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>