the BODY of the message: unsubscribe rasmol If you plan to resubscribe, bookmark http://www.umass.edu/microbio/rasmol/raslist.htm for use later. And you can always check what you missed at the on-line history at the same URL. I don't want to be unfriendly, but I am getting about 100 error messages from the list each day (many are spam-induced despite filters in place). If I don't analyze each one and unsubscribe the non-working or over-quota addresses, soon I'll be getting 200/day, and so forth. So even if your email account goes over quota for only a few days (bouncing your messages back to me), I may go ahead and unsubscribe you. Of course I can't politely inform you of that action since your email isn't working! Sincerely, Eric Martz ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6b) Gecko/20031208 X-Accept-Language: de, en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: Proposed insertion code syntax ^? Date: Thu, 18 Dec 2003 12:30:36 +0100 To: rasmol@lists.umass.edu timothy driscoll schrieb: >at 10.13a EDT on 2003 December 17 Wednesday Jan Reichert said: > > > >>Philippe wrote: >> >> >> >>>Do we really need the caret? Extra semi-colons should be able to >>>remove any ambiguities. Compare the following examples, it is pretty >>>self-explanatory: >>> >>>select 1A >>>select 1:A >>>select 1A: >>>select 1A:A >>>select 1A:-1Z: >>> >>>Philippe >>> >>> >>> >>> >>good idea, but in the current PDB there are some files with digit >>insertion codes >>1bit >>5tra >>1g0u >>1hzp >>I have asked RCSB whether they will alter the above files, >> >> >> > >good morning, > >since I am leaving on vacation for the holidays tomorrow, and I was partly >responsible for starting this thread, I thought I would sum up my position >and make a graceful exit. how graceful is debatable, of course. > >my opinion is that insertion codes are best indicated in scripts by preceding >them with an identifier (ostensibly, the symbol ^). this identifier: > >- allows immediate visual recognition; >- does not conflict with the existing (though undocumented) chain selection; >- can handle numeric insertion codes in those instances where they arise. > > I agree and hope that we (in fact, Herbert J. Bernstein, who actively manged and released the RasMol 2.7 :-) will make a final comment Regards, Jan >using extra colons is an unnecessary kludge, and much less visually intuitive >than ^. for example, the extra mental processing step required to decipher >the above list is not onerous, even at this hour, but hardly intuitive. and >it becomes progressively harder in complex select commands. > >I believe the use of chains does, and will continue to far outweigh the use >of insertion codes in scripting, and so the alternative syntax for chain >selection should be supported. > > There were 1281 (1284) files containing insertion codes in the current PDB http://www.imb-jena.de/~jr/InsertionCode and in the case of e.g. 1hag GLY1^F:E and GLY1^D:E couldn't be separately addressed without insertion codes >for all these reasons, I still suggest using ^ to indicate insertion codes, >and maintaining the alternative chain selection syntax without modification. >I think it is the best way to address all of the relevant issues. > >whether or not ^ is the most natural syntax to use for insertion codes; well, >for some people it is, maybe not for others, and maybe some don't have a >preference. in any case, I don't believe this should be the deciding factor >that trumps ease of implementation, visual recognition, and avoiding conflict >with existing conventions. > > >happy holidays! > >:tim > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <009601c3c478$6d42cd80$424f959f@villa> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: 1h74 (never mind the i-code) Date: Fri, 19 Dec 2003 15:53:46 +0000 (GMT) To: rasmol@lists.umass.edu I have found a perculiar case of "alternate location" usage in the pdb file 1h74. Simply load this file and try "select 227a" "spacefill" and you will see what I mean. "select 227b" "spacefill" shows that something is wrong Can anyone advise me on this PDB? I see strange remarks, but I cant make head or tail of what is going on. Here is an exert... REMARK 500 N A SER A 227 N SER B 227 0.02 REMARK 500 N A SER A 227 CA SER B 227 1.47 REMARK 500 CA A SER A 227 N SER B 227 1.46 REMARK 500 CA A SER A 227 CA SER B 227 0.01 REMARK 500 CA A SER A 227 C SER B 227 1.52 REMARK 500 CA A SER A 227 CB SER B 227 1.53 REMARK 500 O A SER A 227 C SER B 227 1.23 REMARK 500 O A SER A 227 O SER B 227 0.04 REMARK 500 C B SER A 227 CA SER B 227 1.53 REMARK 500 C B SER A 227 C SER B 227 0.02 REMARK 500 C B SER A 227 O SER B 227 1.23 REMARK 500 CB B SER A 227 CA SER B 227 1.53 REMARK 500 CB B SER A 227 CB SER B 227 0.03 REMARK 500 CB B SER A 227 OG SER B 227 1.44 REMARK 500 OG B SER A 227 CB SER B 227 1.43 ... ATOM 1688 N SER A 227 53.338 22.789 75.568 0.50 39.68 N ATOM 1689 CA SER A 227 53.379 21.621 76.461 0.50 39.52 C ATOM 1690 C SER A 227 52.227 20.622 76.388 0.50 39.35 C ATOM 1691 O SER A 227 52.227 19.634 77.126 0.50 40.16 O ATOM 1692 CB SER A 227 53.526 22.074 77.921 0.50 38.96 C ATOM 1693 OG SER A 227 52.364 22.746 78.366 0.50 38.60 O ATOM 1694 N ASER A 227 33.833 25.215 90.996 0.50 40.31 N ATOM 1695 CA ASER A 227 33.341 24.546 89.790 0.50 39.87 C ATOM 1696 C ASER A 227 52.226 20.622 76.385 0.50 39.43 C ATOM 1697 O ASER A 227 33.640 22.656 88.366 0.50 41.43 O ATOM 1698 CB ASER A 227 53.477 22.106 77.918 0.50 39.31 C ATOM 1699 OG ASER A 227 54.636 22.896 78.098 0.50 39.09 O ATOM 1700 N BSER A 227 53.325 22.787 75.560 0.50 39.76 N ATOM 1701 CA BSER A 227 53.365 21.628 76.465 0.50 39.66 C ATOM 1702 C BSER A 227 33.940 23.193 89.430 0.50 40.88 C ATOM 1703 O BSER A 227 52.237 19.626 77.110 0.50 40.19 O ATOM 1704 CB BSER A 227 33.511 25.482 88.588 0.50 37.91 C ATOM 1705 OG BSER A 227 33.104 26.792 88.919 0.50 33.96 O ... ATOM 4018 N SER B 227 33.822 25.225 90.993 0.50 41.08 N ATOM 4019 CA SER B 227 33.334 24.551 89.789 0.50 41.41 C ATOM 4020 C SER B 227 33.926 23.187 89.437 0.50 41.76 C ATOM 4021 O SER B 227 33.609 22.640 88.381 0.50 42.30 O ATOM 4022 CB SER B 227 33.533 25.468 88.583 0.50 40.67 C ATOM 4023 OG SER B 227 34.915 25.584 88.307 0.50 41.43 O MERRY CHRISTMASS !! Anyone got that christmass tree pdb? Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: CONECT hbonds wanted Date: Wed, 24 Dec 2003 15:45:25 +0100 (CET) To: rasmol@lists.umass.edu, pdb-l@sdsc.edu The PDB spec says that hydrogen bonds can be defined by CONECT records. I have not been able to find a .pdb file that has an hbond defined in a CONECT record. I would appreciate it if someone could recommend a .pdb file that has hydrogen bonds defined in CONECT records. Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2.6 SP5 works with PE Date: Tue, 30 Dec 2003 14:11:47 -0500 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com I just found out (by accident) that Chime 2.6 SP5 was released on December 19, 2003. The SP5 version is available for Windows only; 2.6 SP3 remains the current version for the Macintosh OS9 or Classic environment under OSX. Although MDL's installer, website, and release notes might lead you to think otherwise, Chime 2.6 SP5 (as well as SP3, SP4) works just fine with Windows 98, and with Netscape 4.8 (the current version for the 4.X series). My preliminary tests indicate that SP5 is compatible with Protein Explorer 1.982 Beta and 2.1 Alpha. None of the bug fixes documented in SP5 appear likely to affect operation of Protein Explorer. Happy new year! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol--