Beginning Jan 1, 2000: ++++------+------+------+------+------+------+------+------+------+------+ From: James Caras Subject: Structure Tutorials Date: Mon, 3 Jan 2000 19:08:59 -0600 To: rasmol@dhcp-srv2.oit.umass.edu I am a post-doctoral researcher who has always had an interest in the use of multimedia instructional technologies for college-level education. As a graduate student, I obtained a few small grants for this purpose (enough to buy some very nice computers for my lab), and used primarily Chime structure tutorials, flash animation, and QuickTime movies for the development of biochemistry multimedia websites and CD-ROMs to be used by biochemistry instructors at the University of Texas (I instructed one semester following my degree). Because of my past experience, I have recently been asked to complete a fairly comprehensive biochemistry multimedia project. Given the demands of my current research, I will need some help in this endeavor, and would like to contract some of the work out. If any of you would like to put together Chime tutorials, please drop me an email. If you know of anyone who is adept at any of the multimedia technologies I described, such as a talented recently graduated undergraduate or graduate student who would be interested developing instructional technologies, please forward this email on to them. Hope you all had a bug-free Y2K! Jamie Dr. James Caras Dept. of Chemistry and Biochemistry Welch 4.264 The University of Texas at Austin Austin, TX 78712 W: (512) 471-3279 H: (512) 467-8842 caras@mail.utexas.edu http://ccwf.cc.utexas.edu/~caras X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Recognizing Chime in IE5 Date: Tue, 4 Jan 2000 14:01:08 +0100 To: --------------------------------------------------- Dear List members, When creating chemical html-pages with structures, it is good to know in advance whether Chime is available or not. With Javascript functions it is possible then to direct the browser how to build up the page: with embedded interactive Chime graphics, or with simple gif/jpg illustrations etc. In Netscape it is easy to question the browser that is Chime available or not with the aid of the plugins or mimetypes objects. This does not work in the case of Internet Explorer. Although the IE realization of Javascript knows the plugin object, according to MSDN "it is included only for compatibility reasons....". In fact, it is useless. I have found a way to bypass this problem. Although it is an ugly solution, it seems to be useful. Briefly speaking the solution is: 1) In an introductory page let's create a small dummy graphics with Chime 2.0.x. 2) Use an appropriate Chime callback function, which returns "true" if Chime is present and works, "false" otherwise. 3) Save this "true" value in a temporary cookie. 4) In the next pages this cookie can be read and used in the appropriate Javascript codes. This solution looks to be OK under IE 5/Chime 2.0.3 (and under Netscape too, of course), but as I wrote, it is not a very beatyful solution, so I would like to ask, has anybody out there found a better solution? regards Tamas Gunda ...................................... Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Hand-held protein models Date: Sat, 08 Jan 2000 16:23:27 -0500 To: rasmol@dhcp-srv2.oit.umass.edu [Forwarded for Stephen Shaw to circumvent technical difficulties. -E.M.] In silico modeling is wonderful, but there are some occassions when I would like to manipulate peptides or protein models manually. Can you anyone recommend one or more amino acid model sets (with commercial sources if possible) which can be assembled into peptides/structures and manipulated manually (for example explore flexility constraints). I am aware of the CPK Atomic models, but they are rather large. Regards Stephen Shaw, MD SSHAW@NIH.GOV ------------------------------------------------------------ Chief, Human Immunology Section, National Cancer Institute Editor: Protein Reviews on the Web http://www.ncbi.nlm.nih.gov/PROW ------------------------------------------------------------ Experimental Immunology Branch | National Center for National Cancer Insitute | Biotechnology Information National Institutes of Health |National Library of Medicine Bldg 10 Room 4B36 |Bldg 38A Room 8N805 10 CENTER DR MSC 1360 |8600 Rockville Pike BETHESDA MD 20892-1360 |Bethesda MD 20894 Tel: 301-435-6499 FAX: 301-496-0887 ------------------------------------------------------------ charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Bruist, PhD" Subject: RE: Hand-held protein models Date: Mon, 10 Jan 2000 09:31:55 -0500 To: I highly reccomend HGS Biochemistry Molecular Models. See their web site at http://www.sphere.ad.jp/hgs/index.html . These use a 1 cm = 1 angstrom scale and are ball & stick models. This makes them too small for lecture demonstrations, but fine for individual use. A variety of kits for assembling a few small molecules to entire proteins are available Mike Bruist -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz Sent: Saturday, January 08, 2000 4:23 PM From: owner-rasmol@lists.umass.edu Subject: Hand-held protein models To: rasmol@dhcp-srv2.oit.umass.edu [Forwarded for Stephen Shaw to circumvent technical difficulties. -E.M.] In silico modeling is wonderful, but there are some occassions when I would like to manipulate peptides or protein models manually. Can you anyone recommend one or more amino acid model sets (with commercial sources if possible) which can be assembled into peptides/structures and manipulated manually (for example explore flexility constraints). I am aware of the CPK Atomic models, but they are rather large. Regards Stephen Shaw, MD SSHAW@NIH.GOV ------------------------------------------------------------ Chief, Human Immunology Section, National Cancer Institute Editor: Protein Reviews on the Web http://www.ncbi.nlm.nih.gov/PROW ------------------------------------------------------------ Experimental Immunology Branch | National Center for National Cancer Insitute | Biotechnology Information National Institutes of Health |National Library of Medicine Bldg 10 Room 4B36 |Bldg 38A Room 8N805 10 CENTER DR MSC 1360 |8600 Rockville Pike BETHESDA MD 20892-1360 |Bethesda MD 20894 Tel: 301-435-6499 FAX: 301-496-0887 ------------------------------------------------------------ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id MAA23547 ++++------+------+------+------+------+------+------+------+------+------+ From: "Olivier Louvet" Subject: 3D files Date: Mon, 10 Jan 2000 18:02:17 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear All, I am using Rasmol for my 3D protein files. But I also would like to use files that are compatible with CAD softwares (like IGES or STL files). Please, could you tell me if it is possible to convert Rasmol files to such formats? Is there a software that can do that? Thank you. Olivier Louvet ----- La messagerie itinérante sans abonnement NetCourrier ----- Web : www.netcourrier.com Minitel : 3615 et 3623 NETCOURRIER Tél : 08 36 69 00 21 References: ++++------+------+------+------+------+------+------+------+------+------+ From: photon league Subject: Re: 3D files Date: Mon, 10 Jan 2000 12:33:09 -0500 To: rasmol@dhcp-srv2.oit.umass.edu There is a plugin for 3D studio Max (3D imaging and animation software) which allows you to import .pdb files as 3d meshes. From 3D studio Max you could export a .dxf or something that your Cad software will read. This plugin is somewhat limitng when it comes to complex molecules, especially when atoms are closely spaced, but when it works, it works well. This plugin can be downloaded for free at http://www.ktx.com/html/list_files.html . Good luck with it. Let me know if you find other utilities for converting .pdb's to meshes as I've spent many an hour fooling with this stuff, thanks. Alex Laverick The Photon League of Holographers Ontario Inc. Olivier Louvet wrote: > Dear All, > I am using Rasmol for my 3D protein files. > But I also would like to use files that are compatible with CAD softwares (like IGES or STL files). > Please, could you tell me if it is possible to convert Rasmol files to such formats? > Is there a software that can do that? > Thank you. Olivier Louvet > > ----- La messagerie itinérante sans abonnement NetCourrier ----- > Web : www.netcourrier.com Minitel : 3615 et 3623 NETCOURRIER > Tél : 08 36 69 00 21 charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 ++++------+------+------+------+------+------+------+------+------+------+ From: "Shaw, Stephen" Subject: RE: Hand-held protein models Date: Tue, 11 Jan 2000 08:30:37 -0500 To: Dear Mike 1) Thanks for the suggestion. They look interesting 2) Do they give a relatively good sense of rotational flexilibity? 3) Is there a USA distributor with whom you have dealt? 4) If you want to provide your email we can conduct the less interesting issues off-list Thanks Steve Shaw > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Michael Bruist, PhD > Sent: Monday, January 10, 2000 9:32 AM > To: rasmol@dhcp-srv2.oit.umass.edu > Subject: RE: Hand-held protein models > > > I highly reccomend HGS Biochemistry Molecular Models. See > their web site at > http://www.sphere.ad.jp/hgs/index.html . These use a 1 cm = > 1 angstrom > scale and are ball & stick models. This makes them too small > for lecture > demonstrations, but fine for individual use. A variety of kits for > assembling a few small molecules to entire proteins are available > > Mike Bruist > ++++------+------+------+------+------+------+------+------+------+------+ From: Mark Biscone Subject: RasMol Script Problems with Windows 98 and Mac OS 9... Date: Wed, 12 Jan 2000 17:22:11 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu Hi, I am new to this discussion forum so possibly these issues have already been addressed. I am encountering much difficulty in making viable scripts using either RasMol 2.6ucb berkely enhanced or 2.7 on my new laptop which is running windows 98. I ran 2.6 fine on my Windows 95 computer and was able to produce working scripts through the write script command, but am not able on either version on Windows 98. Similairly, I cannot get scripts to work on the new lab Macs, which are running Mac OS 9. Can anyone please give me some insight on addressing these problems so that I do not have to rely on my old machines? Thank you very much for your time and input. Sincerely, Mark Biscone Mark J. Biscone Graduate Student University of Pennsylvania Biscone@mail.med.upenn.edu (215)573-3508 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RasMol Script Problems with Windows 98 and Mac OS 9... Date: Wed, 12 Jan 2000 17:56:26 -0500 To: rasmol@dhcp-srv2.oit.umass.edu To the best of my knowledge, any script which runs under RasMol 2.6 beta-2a runs equally well on all platforms. I can't speak for unix or Mac OS 9, but I've used Windows 3.1, 95, 98 and Mac 68K and PPC. Berkeley RasMol has known bugs, some of which affect scripts. It is not being maintained. I have no experience with RasMol 2.7 (contact the source, info at http://www.umass.edu/microbio/rasmol/getras.htm). You could download the old tried and true RasMol 2.6 beta-2a from the above URL and use it to verify that your scripts are runnable. At 01/12/2000, you wrote: >Hi, > > I am new to this discussion forum so possibly these issues have >already been addressed. I am encountering much difficulty in making >viable scripts using either RasMol 2.6ucb berkely enhanced or 2.7 on my >new laptop which is running windows 98. I ran 2.6 fine on my Windows 95 >computer and was able to produce working scripts through the write script >command, but am not able on either version on Windows 98. Similairly, I >cannot get scripts to work on the new lab Macs, which are running Mac OS >9. Can anyone please give me some insight on addressing these problems >so that I do not have to rely on my old machines? Thank you very much >for your time and input. > >Sincerely, >Mark Biscone > >Mark J. Biscone >Graduate Student >University of Pennsylvania >Biscone@mail.med.upenn.edu >(215)573-3508 > - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Ignacio Valdes Subject: Re: presentation went great! Date: Wed, 12 Jan 2000 19:58:00 -0600 To: "rasmol@lists.umass.edu" Hello all, The presentation on Psychiatric medications went well. The 3-d renderings were neat-o. I now have to transcribe the lecture for a chapter in a book, and I'm wondering about 2-d renderings of these molecules. I have some from another book, but the scans are only okay, they aren't sharp. Can anyone help such that I can have a 2-d rendering that I can embed into a Word-processing doc? -- IV,MD charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "DALE SAMPSON" Subject: RE: presentation went great! Date: Thu, 13 Jan 2000 10:18:31 -0500 To: "Rasmol List (E-mail)" Ignacio, You can use the Export function to save the images you need to .bmp or .gif files to embed into Word. Dale Sampson -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Ignacio Valdes Sent: Wednesday, January 12, 2000 8:58 PM From: owner-rasmol@lists.umass.edu Subject: Re: presentation went great! To: rasmol@lists.umass.edu Hello all, The presentation on Psychiatric medications went well. The 3-d renderings were neat-o. I now have to transcribe the lecture for a chapter in a book, and I'm wondering about 2-d renderings of these molecules. I have some from another book, but the scans are only okay, they aren't sharp. Can anyone help such that I can have a 2-d rendering that I can embed into a Word-processing doc? -- IV,MD References: <000201bf5dd9$749d1040$0264a8c0@dalesnet> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Ignacio Valdes Subject: Re: presentation went great! Date: Thu, 13 Jan 2000 11:54:57 -0600 To: dale_j_sampson@email.msn.com Cc: "Rasmol List (E-mail)" Thanks for your reply, Dale. I am thinking more along the lines of a 2-D stick and letters model that shows the formula clearly. I.e. what people before RasMol used in textbooks. The reason is that if you can't rotate it in space, then a RasMol snapshot of a 3-D structure doesn't seem optimal to me. Am I wrong? -- IV DALE SAMPSON wrote: > > Ignacio, > > You can use the Export function to save the images > you need to .bmp or .gif files to embed into Word. > > Dale Sampson > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of > Ignacio Valdes > Sent: Wednesday, January 12, 2000 8:58 PM > To: rasmol@lists.umass.edu > Subject: Re: presentation went great! > > Hello all, > > The presentation on Psychiatric medications went > well. The 3-d > renderings were neat-o. I now have to transcribe > the lecture for a > chapter in a book, and I'm wondering about 2-d > renderings of these > molecules. I have some from another book, but the > scans are only okay, > they aren't sharp. Can anyone help such that I can > have a 2-d rendering > that I can embed into a Word-processing doc? > > -- IV,MD charset="iso-8859-1" ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: presentation went great! Date: Thu, 13 Jan 2000 13:19:35 -0500 To: "'rasmol@lists.umass.edu'" Igancio, Try one of the following: ISIS Draw from MDLI (http://www.mdli.com/cgi/dynamic/downloadsect.html?uid=$uid&key=$key&id=1) (free for academic/personal use) or ChemDraw Limited from CambridgeSoft (http://products.camsoft.com/ProdInfo.cfm?pid=170)($29.00 with academic discount) or ChemSketch from ACD Labs (http://www.acdlabs.com/download/index.html) (free) All work, each has it's own style, have used all of them with students, can't recommend one over the other. --- Frank ------------------------------------------ Frank R. Gorga, Ph.D., Chair Dept. of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 508-531-1785 (fax) fgorga@bridgew.edu http://topcat.bridgew.edu/~fgorga -----Original Message----- Sent: Thursday, January 13, 2000 12:55 PM From: Ignacio Valdes [mailto:ivaldes@csi.com] Subject: Re: presentation went great! To: FGORGA@mailhost.bridgew.edu Cc: Rasmol List (E-mail) Thanks for your reply, Dale. I am thinking more along the lines of a 2-D stick and letters model that shows the formula clearly. I.e. what people before RasMol used in textbooks. The reason is that if you can't rotate it in space, then a RasMol snapshot of a 3-D structure doesn't seem optimal to me. Am I wrong? -- IV DALE SAMPSON wrote: > > Ignacio, > > You can use the Export function to save the images > you need to .bmp or .gif files to embed into Word. > > Dale Sampson > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of > Ignacio Valdes > Sent: Wednesday, January 12, 2000 8:58 PM > To: rasmol@lists.umass.edu > Subject: Re: presentation went great! > > Hello all, > > The presentation on Psychiatric medications went > well. The 3-d > renderings were neat-o. I now have to transcribe > the lecture for a > chapter in a book, and I'm wondering about 2-d > renderings of these > molecules. I have some from another book, but the > scans are only okay, > they aren't sharp. Can anyone help such that I can > have a 2-d rendering > that I can embed into a Word-processing doc? > > -- IV,MD ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian W. Beck" Subject: Add Berkeley multi-sys functionality Date: Thu, 13 Jan 2000 17:05:27 -0600 (CST) To: rasmol@dhcp-srv2.oit.umass.edu Herbert/Rasmol Community: Is anyone working on adding the Berkeley multi-system functionality into the next maintained version of Rasmol? I end up running both versions depending on what I want to do, but 1) it'd be nice to run one version and 2) I don't think the Berkeley version source code is readily available (so I can modify it) -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Add Berkeley multi-sys functionality Date: Thu, 13 Jan 2000 19:04:49 -0500 (EST) To: "Brian W. Beck" Cc: rasmol@dhcp-srv2.oit.umass.edu Dear Brian and RasMol Community, I believe Brian is absolutely right about the desirability of combining the Berkeley mods into the mainstream of RasMol development. I have asked for access to the source code so that I can do the merge. I have not yet had a final answer. I would be very interested in hearing community sentiment in this matter. Regards, Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Thu, 13 Jan 2000, Brian W. Beck wrote: > Herbert/Rasmol Community: > > Is anyone working on adding the Berkeley multi-system > functionality into the next maintained version of > Rasmol? I end up running both versions depending on > what I want to do, but 1) it'd be nice to run one > version and 2) I don't think the Berkeley version > source code is readily available (so I can modify it) > > -Brian > -- > ============================================================== > | Brian W. Beck |E-mail Address: beck@uh.edu | > | Inst. Molec. Design| | > | Univ. of Houston |URL: | > | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | > | Houston, TX, USA |VOICE (713) 743-3264 | > | 77204-5641 |FAX (713) 743-2709 | > ============================================================== > charset="iso-8859-1" ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: Add Berkeley multi-sys functionality Date: Fri, 14 Jan 2000 09:46:35 -0500 To: "'rasmol@lists.umass.edu'" Herbert, First let me thank you for continuing to develop RasMol. I use RasMol (and CHIME) extensively in teaching both Organic Chemistry & Biochemistry. I can't imagine teaching without it. I would love to see the ability to display multiple structures ala' the Berkeley version added to the current version of RasMol. (The Berkeley version was never particularly useful to me because of its troubles with scripts.) One of the most difficult concepts to get across to students is conformation change. Being able to display two structures side-by-side, or "overlapped" would be a wonderful enhancement. I do this now by running two copies of RasMol, but since the windows are not coordinated, this is not an ideal solution. Another wonderful enhancement would be a command that would automatically align (in 3-D) two structures. I would imagine (based on my dabbler-level programming experience) is that this is a majorly nontrivial request, but it can't hurt to ask! ;-) Thanks again, --- Frank ------------------------------------------ Frank R. Gorga, Ph.D., Chair Dept. of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 508-531-1785 (fax) fgorga@bridgew.edu http://topcat.bridgew.edu/~fgorga -----Original Message----- Sent: Thursday, January 13, 2000 7:05 PM From: Herbert J. Bernstein [mailto:yaya@bernstein-plus-sons.com] Subject: Re: Add Berkeley multi-sys functionality To: FGORGA@mailhost.bridgew.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Dear Brian and RasMol Community, I believe Brian is absolutely right about the desirability of combining the Berkeley mods into the mainstream of RasMol development. I have asked for access to the source code so that I can do the merge. I have not yet had a final answer. I would be very interested in hearing community sentiment in this matter. Regards, Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Thu, 13 Jan 2000, Brian W. Beck wrote: > Herbert/Rasmol Community: > > Is anyone working on adding the Berkeley multi-system > functionality into the next maintained version of > Rasmol? I end up running both versions depending on > what I want to do, but 1) it'd be nice to run one > version and 2) I don't think the Berkeley version > source code is readily available (so I can modify it) > > -Brian > -- > ============================================================== > | Brian W. Beck |E-mail Address: beck@uh.edu | > | Inst. Molec. Design| | > | Univ. of Houston |URL: | > | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | > | Houston, TX, USA |VOICE (713) 743-3264 | > | 77204-5641 |FAX (713) 743-2709 | > ============================================================== > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Add Berkeley multi-sys functionality Date: Fri, 14 Jan 2000 11:02:47 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: shindyal@sdsc.edu At 01/14/2000, Frank Gorga wrote: >One of the most difficult concepts to get across to students is conformation >change. Being able to display two structures side-by-side, or "overlapped" >would be a wonderful enhancement. I do this now by running two copies of >RasMol, but since the windows are not coordinated, this is not an ideal >solution. The Protein Explorer freeware (using Chime) includes a Comparator mode which positions two molecules side by side. In Windows, mouse-driven rotation and zooms can be synched so both molecules remain in the same orientation and zoom. This is much easier than it is to set up two RasMol sessions, and avoids the confusion of which command line goes with which graphic (in PE, there is only one command line and you toggle which molecule is applies to). In fact, you can make a hyperlink which prespecifies the two molecules in advance, and Protein Explorer starts up with them ready to go. Protein Explorer is offered as version 1.0 at the PDB and its mirrors (www.rcsb.org). The latest enhancements (including info on prespecifying molecules in hyperlinks and a link to the alignment server mentioned below) are at www.umass.edu/microbio/chime/explorer before they get released at the PDB. For configuration change, see the Protein Morpher, where large changes induced by calcium, for example, are morphed between two empirical conformations. www.umass.edu/microbio/chime/morpher Such morph movies can also be played in Protein Explorer. Instructions for creating your own toggles or morphs are included in the Morpher site at http://www.umass.edu/microbio/chime/morpher/morphmtd.htm Toggles or morphs can be attached to buttons in presentations. A presentation template is downloadable from http://www.umass.edu/microbio/chime/prsswc/template.htm >Another wonderful enhancement would be a command that would automatically >align (in 3-D) two structures. I would imagine (based on my dabbler-level >programming experience) is that this is a majorly nontrivial request, but it >can't hurt to ask! ;-) Any two or more proteins can be aligned at a site by Ilya Shindyalov and Phil Bourne. This site was recently modified by Ilya to emit Protein-Explorer-ready aligned PDB files (in pseudo-NMR format). These can be toggled in Protein Explorer using the built-in NMR Model Selection page ([Auto] button with adjustable delay). Go to http://cl.sdsc.edu/ce.html and click on Compare All. Specify a PDB ID And chain in the slot and press [Search Database]. The best-aligned structures in the PDB Are listed in order of decreasing alignment, showing % sequence identity and number of residues aligned. (This search is done by 3d structure without reference to sequence.) Check the one or more of interest and press [Get Alignment]. There are several options for viewing, including a direct link to Protein Explorer. Ilya's java applet is very good because it displays the structure-aligned sequence, with options for coloring identical or conserved residues. You can download the aligned PDB file which can be displayed in Protein Explorer (with the NMR control convenience buttons) or in RasMol (using 'select model=n' type commands, automated in Protein Explorer). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: RE: Add Berkeley multi-sys functionality Date: Fri, 14 Jan 2000 10:55:01 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Just in case you didn't know about some of the competition out there, Swiss-PdbViewer can align structures in ein augenblick by several procedures, from 3-point superposition to least-squares on selected groups to fully automatic "magic fit". It can display lots of models at once and "blink" through selected models to make vivid comparisons that are as effective as many animations. It can mutate, alter conformations, add and delete bonds, energy minimize, build oligomers and unit cells, compute and display all sorts of surfaces, and build homology models on site or using the SwissMODEL server in Geneva. It can submit and receive remote-server jobs for GROMOS, CHARMM, and AMBER. It can produce stunning, book-quality graphics for print and for the web. And it's probably the easiest modeling program to learn and use, from the simplest to the most complex operations. It's stable, fast as lightening, friendly, and full of sheer genius (mostly the sheer genius of one Nicolas Guex). And I'm must getting started. If you haven't looked at SPV lately, it has been growing like Topsy, but it's still a small, friendly viewer at heart. It's hard to believe, but it's free. It compares favorably with the best commercial molecular graphics packages. And the basic program still fits on a floppy. I now teach undergraduates to use SPV as part of my first-semester biochemistry course. By the sixth or seventh week of class, all my juniors and seniors can search the PDB for structures, download them, explore them, and compare them, all in open-ended fashion. And from my website, they can download all structures they have seen in class and explore them further. If you want to learn to do this on your Mac, PC, SGI, or Linux machine, check out the SPV Home and my beginner's tutorial. SPV Home http://www.expasy.ch/spdbv/mainpage.htm SPV Tutorial http://www.usm.maine.edu/~rhodes/SPVTut/index.html For some hints about using graphics for student empowerment in your courses, start here: http://www.usm.maine.edu/~rhodes/Biochem/index.html I like RasMol and Chime, too, for certain types of presentations and for making things for students to watch. But for getting them to DO, SPV is unbeatable. I am not on commission. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu WWW Home Page: http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 References: ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Lee Subject: Re: Structure Tutorials Date: Fri, 14 Jan 2000 11:47:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I will send you a CD that contains the tour of myoglobin with the instructions on how to view the tour. How does that sound. James Caras wrote: > I am a post-doctoral researcher who has always had an interest in the use > of multimedia instructional technologies for college-level education. As a > graduate student, I obtained a few small grants for this purpose (enough to > buy some very nice computers for my lab), and used primarily Chime > structure tutorials, flash animation, and QuickTime movies for the > development of biochemistry multimedia websites and CD-ROMs to be used by > biochemistry instructors at the University of Texas (I instructed one > semester following my degree). > > Because of my past experience, I have recently been asked to complete a > fairly comprehensive biochemistry multimedia project. Given the demands of > my current research, I will need some help in this endeavor, and would like > to contract some of the work out. If any of you would like to put together > Chime tutorials, please drop me an email. If you know of anyone who is > adept at any of the multimedia technologies I described, such as a talented > recently graduated undergraduate or graduate student who would be > interested developing instructional technologies, please forward this email > on to them. > > Hope you all had a bug-free Y2K! > > Jamie > > Dr. James Caras > Dept. of Chemistry and Biochemistry > Welch 4.264 > The University of Texas at Austin > Austin, TX 78712 > W: (512) 471-3279 > H: (512) 467-8842 > caras@mail.utexas.edu > http://ccwf.cc.utexas.edu/~caras References: ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Structure Tutorials Date: Fri, 14 Jan 2000 11:57:45 -0600 To: rasmol@dhcp-srv2.oit.umass.edu Adrian- That sounds great. Send them to : Jamies Caras Science Technologies 5410 Avenue G Austin, TX 78751 if you haven't sent them already. If you have already sent them to UT, I can pick them up at work. -Jamie At 11:47 AM 1/14/00 -0500, you wrote: >I will send you a CD that contains the tour of myoglobin with the instructions >on how to view the tour. How does that sound. > >James Caras wrote: > >> I am a post-doctoral researcher who has always had an interest in the use >> of multimedia instructional technologies for college-level education. As a >> graduate student, I obtained a few small grants for this purpose (enough to >> buy some very nice computers for my lab), and used primarily Chime >> structure tutorials, flash animation, and QuickTime movies for the >> development of biochemistry multimedia websites and CD-ROMs to be used by >> biochemistry instructors at the University of Texas (I instructed one >> semester following my degree). >> >> Because of my past experience, I have recently been asked to complete a >> fairly comprehensive biochemistry multimedia project. Given the demands of >> my current research, I will need some help in this endeavor, and would like >> to contract some of the work out. If any of you would like to put together >> Chime tutorials, please drop me an email. If you know of anyone who is >> adept at any of the multimedia technologies I described, such as a talented >> recently graduated undergraduate or graduate student who would be >> interested developing instructional technologies, please forward this email >> on to them. >> >> Hope you all had a bug-free Y2K! >> >> Jamie >> >> Dr. James Caras >> Dept. of Chemistry and Biochemistry >> Welch 4.264 >> The University of Texas at Austin >> Austin, TX 78712 >> W: (512) 471-3279 >> H: (512) 467-8842 >> caras@mail.utexas.edu >> http://ccwf.cc.utexas.edu/~caras > > > > __________________________________ Dr. James W. Caras Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 (512) 471-0416 caras@mail.utexas.edu http://www.sciencetechnologies.com/HomePaige/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Rasmol and conformation change. Date: Fri, 14 Jan 2000 15:24:45 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: shindyal@sdsc.edu [I have forwarded this for Andrew Coulson andrewc@srv0.bio.ed.ac.uk to circumvent technical difficulties. With apologies to Andrew, I then added a comment below. -Eric Martz] Frank Gorga's e-mail suggests that he and maybe others might be interested in the following 'quick fix' : SwissPDBViewer, which is available from http://www.expasy.ch/spdbv/mainpage.htm can be used very simply to produce a PDB file with the superimposed co-ordinates of two related proteins (eg, different conformational states). In SPDBV, open PDB files containing each of the two structures. Then choose 'MagicFit' from the tools menu. Finally, choose 'Save', 'Project' from the File menu, and the output file will be in PDB format with the two sets of overlapping co- ordinates. If anyone would like to see an example, I will e-mail them a file comparing the structures of TIM in the presence and absence of a competitive inhibitor. Substrate binding brings about a loop movement which restricts access of water to the active site cavity. Andrew Coulson [Added by Eric Martz: An example of two molecules aligned by the Shindyalov/Bourne site is at http://www.umass.edu/microbio/chime/beta/x0.992/pdb_files/1cmk1atp.pdb These are the catalytic domains of a C kinase, both with a regulatory peptide bound, but only the latter has ATP bound, which induces a conformational change. They are from pig (1cmk) and mouse (1atp) and are 97% sequence identical. You can display it in Protein Explorer by pasting the above url into the 'browse' slot and pressing [Load]. PE recognizes NMR Files and shows all models by default, in contrast to RasMol which shows only the first by default. PE's default avoids having people fail to realize they've got a multiple-model file. However, the Shindyalov alignment site puts only the aligned chains into the PDB file, hence the regulatory peptide and ATP are lost. A morph between these is at www.umass.edu/microbio/chime/morpher -- I did indeed make this morph-alignment with Swiss PDB Viewer which allowed me to specify the relevant chains for alignment, yet keep the peptide, metals, water, etc. when saving the file. I then had to manually text-edit the two files into one, adding model/endmdl PDB records so they could be independently manipulated in Chime/RasMol. Kudos to Nicolas Guex for his wonderful program! Why did the Shindyalov site leave the myristic acid in? The answer is left as an exercise for the reader, who will be better prepared if she has been following the pdb-l discussion about chain identifiers! -E.M.] References: <9F5E83E17008D31193DD0090274E75056EB834@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: RE: Add Berkeley multi-sys functionality Date: Fri, 14 Jan 2000 13:34:05 -0800 To: rasmol@dhcp-srv2.oit.umass.edu At 10:55 AM 1/14/00 -0500, you wrote: >Just in case you didn't know about some of the competition out there, >Swiss-PdbViewer can align structures in ein augenblick by several >procedures, from 3-point superposition to least-squares on selected groups >to fully automatic "magic fit". Really? I've never gotten it to open more than one thing at a time - I'll read the manual some more. SPDB is a great program - the linux version is slow & a little buggy, but it works....I like the povray export feature.... - - - - _ _ _ _ _ "Written laws are like spiders' webs, and like them will only entangle and hold the poor and weak, while the rich and powerful easily break through them. " Anacharsis (Scythian Philosipher) 600 BCE References: <200001132305.RAA06777@Ba.Chem.UH.EDU> X-pair-Authenticated: 12.79.237.115 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Add Berkeley multi-sys functionality Date: Fri, 14 Jan 2000 17:11:05 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu I am pleased to report that I just got word from Eileen Lewis at Berkeley that Marco Molinaro, the creator of the UCB RasMol mods, will "make the code available to [me] in the next 2-3 weeks." This is wonderful news, which should allow us to bring one of the most important variants of RasMol back into the main line of development. -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== References: <9F5E83E17008D31193DD0090274E75056EB834@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: RE: Add Berkeley multi-sys functionality Date: Fri, 14 Jan 2000 17:24:27 -0500 To: rasmol@dhcp-srv2.oit.umass.edu > >Really? I've never gotten it to open more than one thing at a time - I'll >read the manual some more. SPDB is a great program - the linux version is >slow & a little buggy, but it works....I like the povray export feature.... >- - - - Just use the File: Open command repeatedly to load a series of models in succession. The Layer Information window (Wind: Layer Infos) is handy for selecting which model(s) are visible, can move, are including in blinking (cyclically displaying a series of individual models), or other properties. (I had to look up "cyclically". Still doesn't look right.) The Sequence Alignment window (Wind: Sequence Alignment) is handy for selecting corresponding parts of a model for alignment of models that have some parts not in common. (SPV does structural alignments of sequences, too.) Section 11 of the tutorial takes you through comparisons of a) oxy- vs deoxyhemoglobin and b) Hb alpha chain vs beta chain. Another feature that might be useful to RasMolluscs and Chimeleons is that SPV can build models from scratch (such as small structural elements, helices, sheets (see tutorial assignment #2), loops), or join models to each other, you name it, and then write PDB files that you can use in RasMol/Chime displays. It can also handle such nasty things as structure files in fractional coordinates (don't ask), and then save them in PDB format. Opens several common file formats. Saves coordinates in PDB and mmcif only (also can supply proper formats to remote energy-minimization jobs). About bugs. NOTIFY THE PROGRAMMERS. THEY WILL FIX THEM. Linux and SGI versions are the newest and so are inevitably the least tested by outside users. The PC version has been around long enough that it should be pretty stable. It uses OpenGL for 3D rendering of models for printing, so in theory should be the most powerful in that ONE regard -- can do transparency. The original and probably stablest platform is Mac (OpenGL rendering is coming soon). PLEASE send all bug notices, even minor stuff, to one of the team listed at SPV home. SPV is designed to be THE molecular viewer for use with all ExPASy tools (http://www.expasy.ch/), and has the same high level of support as the other tools. Bugs get fixed quick. I am always happy to answer specific questions about use of SPV. Usually, I will return help messages to individuals, not to the whole RasMol list. Have fun. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu WWW Home Page: http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 X-ZSender: rowland.geoff@zetnet.co.uk ++++------+------+------+------+------+------+------+------+------+------+ From: Geoffrey Rowland Subject: Re: Hand-held protein models Date: Mon, 17 Jan 2000 01:06:55 GMT To: rasmol@dhcp-srv2.oit.umass.edu Edited from the message <0FO100MGTC1NY7@supai.oit.umass.edu> from Eric Martz contains these words: > [Forwarded for Stephen Shaw to circumvent technical difficulties. -E.M.] > In silico modeling is wonderful, but there are some occassions when I would > like to manipulate peptides or protein models manually. Can you anyone > recommend one or more amino acid model sets (with commercial sources if > possible) which can be assembled into peptides/structures and manipulated > manually (for example explore flexility constraints). I am aware of the CPK > Atomic models, but they are rather large. I'm not sure if they will precisely meet your requirements - but you might like to try the Molymod molecular model sets from Spiring Enterprises Ltd, Billinghurst RH14 9HF, UK http://www.molymod.com molymod@globalnet.co.uk These can be assembled as ball-and stick (approx 3.5 cm per Angstrom) or more compact semi-spacefilling models(approx 1.5 cm per Angstrom). As well as general sets, there are specific kits for building display models of alpha-helices and beta-pleated sheets. Also, they have just brought out rather neat molecular obital parts which would give a good representation of the delocalised rigid trans-planar nature of the peptide link. I don't think details of the molecular orbital parts are yet posted on their web site so you may need to email for more info. An alternative is to use the Orbit (3cm per Angstom), Minit (2cm per Angstrom) or Micrit (1.25 cm per Angstrom) systems from Cochranes of Oxford Ltd, Leafield Witney, Oxford OX8 5NY, UK. http://www.cochranes.co.uk cochranes@mailbox.co.uk These give a more 'skeletal' structure with atom centres linked with 'straws'. I particularly like the Minit 'peptide' units which allow rapid building of hydrogen bonded alpha-helices and beta-sheets. They are also good for synthetic polyamides like nylon-6,6 and Kevlar. The peptide units are molded in black plastic and one 'trick' is to use small circular white, red and blue stickers (available from all good stationers!)to allow ready identification the H, O and N centres. Again, I don't think details of the peptide units are posted on the Cochranes website. The Micrit system is described as being specifically for the construction of macromolecular structures, having more rigid straws than the Minit system, although I have no direct experience of using this. Hope this is of some use. Regards, Geoff Rowland Yeovil College charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 ++++------+------+------+------+------+------+------+------+------+------+ From: "Shaw, Stephen" Subject: RE: Hand-held protein models Date: Sun, 16 Jan 2000 21:07:11 -0500 To: Dear Geoff Thank you for your thoughtful and informative reply. Together with your information I am aware of four distributors of assemblable kits: 1. CPK - Harvard Apparatus 2. Cochranes 3 MolyMod 4. HGS I am getting samples of several, and will see how they meet my needs. I will summarize my findings briefly on this listserv when I have more to share Regards Steve Shaw charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Bruist, PhD" Subject: coloring nucleic acid surfaces by potential Date: Mon, 17 Jan 2000 15:33:51 -0500 To: I am using Protein Explorer to view protein-nucleic acid complexes. I would like to color the surfaces of the protein and the dna by potential. I have tried this on the gal4 complex used in the tutorial. The protein gets colored but the nucleic acid is a uniform red. Is there a different MPE function or something else that will give the DNA potential colors? Thanks Mike Dr. Michael F. Bruist Associate Professor of Biochemistry Department of Chemistry and Biochemistry Griffith Hall 142 University of the Sciences in Philadelphia 600 South 43rd Street Philadelphia, PA 19104-4495 Phone (Office & Voice Mail):(215) 596-8530 Phone (Lab): -8553 Dept. Phone: -8839 Dept. Fax: -8543 E-mail: m.bruist@usip.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: RasMol-2.6b2 Date: Mon, 17 Jan 2000 17:10:16 -0800 (PST) To: , Hi, I'm trying to get my SpaceOrb 360 (a cheap 6DOF device) going with LibOrb http://www.spacetec.com/product/profile/index.cfm?ProductID=154 http://www.umr.edu/~johns/projects/liborb/ using a modified RasMol-2.6b2 from http://www.in-machina.com/~reece/RasMol/ Unfortunately, I'm running into the following problems during build: eugene.leitl@lrz:~/download/rasmol/RasMol-2.6b2 > make gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT -c rasmol.c -o rasmol.o rasmol.c:52: sys/termio.h: No such file or directory make: *** [rasmol.o] Error 1 Before you ask: RasMol 2.7.1 builds just fine, unfortunately the patch is RasMol-2.6b2-spaceorb-01.patch only applicable on RasMol-2.6b2. I seem to recall there is an easy fix for this, but I don't remember the specifics. I've tried some websearches, but so far found anything. Can anyone help? TIA, Regards, Eugene Leitl ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: CCL:RasMol-2.6b2 Date: Tue, 18 Jan 2000 12:10:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: saturka@daisy.imc.cas.cz [resent by Eric Martz to circumvent technical difficulties] On Mon, 17 Jan 2000, Eugene Leitl wrote: > eugene.leitl@lrz:~/download/rasmol/RasMol-2.6b2 > make > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT -c rasmol.c -o rasmol.o > rasmol.c:52: sys/termio.h: No such file or directory > make: *** [rasmol.o] Error 1 > it just means, that you haven't got file /usr/include/sys/termio.h. it's obsolete file, try either to overwrite #include to #include or to #include in your source code of rasmol or copy /usr/include/sys/termio.h to /usr/include/sys/termios.h or into directory you have permissions for /home/guy/include/sys/termio.h and (in the last case) add directive -I/home/guy/include to your compilation or add that directory into your makefile. I hope, it will work. PS what experiences do you have with such (virtual reality) devices under linux box (including SGI dials and others) - applications, prices, ...? Thank you, Martin Saturka ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: success in patching RasMol 2.7.1 for use with SpaceOrb 360 Date: Tue, 18 Jan 2000 20:43:29 -0800 (PST) To: , , It is possible to successfully patch RasMol 2.7.1 http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.tar.gz with the patch for the SpaceOrb 360 6DOF input device http://www.spacetec.com/product/profile/index.cfm?ProductID=154 using the patch for RasMol-2.6b2 http://www.in-machina.com/~reece/RasMol/RasMol-2.6b2-spaceorb-01.patch.gz under Linux 2.2.14 with the following modifications: unpack the RasMol tarball. Unzip and put the patch into the RasMol_2.7.1/src directory. Go there. Apply the patch via patch Subject: RasMol bond assignment mystery? Date: Wed, 19 Jan 2000 17:31:50 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Tim Driscoll has discovered the following mystery. In 1c8r, neither RasMol nor Chime show atomno=2046 (carbon in hetero ret group) bonded to atomno=1606 (NZ in K216:A). Note that one is HETATM, the other ATOM. The C-N distance is 1.33 Angstroms, closer than some nearby C-N distances which show bonds. For here on my tests are in RasMol 2.6 beta2a, parent of Chime. I'm assuming Chime behaves similarly but have not tested it. Show info reports 2083 bonds, regardless of 'connect false' or 'connect true'. However, try this: select within(5., atomno=2046) 25 atoms selected save pdb 1c8r-x.pdb zap load 1c8r-x.pdb Now the two atoms in question ARE bonded! Note that this file has only 18 atoms so falls below the 255 atom rule. Again, 'connect' commands report 9 bonds either way. According to my understanding (evidently incorrect or incomplete) of how bonds are assigned, in the original 1c8r (1,720 atoms, no hydrogens), any carbon and nitrogen within 1.9 Angstroms of each other should be bonded. These two are 1.33 Angstroms apart. Therefore there should be a bond. For the 18-atom excerpt, there should be a bond between any two atoms within a distance of the sum of their covalent radii + 0.56 Angstroms. For C-N, this value is 1.96 Angstroms. So there should be a bond here too. The sum of my understanding of RasMol and Chime's bonding rules is in http://www.umass.edu/microbio/rasmol/rasbonds.htm (This document omits an adjustment of van der Waals radii for pdb files lacking hydrogens; see ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/99.01-02 and search for the first message by Sayle. But vdW radii are irrelevant for the issue at hand, I think. Also I just realized that the 'set connect' command was an enhancement in Chime missing from RasMol 2.6) THE MYSTERIES: Why isn't there a bond in 1c8r? Why doesn't 'connect true' force a bond in 1c8r? Why do 1c8r and the 18-atom excerpt get different bond assignments? Why doesn't 'connect false' do anything in the 18-atom excerpt? Does anyone know a case where the 'connect' command makes a difference? Help, please, Roger! -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id BAA27379 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Rasmol default window size Date: Thu, 20 Jan 2000 17:42:59 +1100 To: Is it possible to set the window size of Rasmol ( the PC or Unix version) e.g. to 640x480 pixels either by hacking the code or using a command line option? ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Rasmol default window size Date: Thu, 20 Jan 2000 13:06:17 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Win95 and Win3.1 solutions for making RasMol 2.6b2a start up with a desired window size and placement are listed under Retaining RasMol's window sizes/positions at http://www.umass.edu/microbio/rasmol/faq_em.htm I don't know of solutions for Macintosh or unix. There is no relevant command line option for Windows RasMol 2.6b2a. At 01/20/2000, Brendan O'Malley wrote: > >Is it possible to set the window size of Rasmol >( the PC or Unix version) e.g. to 640x480 pixels >either by hacking the code or using a >command line option? > - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: RasMol bond assignment mystery? Date: Thu, 20 Jan 2000 15:31:41 -0700 (MST) To: rasmol@dhcp-srv2.oit.umass.edu Hi Eric and Tim, The confusion is caused by the fact that RasMol's internal bonding calculations do not add bonds between molecules in different chains, models or segments separated by TER records. This definition of a chain in RasMol is quite subtle, and the "TER" record (at PDB serial number 1721 in 1c8r) is interpreted as disconnecting the atoms before it from those after it. The presence of this TER record overrides the same chain identifier (much like a "MODEL" or "ENDMDL" record). The PDB more recently use "LINK" records to explicitly add bonds across TER records, but unfortunately these are currently not interpreted by either RasMol or Chime. When writing out a PDB file, RasMol does not preserve these explicit "TER" records, only placing TER records between atoms with differing chain identifiers. This explains why writing out a subset of atoms and reading them back results in an additional bond. The inability to discover a difference between "connect true" and "connect false" in the peptides that you've been investigating is a credit to the fast bonding heuristics used in RasMol. The faster "connect false" command assumes that any pair of heavy atoms between 0.4 and 1.9 Angstroms are bonded. This is a gross simplification that works well for unstrained, organic structures containing carbon, nitrogen, oxygen and sulphur. It is totally inadequate for strained caged structures (such as cubane) or inorganic molecules. In addition to protein biochemists, RasMol is also used by semiconductor physicists who rely on "connect true" to give accurate bonding lattices in Gallium-Arsenide semiconductors and similar exotic chemistries. RasMol automatically selects the fast heuristics for molecules with over 256 atoms as these tend to be large biomolecules for which the heuristics work well and benefit most from the improved performance. > Also I just realized that the 'set connect' command > was an enhancement in Chime missing from RasMol 2.6) Unfortunately your chosen version of RasMol, predates the RasMol upon which Chime is based. The "set connect" command has been is RasMol since atleast 1996, and this functionality subsequently copied by Chime. It appears that you've been updating your copy of RasMol less frequently than MDL has theirs! :> Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ Office 104, 441 Greg Avenue, Tel: (+1) 505-954-3281 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ++++------+------+------+------+------+------+------+------+------+------+ From: Tansu KINIKLI Subject: Web site info Date: Sat, 22 Jan 2000 13:44:52 +0300 (MEST) To: rasmol@dhcp-srv2.oit.umass.edu Hello, do you know any web site which contains polymer modells. Regards. Tansu KINIKLI Hacettepe University Bioengineering Department Beytepe, ANKARA, TURKEY References: charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-MIME-Autoconverted: from base64 to 8bit by dhcp-srv2.oit.umass.edu id KAA08430 ++++------+------+------+------+------+------+------+------+------+------+ From: "Liu Tao" Subject: Re: Web site info Date: Sat, 22 Jan 2000 23:20:29 +0800 To: I am so sorry that I don't know. ----- Original Message ----- Sent: Saturday, January 22, 2000 6:44 PM From: Tansu KINIKLI Subject: Web site info To: > > > Hello, do you know any web site which contains polymer modells. > > Regards. > > Tansu KINIKLI > Hacettepe University > Bioengineering Department > Beytepe, ANKARA, TURKEY > > > > X-Operating-System: Debian GNU/Linux ++++------+------+------+------+------+------+------+------+------+------+ From: "K. Arun" Subject: Re: Add Berkeley multi-sys functionality Date: 23 Jan 2000 09:51:30 +0530 To: rasmol@dhcp-srv2.oit.umass.edu >>>>> "G. Rhodes" == Gale Rhodes writes: G. Rhodes> If you haven't looked at SPV lately, it has been growing G. Rhodes> like Topsy, but it's still a small, friendly viewer at G. Rhodes> heart. It's hard to believe, but it's free. It compares G. Rhodes> favorably with the best commercial molecular graphics G. Rhodes> packages. And the basic program still fits on a floppy. Is there a forum such as this for SPDBV users ? Specifically, users of the Linux port ? Thanks, - K. Arun References: <200001230523.KAA12436@giasmda.vsnl.net.in> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Add Berkeley multi-sys functionality Date: Sun, 23 Jan 2000 14:38:56 -0800 To: rasmol@dhcp-srv2.oit.umass.edu > > Is there a forum such as this for SPDBV users ? Specifically, > users of the Linux port ? > I don't know about the mailing list, but have found SPDBV to be excellent under win9* but a little buggy under linux. This may be my compilation, but it seems to take a long time for windows to open compared to windows. I'm using RH 6.1 & also would be interested in other peoples experiences under linux. The rasmol linux versions are pretty good, but still not as good as windows. The file menu doesn't work at all - pretty much everything has to be command line (which has it's advantages and disadvantages). But the scripts work, and output to pov files is great in both programs... ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Add Berkeley multi-sys functionality Date: Sun, 23 Jan 2000 18:44:08 -0500 To: rasmol@dhcp-srv2.oit.umass.edu > Is there a forum such as this for SPDBV users ? Specifically, >users of the Linux port ? > > Thanks, > > - K. Arun Gale Rhodes wrote to Nicolas Guex: >Maybe it's time to set up something like the RasMol discussion list for >SPdbV. Would you like for me to see if I can set it up here? Or would you >prefer it to be there? I will be happy to take responsibility for it if we >can do it here, or to help out in any way I can if it's there. Nicolas Guex replied: >yes, I guess it is time. >I still hesitate between Eric Martz proposition to add >it to the rasmol list, or to launch a different one... >I guess that the questions from the two users communities are >slightly different. I wonder if it is appropriate to swamp the >rasmol list with spdbv questions and conversely, although some >general questions/answers will benefit to both lists... >any Idea regarding what eould be best? RasMolluscs and Chimeleons: Any opinions? We'll try to act on this soon. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu WWW Home Page: http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Soerge Kelm Subject: Re: Add Berkeley multi-sys functionality Date: Mon, 24 Jan 2000 08:25:02 +0100 To: rasmol@dhcp-srv2.oit.umass.edu I think that having one list dealing with both Rasmol and SPDBV would be more useful since probably many people use both programs. Soerge Gale Rhodes wrote: > > Is there a forum such as this for SPDBV users ? Specifically, > >users of the Linux port ? > > > > Thanks, > > > > - K. Arun > > Gale Rhodes wrote to Nicolas Guex: > > >Maybe it's time to set up something like the RasMol discussion list for > >SPdbV. Would you like for me to see if I can set it up here? Or would you > >prefer it to be there? I will be happy to take responsibility for it if we > >can do it here, or to help out in any way I can if it's there. > > Nicolas Guex replied: > > >yes, I guess it is time. > >I still hesitate between Eric Martz proposition to add > >it to the rasmol list, or to launch a different one... > >I guess that the questions from the two users communities are > >slightly different. I wonder if it is appropriate to swamp the > >rasmol list with spdbv questions and conversely, although some > >general questions/answers will benefit to both lists... > >any Idea regarding what eould be best? > > RasMolluscs and Chimeleons: Any opinions? > > We'll try to act on this soon. > > Cheers! > > ***************************** > > "Some people place favorite quotations at the end of their e-mails, but I > don't." > Anonymous, Greece, 3rd century BC. > > Gale Rhodes mailto:rhodes@usm.maine.edu > WWW Home Page: http://www.usm.maine.edu/~rhodes/GRHomePage.html > Professor of Chemistry > Chemistry Department > University of Southern Maine > PO Box 9300 > Portland, Maine 04104-9300 > Phone: (207)780-4734 > Fax: (207) 228-8288 -- Soerge Kelm Biochemisches Institut Universitaet Kiel Olshausenstrasse 40 D-24098 Kiel Germany Phone: x49-431-8802215 FAX: x49-431-8802007 email: skelm@biochem.uni-kiel.de home page: http://www.uni-kiel.de/Biochemie/kelm/ X-Operating-System: Debian GNU/Linux ++++------+------+------+------+------+------+------+------+------+------+ From: "K. Arun" Subject: Re: Add Berkeley multi-sys functionality Date: 24 Jan 2000 16:33:58 +0530 To: rasmol@dhcp-srv2.oit.umass.edu >>>>> "Soerge" == Soerge Kelm writes: Soerge> I think that having one list dealing with both Rasmol and Soerge> SPDBV would be more useful since probably many people use Soerge> both programs. Soerge How about keeping it within this list for now, and moving to a two list setup, if and when SPdbV traffic justifies it ? -arun References: <388BFE4E.3715F27@biochem.uni-kiel.de> boundary="------------D42A03674FDFAD25D4207AA2" X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: odin Subject: unsubscribe Date: Mon, 24 Jan 2000 19:37:16 -0700 To: rasmol@dhcp-srv2.oit.umass.edu --------------D42A03674FDFAD25D4207AA2 > --------------D42A03674FDFAD25D4207AA2
 
--------------D42A03674FDFAD25D4207AA2-- Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id AAA25157 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Re: Rasmol default window size Date: Wed, 26 Jan 2000 16:28:32 +1100 To: Thanks for the help Eric. I found that for Windows NT (for which Softarts program doesnt work) that a shareware program ($22) PowerPro can be used (www.inforamp.net/~crs2086/index.html). This program will pop up a little window showing the size of an active window when you reposition or scale it. Brendan O'Malley (brendan.omalley@rmit.edu.au) Applied Physics RMIT Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id DAA25409 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Rasmol/Chime Script Animations Date: Wed, 26 Jan 2000 19:07:16 +1100 To: I use a script file in rasmol to view the results of molecular dynamics simulations of model atomic systems. The script file loads in a pdb file, writes an image file, zaps it, and then loads another pdb file, ad nauseum. I would like, if possible, to be able to use the script file to simply view an animation directly using rasmol but I find that in loading a new pdb file the screen goes temporarily blank after each pdb file is 'zapped'. This makes it difficult to view as the image of the atoms rapidly flashes on and off. The number of atoms is large in these animations and bond information is also included so generating an xyz file for viewing with Chime is not an option. Is there any way around this problem in Rasmol? I have used a script file within a web page to partially circumvent this problem but I find that the colours of atoms bleed severely. Bizarrely it only happens with some colors. This is using an SGI with IRIX 6.2, the problem doest occur on Windows. Any ideas as to why this would occur? Brendan O'Malley (brendan.omalley@rmit.edu.au) Applied Physics RMIT ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Rasmol/Chime Script Animations Date: Wed, 26 Jan 2000 12:39:36 -0800 To: rasmol@dhcp-srv2.oit.umass.edu At 07:07 PM 1/26/00 +1100, you wrote: > >I use a script file in rasmol to view the results of molecular >dynamics simulations of model atomic systems. The script >file loads in a pdb file, writes an image file, zaps it, and then >loads another pdb file, ad nauseum. Why can't you animate the results using something like Re_view or povray and aawin?? - - - - _ _ _ _ _ "Written laws are like spiders' webs, and like them will only entangle and hold the poor and weak, while the rich and powerful easily break through them. " Anacharsis (Scythian Philosipher) 600 BCE References: <3.0.6.32.20000126123936.0079b370@asis.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: odin Subject: unsubscribe Date: Wed, 26 Jan 2000 14:02:17 -0700 To: rasmol@dhcp-srv2.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: GODFREY HENRY Subject: unsubscribe Date: Wed, 26 Jan 2000 16:16:19 -0500 To: "'rasmol@dhcp-srv2.oit.umass.edu'" ++++------+------+------+------+------+------+------+------+------+------+ From: jromeo@sfsu.edu (Joseph Romeo) Subject: unsubscribe Date: Wed, 26 Jan 2000 14:13:26 -0700 To: rasmol@dhcp-srv2.oit.umass.edu ______________________________________________________________________________ Joseph Romeo, Associate Professor Center for Biomedical Laboratory Sciences San Francisco State University 1600 Holloway Ave San Francisco, CA 94132 Phone: 415 338-6008 FAX: 415 338-7747 ++++------+------+------+------+------+------+------+------+------+------+ From: "Hopkins, Nancy" Subject: RE: unsubscribe Date: Wed, 26 Jan 2000 16:56:59 -0600 To: "'rasmol@lists.umass.edu'" Help! Is there anyway for people to unsubscribe and not send the message to the entire list? For some reason I've started getting two or three of these messages a day. Thanks, NEH Nancy Eddy Hopkins, PhD Box 150214 Millsaps College Jackson MS 39210 601-974-1409 601-974-1401 FAX > -----Original Message----- > From: GODFREY HENRY [SMTP:HGODFREY@NYMC.EDU] > Sent: Wednesday, January 26, 2000 3:16 PM > To: hopkine@topaz2.millsaps.edu > Subject: unsubscribe > > References: charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Roy Fultun" Subject: Re: unsubscribe Date: Wed, 26 Jan 2000 23:20:30 -0800 To: Thanks for being vocal. I've had the same thing here. ----- Original Message ----- Sent: Wednesday, January 26, 2000 2:56 PM From: Hopkins, Nancy Subject: RE: unsubscribe To: 'rasmol@lists.umass.edu' > Help! Is there anyway for people to unsubscribe and not send the message to > the entire list? For some reason I've started getting two or three of these > messages a day. > > Thanks, > NEH > Nancy Eddy Hopkins, PhD > Box 150214 > Millsaps College > Jackson MS 39210 > > 601-974-1409 > 601-974-1401 FAX > > > -----Original Message----- > > From: GODFREY HENRY [SMTP:HGODFREY@NYMC.EDU] > > Sent: Wednesday, January 26, 2000 3:16 PM > > To: hopkine@topaz2.millsaps.edu > > Subject: unsubscribe > > > > > Content-MD5: 1B2M2Y8AsgTpgAmY7PhCfg== ++++------+------+------+------+------+------+------+------+------+------+ From: Julien Textoris Subject: unsubscribe Date: Thu, 27 Jan 2000 08:45:39 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id DAA03683 ++++------+------+------+------+------+------+------+------+------+------+ From: Lennart Nilsson Subject: How to unsubscribe Date: Thu, 27 Jan 2000 09:04:57 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is the information I received when I first subscribed to the rasmol list: Please do not send command requests (e.g., subscribe/unsubscribe) to the list; instead direct them to the ListProc server account: listproc@lists.umass.edu ie, if you wish to unsubscribe: send a message with the text unsubscribe in the subject field to listproc@lists.umass.edu Best regards, Lennart Nilsson ==========================///////////\\\\\\\\\\\============================ Professor Lennart Nilsson Phone: Int+46-8-6089228 Karolinska Institutet FAX: Int+46-8-6089290 Department of Bioscience, CSB Hälsovägen 7, floor 7 S-141 57 HUDDINGE, Sweden E-mail: Lennart.Nilsson@biosci.ki.se URL http://www.csb.ki.se/md/md.html boundary="----=_NextPart_000_001E_01BF68A1.C3B22A80" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 ++++------+------+------+------+------+------+------+------+------+------+ From: "Scott Lammas" Subject: unsubscribe Date: Thu, 27 Jan 2000 08:37:37 -0000 To: This is a multi-part message in MIME format. ------=_NextPart_000_001E_01BF68A1.C3B22A80 charset="iso-8859-1" ------=_NextPart_000_001E_01BF68A1.C3B22A80 charset="iso-8859-1"
 
------=_NextPart_000_001E_01BF68A1.C3B22A80-- References: <200001270745.IAA02888@jamaique.ens-lyon.fr> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Shoba Ranganathan Subject: unsubscribe Date: Fri, 28 Jan 2000 10:09:41 +1100 To: rasmol@dhcp-srv2.oit.umass.edu Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id WAA05562 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Re: Rasmol/Chime Script Animations Date: Fri, 28 Jan 2000 14:32:12 +1100 To: >>> skg@asis.com 01/27 7:39 AM >>> At 07:07 PM 1/26/00 +1100, you wrote: > >I use a script file in rasmol to view the results of molecular >dynamics simulations of model atomic systems. The script >file loads in a pdb file, writes an image file, zaps it, and then >loads another pdb file, ad nauseum. Why can't you animate the results using something like Re_view or povray and aawin?? The reason is that my MD simulations are on growing crystal nuclei and hence its useful to be able to reorientate the nuclei within Rasmol and rerun a script rather than go through the time-consuming process of generating hundreds of images and then making an AVI movie with them. Can you tell me what aawin and Re_view are? References: <3.0.6.32.20000127090457.00c8e0e0@whale.csb.ki.se> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 ++++------+------+------+------+------+------+------+------+------+------+ From: "Ronald Frisch" Subject: How to unsubscribe Date: Fri, 28 Jan 2000 10:33:35 -0800 To: Here is what I got back then(Lennart is right but you have to name the list (RASMOL)): ********** HOW TO GET OFF THE LIST ********** To sign off from the list, email to listproc@lists.umass.edu with the following request: signoff RASMOL or unsubscribe RASMOL ********** GETTING YOUR SUBSCRIPTION ATTRIBUTES ********** You may get your current subscription attributes at any time by sending the following request to listproc@lists.umass.edu: query RASMOL :)) I hope this matter will be dealt with then. Best regards, Ronald Frisch University of Mannheim, Germany Student of Computer Science, Protein Structure Prediction Project ----- Original Message ----- Sent: Thursday, January 27, 2000 12:04 AM From: "Lennart Nilsson" Subject: How to unsubscribe To: > This is the information I received when I first subscribed to the > rasmol list: > > Please do not send command requests (e.g., subscribe/unsubscribe) > to the list; instead direct them to the ListProc server account: > > listproc@lists.umass.edu > > > ie, if you wish to unsubscribe: > send a message with the text unsubscribe in the subject field to > listproc@lists.umass.edu > > Best regards, > Lennart Nilsson > > > > > ==========================///////////\\\\\\\\\\\============================ > Professor Lennart Nilsson Phone: Int+46-8-6089228 > Karolinska Institutet FAX: Int+46-8-6089290 > Department of Bioscience, CSB > Hälsovägen 7, floor 7 > S-141 57 HUDDINGE, Sweden > E-mail: Lennart.Nilsson@biosci.ki.se URL http://www.csb.ki.se/md/md.html > > boundary="Boundary_(ID_/C0T61Xd6sphhyRle2k+OA)" ++++------+------+------+------+------+------+------+------+------+------+ From: Ross Feldberg Subject: New Chime Site Date: Fri, 28 Jan 2000 15:20:42 -0500 To: rasmol@dhcp-srv2.oit.umass.edu --Boundary_(ID_/C0T61Xd6sphhyRle2k+OA) Hi all; I am pleased to announce that I have developed a new Chime-based site for student instruction in structural biochemistry. The site is designed to integrate structural instruction into several courses at Tufts. http://ase.Tufts.edu/biology/MolecVisual/open.html Currently, tutorials for introductory biology and for biochemistry are up and running, but I will be adding tutorals for Genetics and Molecular Biology in the next few months. Current tutorials include: Intro Bio Alpha helix and beta sheet Tertiary structure (myoglobin and hemoglobin) Aspects of enzyme active sites Lipids and membranes Biochem Reverse turns Hemoglobin Ras protein Lysozyme Chymotrypsin The tutorials are a bit different from many currently on the web as they tend to focus only on one or two aspects of a given protein and to provide more explanatory text. I have also tried to begin to address the didactic nature of Chime, by having some of the tutorials require that students make use of the Chime menu to answer specific questions on structure (and a tutorial to menu use is provided). Although the intro page tends to load a bit slower than I would like, I think the site design is attractive and functional (thanks to a talented undergrad). All pdb files are gzipped for speed of loading. Any suggestions or comments gratefully appreciated. Ross Feldberg Dept of Biology Tufts University --Boundary_(ID_/C0T61Xd6sphhyRle2k+OA) TimesHi all; I am pleased to announce that I have developed a new Chime-based site for student instruction in structural biochemistry. The site is designed to integrate structural instruction into several courses at Tufts. 0000,0000,00FFhttp://ase.Tufts.edu/biology/MolecVisual/open.html TimesCurrently, tutorials for introductory biology and for biochemistry are up and running, but I will be adding tutorals for Genetics and Molecular Biology in the next few months. Current tutorials include: Intro Bio Alpha helix and beta sheet Tertiary structure (myoglobin and hemoglobin) Aspects of enzyme active sites Lipids and membranes Biochem Reverse turns Hemoglobin Ras protein Lysozyme Chymotrypsin The tutorials are a bit different from many currently on the web as they tend to focus only on one or two aspects of a given protein and to provide more explanatory text. I have also tried to begin to address the didactic nature of Chime, by having some of the tutorials require that students make use of the Chime menu to answer specific questions on structure (and a tutorial to menu use is provided). Although the intro page tends to load a bit slower than I would like, I think the site design is attractive and functional (thanks to a talented undergrad). All pdb files are gzipped for speed of loading. Any suggestions or comments gratefully appreciated. Ross Feldberg Dept of Biology Tufts University --Boundary_(ID_/C0T61Xd6sphhyRle2k+OA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: How to Unsubscribe -- and the flurry of same Date: Sat, 29 Jan 2000 20:30:05 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmoleans: I was called out of town for 5 days unexpectedly, during which I was unable to do email daily. As luck would have it, more than a dozen people submitted unsubscribe requests during this 5 days (a highly unusual burst), and every one was inadvertantly broadcast to all of you. Unfortunately, the instructions for unsubscribing are not as accessible as they should be (for reasons given below). They are at the URL below, but it is not in front of people at the moment they wish to unsubscribe. The URL below says: ----BEGIN QUOTE---- Unsubscribing To unsubscribe, from the address you wish to unsubscribe send to listproc@lists.umass.edu this message: unsubscribe rasmol ----END QUOTE---- Note that this listproc ignores 'unsubscribe' if placed in the SUBJECT, and anyway wouldn't know which of the several lists it manages was relevant. The request must be in the BODY of the message. If you don't have access to the email account you wish to unsubscribe, just send the old email address to me (ME, not the list) and I'll be happy to do it. The reason the automatic mechanism insists on your sending the request from the address to be unsubscribed is so it can be sure to get the correct email address. Very commonly, when people type the email address manually, either it is misspelled, or they give an alternative form of the address which the list processor doesn't find and can't unsubscribe. The listproc I am using is no longer supported by my University's computer staff and I have been unable to get it to respond to erroneous unsubscribe requests with a more helpful message, nor have I been able to append the unsubscribe instructions to EVERY broadcast message (following the excellent example of pdb-l). I am reluctant to invest the time to move this list to a newer support system, since I have already invested a lot of time to get it this far. Someday, moving it will probably become necessary, but until then, please excuse the occasional rough spots. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Discussing Swiss-PDBViewer Here Date: Sat, 29 Jan 2000 20:39:21 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Discussions of Swiss-PDBViewer are very welcome here, on this list. If Nicolas Guex and Gale Rhodes link the URL for this list (http://www.umass.edu/microbio/rasmol/raslist.htm) to their documentation for Swiss-PDBViewer, they may designate it officially as the primary venue for such discussions. Once we see how much SPDBV traffic occurs, we could discuss whether a new separate list needs to be created for SPDBV (as K. Arun recently suggested). I use Chime, RasMol, or Swiss-PDBViewer depending on what best suits my needs in a given situation. Subscribers unfamiliar with Swiss-PDBViewer will benefit from knowing more about it. Over a year ago, I invited Nicolas Guex (author of the excellent Swiss-PDBViewer freeware) to make this email list the offical place for discussing Swiss-PDBViewer. Nicolas and Gale Rhodes (evidently Swiss-PDBViewer's strongest advocate, and author of its introduction for beginners) seemed to like the idea, but none of us ever got around to making any kind of official announcement. Some time ago I did, however, explicitly list RasMol, Chime, and Swiss-PDBViewer as particularly appropriate topics for discussion at the list's website, http://www.umass.edu/microbio/rasmol/raslist.htm So a better name for this list would be the "Molecular Visualization and Modeling Freeware Discussion" or some such, but it hardly seems worth the effort to change it officially from the "RasMol List" which rolls off the tongue so nicely (and has established name recognition). Nevertheless, suggestions for rewording of http://www.umass.edu/microbio/rasmol/raslist.htm are welcome. The list broadcast 525 messages in 1999 (average 1.4 messages/day). We have 505 subscribers at the moment. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at rasmol@dhcp-srv2.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Stephen Koch Subject: Scifinder Scholar 3.0 provides 3D structures of molecules Date: Mon, 31 Jan 2000 17:32:41 -0500 To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST , There is a an interesting feature in version 3.0 of SciFinder Scholar and I presume SciFinder. SciFinder Scholar is a rather expensive (subscription based) way to search Chemical Abstracts. As is described in the help manual, if you install MDL Web Viewer Lite (which is free) then when you do a search you automatically get for many compounds a link to the 3D structure of the molecule. It is a convenient way to get the three-dimensional coordinates of compounds. The coordinates are not those from X-ray crystal structures but rather are likely the results of simple molecular mechanics calculations. There is however a problem with the structure of some inorganic compounds. It appears to assume that all four-coordinate compounds are tetrahedral. This is an excellent approach for organic compounds but not for inorganic compounds. Stephen A. Koch 516-632-7944 (7931) Koch@sbchem.sunysb.edu Fax 516-632-7960 Department of Chemistry, SUNY,Stony Brook, NY 11794-3400 Bioinorganic WWW Server: http://www.chem.sunysb.edu/koch/biic.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: ChemInt2000 - Web Abstract Submission Form Now Operational Date: Wed, 02 Feb 2000 12:34:02 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Chimeleons who don't subscribe to pdb-l may find this of interest. -Eric >Date: Wed, 2 Feb 2000 08:21:47 -0500 (EST) >From: Steve Heller >Subject: ChemInt2000 - Web Abstract Submission Form Now Operational >Sender: owner-pdb-l@rcsb.org > >This note is to announce that web Abstract Submission form is now >operational for the Chemistry and the Internet (ChemInt2000) meeting >being held in at Georgetown University in Washington DC on September >23-26, 2000. > >The draft program of invited speakers, workshops, markup langauge >tutorial, and panel sessions is available on the meeting web site: > > >http://www.chemint.org > >You are urged to look at the program and to consider submitting a >poster paper to the meeting. Some 8-10 of poster papers will be selected >for oral presentation at the meeting. > >The main lecturers for the meeting will be: > >Rene DePlanque, FIZ - Berlin >Jim Myers, Pacific Northwest Labs >Glen Hopkinson, Synopsys Scientific Systems >Wolf-Dietrich Ihlenfeldt, University of Erlangen-Nurenberg >Jim Ostell, NIH/NLM/NCBI >Engelbert Zass, ETH >Henry Rzepa, Imperial College, London >Peter Murray-Rust, Nottingham University > > >The (current) corporate sponsors for the meeting are: >SciVision >Internet Journal of Chemistry > > >Technical Sponsors are: > >ACS CINF Division >ACS COMP Division >The Chemical Structure Association (CSA) >Georgetown University - Department of Chemistry >Special Libraries Association (SLA) Chemistry Division >Royal Society of Chemistry (RSC) > > >Steve Heller > > > >Steve Heller, Guest Researcher >NIST/SRD, Mail Stop: 820/113 >820 Diamond Avenue, Room 101 >Gaithersburg, MD 20899-2310 USA >E-mail: chem@feldmann.nist.gov - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Stephen Koch Subject: Re: Scifinder Scholar 3.0 provides 3D structures of molecules Date: Wed, 02 Feb 2000 17:02:14 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I accidently confused companies in referring to Web Viewer Lite and its use in Scifinder Scholar. It is produced by MSI. http://www.msi.com/life/products/weblab/viewer/register/lite/download_lite.html Stephen A. Koch 516-632-7944 (7931) Koch@sbchem.sunysb.edu Fax 516-632-7960 Department of Chemistry, SUNY,Stony Brook, NY 11794-3400 Bioinorganic WWW Server: http://www.chem.sunysb.edu/koch/biic.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Scifinder Scholar 3.0 provides 3D structures of molecules Date: Wed, 02 Feb 2000 18:08:28 -0500 To: rasmol@dhcp-srv2.oit.umass.edu [Forwarded to the list for Stephen Koch. -Eric Martz] I accidently confused companies in referring to Web Viewer Lite and its use in Scifinder Scholar. It is produced by MSI. http://www.msi.com/life/products/weblab/viewer/register/lite/download_lite. html Stephen A. Koch 516-632-7944 (7931) Koch@sbchem.sunysb.edu Fax 516-632-7960 Department of Chemistry, SUNY,Stony Brook, NY 11794-3400 Bioinorganic WWW Server: http://www.chem.sunysb.edu/koch/biic.html X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id DAA28117 ++++------+------+------+------+------+------+------+------+------+------+ From: "Olivier Louvet" Subject: file format Date: Thu, 3 Feb 2000 09:51:54 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear All, How can I obtain (or convert) protein 3D files in mdl, alchemy, mol2, charmm and xyz formats? Can anybody explain me what is the informatic structure of the pdb files (that means, how is it structured and how Rasmol extract the informations from it)? Thank you for yourhelp. Sincerely Olivier Louvet ----- La messagerie itinérante sans abonnement NetCourrier ----- Web : www.netcourrier.com Minitel : 3615 et 3623 NETCOURRIER Tél : 08 36 69 00 21 References: X-Accept-Language: de ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Frank Eblinger" Subject: Re: file format Date: Thu, 03 Feb 2000 10:24:58 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi Olivier with RasMol 2.7 you can save the pdb files as different formats save mdl filename.mdl etc. you get more infos with help write Frank Olivier Louvet schrieb: > Dear All, > > How can I obtain (or convert) protein 3D files in mdl, alchemy, mol2, charmm and xyz formats? > > Can anybody explain me what is the informatic structure of the pdb files (that means, how is it structured and how Rasmol extract the informations from it)? > > Thank you for yourhelp. > > Sincerely Olivier Louvet > > ----- La messagerie itinérante sans abonnement NetCourrier ----- > Web : www.netcourrier.com Minitel : 3615 et 3623 NETCOURRIER > Tél : 08 36 69 00 21 charset="iso-8859-1" X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id JAA28644 ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: file format Date: Thu, 3 Feb 2000 09:43:45 -0500 To: "'rasmol@lists.umass.edu'" Olivier, >How can I obtain (or convert) protein 3D files in mdl, alchemy, >mol2, charmm and xyz formats? You might take a look at Babel (http://www.eyesopen.com/babel.html) it is sort of the master translator for between molecular modeling file formats. >Can anybody explain me what is the informatic structure of the pdb files >(that means, how is it structured and how Rasmol extract the >informations from it)? You can get information on the pdb file structure from the PDB at http://www.rcsb.org/pdb/info.html#File_Formats_and_Dictionaries As for how RasMol extracts the info... all I know is that I am glad it does! ;-) Hope this helps, --- Frank ------------------------------------------ Frank R. Gorga, Ph.D. Dept. of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 508-531-1785 (fax) fgorga@bridgew.edu http://topcat.bridgew.edu/~fgorga -----Original Message----- Sent: Thursday, February 03, 2000 3:52 AM From: Olivier Louvet [mailto:louvet@netcourrier.com] Subject: file format To: FGORGA@mailhost.bridgew.edu Dear All, How can I obtain (or convert) protein 3D files in mdl, alchemy, mol2, charmm and xyz formats? Can anybody explain me what is the informatic structure of the pdb files (that means, how is it structured and how Rasmol extract the informations from it)? Thank you for yourhelp. Sincerely Olivier Louvet ----- La messagerie itinérante sans abonnement NetCourrier ----- Web : www.netcourrier.com Minitel : 3615 et 3623 NETCOURRIER Tél : 08 36 69 00 21 X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Gitte Iversen Subject: Can I get a molecules menu in Rasmol running on Unix Date: Fri, 04 Feb 2000 12:17:17 +0100 To: Rasmol Mailinglist Dear Rasmol Users. Normally I use rasmol vs. 2.6.4 or 2.7.0.1. in a Unix environment. However, lately I saw a pc-version of rasmol with a very nice "Molecules menu", where one could also directly activate monitors for distance, angle etc. The pc version is RasWin 2.6-ucb. I do not find this "molecules menu" in the versions compiled for Unix - should it be there? And if yes, in which version? Hope someone can help me further. Gitte -- ************************************************************** Gitte Iversen, Ph.D. Applied Bioinformatics Centre Phone: +45 3587 8979 DTU, Bldg. 208 Room 018 Fax: +45 3587 8990 DK-2800 Lyngby E-Mail: gitte.iversen@ab-c.dk Denmark WWW: www.ab-c.dk ************************************************************** References: X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: file format Date: Fri, 4 Feb 2000 14:27:34 +0100 To: Olivier, You may have to consider Mol2Mol, which is capable of interconverting a number of different file formats Have a look on http://www.compuchem.com/mol2mol.htm Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Thursday, February 03, 2000 9:51 AM From: Olivier Louvet Subject: file format To: Dear All, How can I obtain (or convert) protein 3D files in mdl, alchemy, mol2, charmm and xyz formats? Can anybody explain me what is the informatic structure of the pdb files (that means, how is it structured and how Rasmol extract the informations from it)? Thank you for yourhelp. Sincerely Olivier Louvet ----- La messagerie itinérante sans abonnement NetCourrier ----- Web : www.netcourrier.com Minitel : 3615 et 3623 NETCOURRIER Tél : 08 36 69 00 21 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian W. Beck" Subject: cartoons command vs menu Date: Fri, 4 Feb 2000 10:18:54 -0600 (CST) To: rasmol@dhcp-srv2.oit.umass.edu (Rasmol Listserv) Hey Rasmolians: I've poked around in the documentation, but I can't determine why the "cartoons" command draws non-helix/non-sheet as ribbon but the cartoons menu draws the same with "trace 0.5". Was this done on purpose for some reason? I personally like the trace (tube) over the ribbon, but I'm curious why there's a difference. -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== References: <200002041618.KAA03140@Ba.Chem.UH.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: cartoons command vs menu Date: Fri, 04 Feb 2000 16:46:24 +0000 To: Rasmol Listserv This came up on the list a few years back, and I think Roger Sayle answered it. I don't think there is a 'why' except that's the way it was programmed. The command line way to do it is something like select helix or sheet cartoon select not helix and not sheet trace 100 which is more like what happens when you choose 'Cartoons' from the menu (I think it's actually a little more complicated by specifying each of sheet and helix with a respective size, but the above is the shortest way of writing it). Kurt -- Dr Kurt Giles kurt.giles@oxford.ac.uk Glaxo Wellcome Graduate Centre for Biosciences Departments of Experimental Psychology and Zoology Oxford OX1 3UD Phone: +44-1865-271342 Fax: +44-1865-310447 ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook Seng Subject: Re: file format Date: Fri, 11 Feb 2000 00:58:40 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Hello, I can give you some information about PDB file format. I know how to represent xyz co-ordinate in PDB format. If you are interested , let me know . (perhaps i will take time to reply to you, sorry in advance) James ===== James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com References: <20000211085840.5279.qmail@web112.yahoomail.com> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 ++++------+------+------+------+------+------+------+------+------+------+ From: "VAN DE WIELE" Subject: Re: file format Date: Sat, 12 Feb 2000 19:55:30 +0100 To: , I should be very interested too with the reply. Thank you in advance for a copy for a baby chimeleon ! Annie avandewiele@nordnet.fr ----- Original Message ----- Sent: Friday, February 11, 2000 9:58 AM From: James Leong Mook Seng Subject: Re: file format To: > Hello, > I can give you some information about PDB file > format. I know how to represent xyz co-ordinate in PDB > format. If you are interested , let me know . > (perhaps i will take time to reply to you, sorry in > advance) > > James > > ===== > > > James Leong Mook seng > Clairfonds No 2, Vacoas > Mauritius. > > > __________________________________________________ > Do You Yahoo!? > Talk to your friends online with Yahoo! Messenger. > http://im.yahoo.com > James Leong Mook Seng References: <20000211085840.5279.qmail@web112.yahoomail.com> X-Apparently-From: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: DavinciXXI Subject: Re: file format Date: Sun, 13 Feb 2000 12:01:07 -0300 To: rasmol@dhcp-srv2.oit.umass.edu Cc: VAN DE WIELE , Hi! The protein Data Bank (PDB) has a good tutorial related to PDB file formats http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html Sincerely, James Leong Mook Seng wrote: > Hello, > I can give you some information about PDB file > format. I know how to represent xyz co-ordinate in PDB > format. If you are interested , let me know . > (perhaps i will take time to reply to you, sorry in > advance) > > James > > ===== > > James Leong Mook seng > Clairfonds No 2, Vacoas > Mauritius. > > __________________________________________________ > Do You Yahoo!? > Talk to your friends online with Yahoo! Messenger. > http://im.yahoo.com __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PDB Lite now with Protein Explorer Date: Sun, 20 Feb 2000 13:38:08 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: lsprilus@weizmann.weizmann.ac.il PDB Lite, released in 1998, is designed for nonspecialists who search for atomic coordinate ("PDB") files at the Protein Data Bank on an occasional basis. It is especially aimed at students and educators. The PDB Lite search interface home page, www.umass.edu/microbio/rasmol/pdblite.htm, has been updated. PDB Lite is now available with direct links to Protein Explorer. When you find a molecule, clicking the link to Protein Explorer automatically loads that molecule and displays it in Protein Explorer. PDB Lite constantly updated with the weekly releases from RCSB is currently available from Israel, USA, Poland, and Australia. PDB Lite is a collaboration between myself and Jaime Prilusky. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Swiss-PdbViewer Discussion Group Date: Mon, 21 Feb 2000 14:34:32 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Today I activated a discussion group for users of Swiss-PdbViewer. If you are interested in participating or learning more, please visit http://www.usm.maine.edu/~rhodes/SPVTut/text/DiscuSPV.html Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu WWW Home Page: http://www.usm.maine.edu/~rhodes Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 ++++------+------+------+------+------+------+------+------+------+------+ From: Alfredo Lopez De Leon Subject: Yet Another LINUX Installation Question Date: Thu, 17 Feb 2000 14:03:02 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmol List Subscribers: I have been trying to install RasMol 2.7 on my Laptop (Caldera Open Linux 2.3) but I get this anoying "Error 1" and then everything stops. I will appreciate any suggestions you may have. Thanks in advance Alfredo This is the out put that I get after I do make. ******************************************************************************* $ make gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -Dlinux -D__i386__ -D_PO SIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_ SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -D EIGHTBIT -c rasmol.c -o rasmol.o In file included from /usr/include/signal.h:294, from rasmol.c:10: /usr/include/bits/sigcontext.h:28: asm/sigcontext.h: No such file or directory In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:30, from /usr/lib/gcc-lib/i386-linux/egcs-2.91.66/include/limits.h:117, from /usr/lib/gcc-lib/i386-linux/egcs-2.91.66/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-linux/egcs-2.91.66/include/limits.h:11, from /usr/include/bits/socket.h:31, from /usr/include/sys/socket.h:34, from rasmol.c:76: /usr/include/bits/local_lim.h:27: linux/limits.h: No such file or directory In file included from /usr/include/sys/socket.h:34, from rasmol.c:76: /usr/include/bits/socket.h:275: asm/socket.h: No such file or directory make: *** [rasmol.o] Error 1 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Sequence numbering pecularities in PDB files Date: Mon, 28 Feb 2000 14:16:31 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I am working on the sequence reporting and sequence-to-structure interface for the forthcoming enhanced version of Protein Explorer. This requires that I handle the various peculiarities in PDB file sequence numbering. (At present, Chime can only report the sequences of ATOM records; not the SEQRES records. So I am only dealing with the ATOM record group/residue numbering at this time. I am aware that the SEQRES records and ATOM record residue numbering schemes may not agree.) I am aware of these pecularities for ATOM record sequence numbering: 1. Sequence numbering can start at a number higher than one and contain gaps. Examples: chain B in 1avp starts at 205; chain 4 in 1fod contains a 24-residue gap. According to the "PDB Format Description Version 2.3" (http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html) gaps may signify unresolved atomic positions, or gaps in multiple sequence alignments required to preserve sequence numbering alignment with a reference chain. 2. Sequence numbering can start with a negative number and/or include a residue numbered zero. Example: 1avq. 3. Two or more consecutive residues can be given the same sequence number. In the examples I've seen, the redundant numbers are distinguished with letters, e.g. 82, 82A, 82B, 82C. Example: chain A residues 52x2, 82x4, 100x4 in 1igt. The letters are called an 'insertion code' and are part of the official PDB format. They are allocated a single column, 27, following columns 23-26 reserved for the sequence number. 4. A hetero moiety covalently attached to standard residue can be given the same residue number in the same chain. Example: MYR 1 and GLY 1 in 1jsa. Are there other categories of exceptions upon which I haven't yet stumbled? Do sequence numbers ever go in reverse (for example ... 22 23 24 25 *24 25 26 27 ...) ? Are residues in the middle of a numbered sequence ever simply not given a number? Please share any exceptional cases or juicy examples you know about. Thanks, -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at X-Envelope-To: ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: Sequence numbering pecularities in PDB files Date: Mon, 28 Feb 2000 14:48:48 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu Dear Eric, Here are the rules for the residue identification fields in PDB entries: 1. The four-digit residue number cannot be blank. The one-character insertion code may be blank or not, as necessary. The residue numbers can be in ascending or decreasing order. Zero and negative numbers are permitted. Residues of one chain must be presented together and must start with the N or 5' terminus. 2. The residue number together with the insertion code forms the residue identification. A chain is defined as a linked series of residues that appear on one set of SEQRES records. Each residue within a chain must have a unique residue identification. Het groups associated with a chain may have the same residue identification as residues within that chain. It would be 'simpler' if all chains were numbered from 1 to N. Many proteins, however, are numbered by homology with the same protein from other species or with similar proteins. People studying related proteins wish to be able, say, to discuss the catalytic residue 195 and have that residue be numbered 195 in all related proteins. Because the sequences can vary in length relative to one another and have gaps/insertions relative to one another, it is necesary to have the insertion code field and allow for gaps in numbering. Even in proteins that are numbered sequentially from 1 to N, there may be gaps in the residue numbering in the ATOM records because some residues may not have been located in the experiment. Residue numbering may be based on the protein that was expressed and then cleaved. I hope that this is helpful. Sincerely, Frances C. Bernstein P.S. There is at least one entry where a chain in numbered in decreasing order but I do not recall which one it is. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Mon, 28 Feb 2000, Eric Martz wrote: > I am working on the sequence reporting and sequence-to-structure interface > for the forthcoming enhanced version of Protein Explorer. This requires > that I handle the various peculiarities in PDB file sequence numbering. (At > present, Chime can only report the sequences of ATOM records; not the > SEQRES records. So I am only dealing with the ATOM record group/residue > numbering at this time. I am aware that the SEQRES records and ATOM record > residue numbering schemes may not agree.) > > I am aware of these pecularities for ATOM record sequence numbering: > > 1. Sequence numbering can start at a number higher than one and contain > gaps. Examples: chain B in 1avp starts at 205; chain 4 in 1fod contains a > 24-residue gap. According to the "PDB Format Description Version 2.3" > (http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html) gaps > may signify unresolved atomic positions, or gaps in multiple sequence > alignments required to preserve sequence numbering alignment with a > reference chain. > > 2. Sequence numbering can start with a negative number and/or include a > residue numbered zero. Example: 1avq. > > 3. Two or more consecutive residues can be given the same sequence number. > In the examples I've seen, the redundant numbers are distinguished with > letters, e.g. 82, 82A, 82B, 82C. Example: chain A residues 52x2, 82x4, > 100x4 in 1igt. The letters are called an 'insertion code' and are part of > the official PDB format. They are allocated a single column, 27, following > columns 23-26 reserved for the sequence number. > > 4. A hetero moiety covalently attached to standard residue can be given the > same residue number in the same chain. Example: MYR 1 and GLY 1 in 1jsa. > > Are there other categories of exceptions upon which I haven't yet stumbled? > > Do sequence numbers ever go in reverse (for example ... 22 23 24 25 *24 25 > 26 27 ...) ? > > Are residues in the middle of a numbered sequence ever simply not given a > number? > > Please share any exceptional cases or juicy examples you know about. > Thanks, -Eric > > - - - > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 01003-5720 > > RasMol Email List > TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. > History -- all messages sent to this list are searchable at > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Helge Weissig Subject: selecting hetero's which are part of solvent Date: Mon, 28 Feb 2000 17:10:17 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Hi, I am trying to generate a rasmol script that would select a specific hetero group and render it spacefilled. Using select XYZ spacefill works for all cases where XYZ is NOT part of what rasmol considers solvent. However, if XYZ is part of the solvent set, nothing is selected. I can select specific XYZ's in structures that I know. For example: select hetero and not HOH and not HEM spacefill works for the PO4 group in 4hhb for example. However, I am trying to code something generic and the above approach would thus not work. any help is highly appreciated! best regards, h. +--------------------------------------------+ | Helge Weissig, PhD | | Technical Project Manager, PDB | | San Diego Supercomputer Center +-----------------------------------+ | voice: +1 858 534 8399 | mail: PO Box 85608 | | fax: +1 858 822 0873 | San Diego, CA 92186-5608 | +---------------------------------| direct: 10100 John J. Hopkins Dr. | | La Jolla, CA 92093-0537 | +-----------------------------------+ References: X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: selecting hetero's which are part of solvent Date: Tue, 29 Feb 2000 07:50:23 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi Helge, I suggest using select PO? and hetero or select SO? and hetero may be its a problem RasMol has with digits in residue names. Regards, Jan > I am trying to generate a rasmol script that would select a > specific hetero group and render it spacefilled. Using > > select XYZ > spacefill > > works for all cases where XYZ is NOT part of what rasmol considers > solvent. However, if XYZ is part of the solvent set, nothing is selected. > I can select specific XYZ's in structures that I know. For example: > > select hetero and not HOH and not HEM > spacefill > > works for the PO4 group in 4hhb for example. However, I am trying to code > something generic and the above approach would thus not work. > > any help is highly appreciated! > > best regards, > h. > > +--------------------------------------------+ > | Helge Weissig, PhD | > | Technical Project Manager, PDB | > | San Diego Supercomputer Center +-----------------------------------+ > | voice: +1 858 534 8399 | mail: PO Box 85608 | > | fax: +1 858 822 0873 | San Diego, CA 92186-5608 | > +---------------------------------| direct: 10100 John J. Hopkins Dr. | > | La Jolla, CA 92093-0537 | > +-----------------------------------+ -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: selecting hetero's which are part of solvent Date: Tue, 29 Feb 2000 10:24:34 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Helge, I suspect you are running into the problem that if a group name includes a digit, it must be enclosed in [] for selection. For example select po4 fails but select [po4] succeeds. This is documented in the RasMol reference manual http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual (also available in Spanish) and in my guide "Select Commands in Chime and RasMol" http://www.umass.edu/microbio/rasmol/seleccmd.htm Also perhaps the predefined term 'solvent' would be useful? for example 'select solvent and not water' If this is not the problem, please give specific examples with PDB codes. -Eric At 02/28/2000, you wrote: >Hi, > > I am trying to generate a rasmol script that would select a >specific hetero group and render it spacefilled. Using > >select XYZ >spacefill > >works for all cases where XYZ is NOT part of what rasmol considers >solvent. However, if XYZ is part of the solvent set, nothing is selected. >I can select specific XYZ's in structures that I know. For example: > >select hetero and not HOH and not HEM >spacefill > >works for the PO4 group in 4hhb for example. However, I am trying to code >something generic and the above approach would thus not work. > >any help is highly appreciated! > >best regards, >h. > >+--------------------------------------------+ >| Helge Weissig, PhD | >| Technical Project Manager, PDB | >| San Diego Supercomputer Center +-----------------------------------+ >| voice: +1 858 534 8399 | mail: PO Box 85608 | >| fax: +1 858 822 0873 | San Diego, CA 92186-5608 | >+---------------------------------| direct: 10100 John J. Hopkins Dr. | > | La Jolla, CA 92093-0537 | > +-----------------------------------+ > - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at Content-Disposition: inline X-Lotus-FromDomain: BIOGEN ++++------+------+------+------+------+------+------+------+------+------+ From: Herman_Van_Vlijmen@biogen.com Subject: atomic radii again Date: Tue, 29 Feb 2000 11:04:14 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I am trying to create transparent spheres in Rasmol (Chime actually) to display pharmacophoric features. I have been using the "dots" command, and this works and looks fine. The problem is that you are limited to the radii you can assign to these spheres, since it looks at the atomic radius which is hard coded (in abstree.h). I have been assigning atom types like "V" (radius 1.06) to display pharmacophoric features with a radius of 1 A, but I would like to have a cleaner solution. I have also noticed that Chime does not display atom types such as "Be" (radius 0.63), "As" (radius 0.83), etc. correctly. The easy solution is of course to use the spacefill command, but I cannot make the spheres transparent, and I need that to display molecules that fit the pharmacophore sphere. Any suggestions? Thanks, Herman van Vlijmen The top of the list of smallest radii (processed from abstree.h; The 4th column shows the atomic radius in A): Be 88 157 0.63 12 "BERYLLIUM" As 302 207 0.83 12 "ARSENIC" Se 305 225 0.90 12 "SELENIUM" V 332 265 1.06 12 "VANADIUM" H 80 275 1.10 4 "HYDROGEN" At 302 280 1.12 12 "ASTATINE" Sb 365 280 1.12 12 "ANTIMONY" Co 332 282 1.13 12 "COBALT" Cr 338 282 1.13 9 "CHROMIUM" Cu 380 287 1.15 10 "COPPER" Zn 362 287 1.15 10 "ZINC" Mn 338 297 1.19 9 "MANGANESE" Ru 350 300 1.20 12 "RUTHENIUM" Po 420 302 1.21 12 "POLONIUM" Ir 330 305 1.22 12 "IRIDIUM" Li 170 305 1.22 14 "LITHIUM" Rh 362 305 1.22 12 "RHODIUM" Ta 358 305 1.22 12 "TANTALUM" Ni 405 310 1.24 10 "NICKEL" Te 368 315 1.26 12 "TELLURIUM" W 342 315 1.26 12 "TUNGSTEN" F 160 325 1.30 6 "FLUORINE" Re 338 325 1.30 12 "RHENIUM" Sc 360 330 1.32 12 "SCANDIUM" Nb 370 332 1.33 12 "NIOBIUM" O 170 337 1.35 2 "OXYGEN" Hf 392 350 1.40 12 "HAFNIUM" N 170 350 1.40 1 "NITROGEN" Zr 390 355 1.42 12 "ZIRCONIUM" Pd 375 360 1.44 12 "PALLADIUM" Au 375 362 1.45 6 "GOLD" In 408 362 1.45 12 "INDIUM" Al 338 375 1.50 9 "ALUMINIUM" Mg 275 375 1.50 15 "MAGNESIUM" Lu 430 382 1.53 12 "LUTETIUM" Yb 485 385 1.54 12 "YTTERBIUM" Ag 398 387 1.55 9 "SILVER" B 208 387 1.55 13 "BORON" C 180 387 1.55 0 "CARBON" References: <85256894.005843AB.00@camb020.biogen.com> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 ++++------+------+------+------+------+------+------+------+------+------+ From: "Ronald Frisch" Subject: Re: atomic radii again Date: Fri, 3 Mar 2000 07:31:49 -0800 To: Hi Herman, I had a similar problem a while ago, wanting to color atoms individually. The same is possible with radii, I think. You have to modify PDB files though, please read through the attached messages I took from my email archive. The last message from Roger Sayle is the most important I guess, because he mentions how to actually use the radius data from a PDB file. Hope that helps. Regards, Ronald Frisch frisch@rumms.uni-mannheim.de University of Mannheim, Germany Student ---------------------------------------------------------------------------------------- (Ronald Frisch).... trying to visualize certain protein atom properties like accessible surface / solvation contact I came upon the "user color" menu option in RasMol. I found how to build those COLO records and quickly implemented into my project so that the result is a PDB file with a COLO record for each atom. I have found that RasMol accepts no more than roughly 25 COLO records, otherwise it won't display the PDB file giving this error message: "Too many color records in file." Is there a way to make RasMol display much more COLO records? (like 200) The most likely source for an answer is Roger Sayle -- or maybe Herbert Bernstein if he is familiar with this zone of the source code. Meanwhile, please enlighten the rest of us about the format for COLO records! Send a description to the list, please. I have never used COLO records and neither has anyone else I know of because in most cases a simple script with select commands followed by color commands does the job more effectively. For an example, see http://www.umass.edu/microbio/rasmol/makescrp.htm#allmol -Eric Martz --------------- If you read the Rasmol source or look in the Raster3d distribution (mycolours.pdb), I believe the COLO record is something like the following: 1-6 COLOUR 7-30 ATOM and/or SEQ and/or CHAIN MASK (Mask format same as ATOM) 31-54 Red(F8.3),Blue(F8.3),Green(F8.3) (0-1 range) 55-60 ??Radius(F6.2)?? (I don't know that it's actually radius) eg. COLOUR#######C################ 1.000 1.000 1.000 1.70 is equal to all carbons white with a radius of 1.70A COLOUR#######CA##GLY########## 0.200 1.000 0.200 2.00 is equal to all GLY alpha carbons greenish with a radius of 2.00A It seems also that the first mask to equate takes precedence over subsequent masks. Regarding the limit of 25 masks, alter MAXMASK in molecule.h. -Brian W. Beck -------------------------- Hi all, thank you for the information, Brian, changing the MAXMASK constant in molecule.h definitely solved my problem. Usually it is 40, I think, I tried 400 and it works just fine. That way, 400 user colour masks can be applied to a molecule which is enough for me. The way I use the COLO records is like this, I create a mask for each atom I want to colour and also provide a default mask/colour for all atoms that are not described by a preceding mask. I have not figured out the use of the last value, you should be able to actually set something like a radius, since I don't need it, I just leave it away. .... ATOM 194 N THR 28 3.827 14.802 6.358 1.00 4.53 ATOM 195 CA THR 28 2.691 15.221 7.194 1.00 5.08 ATOM 196 C THR 28 1.672 14.132 7.434 1.00 4.62 ATOM 197 O THR 28 .947 14.112 8.468 1.00 7.80 ATOM 198 CB THR 28 1.986 16.520 6.614 1.00 6.03 COLO 194 N ### ##### 0.707 0.707 1.000 COLO 195 CA ### ##### 0.610 0.610 1.000 COLO 196 C ### ##### 0.617 0.617 1.000 COLO 197 O ### ##### 0.425 0.425 1.000 COLO 198 CB ### ##### 0.437 0.437 1.000 COLO ######################## 0.100 0.100 0.100 .... (For the mask, the atom number only would suffice of course, the atom type is not needed. the colours are values from white to blue, default is almost black...) -Ronald Frisch ------------------------ > The way I use the COLO records is like this, I create a mask for each > atom I want to colour and also provide a default mask/colour for all > atoms that are not described by a preceding mask. I have not figured out > the use of the last value, you should be able to actually set > something like a radius, since I don't need it, I just leave it away. The final column in a COLOR record is indeed the radius. The appropriate RasMol command to use these radii is "spacefill user" or "cpk user". This behaves almost the same as "spacefill temperature" (or "cpk temperature") but in the later the radius is defined by the bfactor field in the PDB file. Roger Sayle -------------------------------------------------------------------------------------------------------------- -------------------- ----- Original Message ----- Sent: Tuesday, February 29, 2000 8:04 AM From: Subject: atomic radii again To: > > > I am trying to create transparent spheres in Rasmol (Chime actually) to display > pharmacophoric features. I have been using the "dots" command, and this works > and looks fine. The problem is that you are limited to the radii you can assign > to these spheres, since it looks at the atomic radius which is hard coded (in > abstree.h). I have been assigning atom types like "V" (radius 1.06) to display > pharmacophoric features with a radius of 1 A, but I would like to have a cleaner > solution. I have also noticed that Chime does not display atom types such as > "Be" (radius 0.63), "As" (radius 0.83), etc. correctly. > The easy solution is of course to use the spacefill command, but I > cannot make the spheres transparent, and I need that to display molecules that > fit the pharmacophore sphere. > Any suggestions? > > Thanks, > Herman van Vlijmen > > The top of the list of smallest radii (processed from abstree.h; The 4th column > shows the atomic radius in A): > > Be 88 157 0.63 12 "BERYLLIUM" > As 302 207 0.83 12 "ARSENIC" > Se 305 225 0.90 12 "SELENIUM" > V 332 265 1.06 12 "VANADIUM" > H 80 275 1.10 4 "HYDROGEN" > At 302 280 1.12 12 "ASTATINE" > Sb 365 280 1.12 12 "ANTIMONY" > Co 332 282 1.13 12 "COBALT" > Cr 338 282 1.13 9 "CHROMIUM" > Cu 380 287 1.15 10 "COPPER" > Zn 362 287 1.15 10 "ZINC" > Mn 338 297 1.19 9 "MANGANESE" > Ru 350 300 1.20 12 "RUTHENIUM" > Po 420 302 1.21 12 "POLONIUM" > Ir 330 305 1.22 12 "IRIDIUM" > Li 170 305 1.22 14 "LITHIUM" > Rh 362 305 1.22 12 "RHODIUM" > Ta 358 305 1.22 12 "TANTALUM" > Ni 405 310 1.24 10 "NICKEL" > Te 368 315 1.26 12 "TELLURIUM" > W 342 315 1.26 12 "TUNGSTEN" > F 160 325 1.30 6 "FLUORINE" > Re 338 325 1.30 12 "RHENIUM" > Sc 360 330 1.32 12 "SCANDIUM" > Nb 370 332 1.33 12 "NIOBIUM" > O 170 337 1.35 2 "OXYGEN" > Hf 392 350 1.40 12 "HAFNIUM" > N 170 350 1.40 1 "NITROGEN" > Zr 390 355 1.42 12 "ZIRCONIUM" > Pd 375 360 1.44 12 "PALLADIUM" > Au 375 362 1.45 6 "GOLD" > In 408 362 1.45 12 "INDIUM" > Al 338 375 1.50 9 "ALUMINIUM" > Mg 275 375 1.50 15 "MAGNESIUM" > Lu 430 382 1.53 12 "LUTETIUM" > Yb 485 385 1.54 12 "YTTERBIUM" > Ag 398 387 1.55 9 "SILVER" > B 208 387 1.55 13 "BORON" > C 180 387 1.55 0 "CARBON" > > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Sequence numbering pecularities in PDB files Date: Fri, 03 Mar 2000 10:16:20 -0500 To: rasmol@dhcp-srv2.oit.umass.edu [I have forwarded this for Torsten Schwede to circumvent technical difficulties. -Eric Martz] Dear Eric, > Are there other categories of exceptions upon which I haven't yet stumbled? .... there is (at least) one more sequence format problem in PDB files: If a protein sample is non homogenous, there might be two different amino acid at the same position in the sequence. It is not possible to annotate this correctly in the current PDB file format. E.g. in the high resolution structure of crambin (1CBN) it looks like this: ATOM 352 N PRO 22 4.909 12.659 -3.127 0.60 3.03 ATOM 353 CA PRO 22 6.035 13.459 -2.622 0.60 3.04 ATOM 354 C PRO 22 6.362 13.139 -1.174 0.60 3.08 ATOM 355 O PRO 22 5.473 12.959 -0.323 0.60 3.67 .... and so on ... ATOM 366 N SER 22B 4.909 12.659 -3.127 0.40 3.03 ATOM 367 CA SER 22B 6.035 13.459 -2.622 0.40 3.04 ATOM 368 C SER 22B 6.362 13.139 -1.174 0.40 3.08 ATOM 369 O SER 22B 5.473 12.959 -0.323 0.40 3.67 .... and so on ... As stated in the REMARK record, PRO 22 and SER 22B are alternative residues at the same sequence position, i.e. they have identical backbone coordinates. A sequence derived from the co-ordinates should either state a PRO or a SER at psoition 22, but not both of them. Looks like our scripts also have to read the REMARK records ;-) Cheers Torsten ---------------------------------------------------------- Dr. Torsten Schwede GlaxoWellcome Experimental Research SA 16 Chemin des Aulx 1228 Plan-les-Ouates, Geneva, Switzerland Phone +41 (0)22 884 86 52 Fax +41 (0)22 884 86 50 email: ts80960@GlaxoWellcome.co.uk ---------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook Seng Subject: unsubscribe Date: Fri, 3 Mar 2000 11:46:29 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu ===== James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com charset="koi8-r" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: Chime + IIS3 + Netscape Date: Sat, 11 Mar 2000 23:10:17 +0300 To: Hi Chimers! I have an idea to add some Chime matirials on our project web server (we use IIS 3). After installing various chemical mime types in my WWW server I can work with it only from IE (I tested 4 & 5 version for Win9x and WinNT) but not form Netscape 4.08 :( Chime version is 2.0.3 http://dpidb.genebee.msu.ru/Reviews/Chime/homeo.htm Have any ideas? Thank you very much in advance Sergey Vasil'ev, Ph.D. /*----------------------------------------------- DNA-Protein Interaction DataBase project team. Department of Mathematical Methods in Biology. Belozersky Institute of Physico-Chemical Biology, Moscow State University. Vorobyevy gory, Moscow 119899, RUSSIA. email: vasil@genebee.msu.ru vasil@iab.ac.ru tel: +7-095-9395414 fax: +7-095-9390338 -----------------------------------------------*/ References: <002701bf6f13$9b4f7200$3b8506c1@chem.klte.hu> X-Accept-Language: de ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Frank Eblinger" Subject: compiling RasMol for SuSe Linux 6.3 Date: Mon, 13 Mar 2000 10:30:32 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi all, Just recently I installed SuSe Linux 6.3. on my PC, works fine. The software package includes RasMol 2.6, but if I try to start it I get an error message: No graphical display I have no experience with compiling and I would like to have rasmol 2.7 (for working with cif files) installed on Linux. Is there anybody who can give me a detailed description how to do this?? thanks in advance Frank References: <002701bf6f13$9b4f7200$3b8506c1@chem.klte.hu> <38CCB538.275B83BF@rz.uni-sb.de> X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Sarnow Subject: Re: compiling RasMol for SuSe Linux 6.3 Date: Mon, 13 Mar 2000 14:19:36 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu "Dr. Frank Eblinger" wrote: > > Hi all, > > Just recently I installed SuSe Linux 6.3. on my PC, works fine. > The software package includes RasMol 2.6, but if I try to start it I get an > error message: No graphical display > I have no experience with compiling and I would like to have rasmol 2.7 (for > working with cif files) installed on Linux. Is there anybody who can give me a > detailed description how to do this?? > > thanks in advance > > Frank On my homepage you will find a compiled version, which runs under 32 bit display. It is a problem which arises from the compiled program, which is compiled fopr 8 bit displays. CU Karl -- Dr. Karl Sarnow Teacher at Gymnasium Isernhagen German national co-ordinator of the European Schools Project e-Mail: karl@dadoka.h.ni.schule.de Attention: New URL: http://www.shuttle.schule.de/h/dadoka charset="koi8-r" ++++------+------+------+------+------+------+------+------+------+------+ From: Alan Wolfson Subject: RE: Chime + IIS3 + Netscape Date: Mon, 13 Mar 2000 11:01:39 -0500 To: "'Sergey Vasil'ev'" , rasmol@dhcp-srv2.oit.umass.edu Try changing the embed tag from Subject: programs Date: Tue, 14 Mar 2000 08:20:48 -0500 To: rasmol mailing list Can anyone help with this problem?Are there any programs that can help me determine or speculate about the structure of a protein whose conformation is not known, but where the sequence is? Thank you, Dixie-Ann Persaud Duke University ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: programs Date: Tue, 14 Mar 2000 08:47:35 -0500 To: rasmol@dhcp-srv2.oit.umass.edu You can put the sequence in FASTA format into Swiss-PdbViewer and conduct a search for homologous proteins of known structure. Then you can import those structures and thread your sequence onto them as templates. In the process, if your sequence is already present in various databases, you might find that someone has already made and deposited such a model of your sequence. Recently, about 64,000 such models were made automatically from open reading frames in databases. For more information, go to the Swiss-PdbViewer Home Page http://www.expasy.ch/spdbv/mainpage.htm and take the Homology Modeling tutorial. For an introduction to the program, see http://www.usm.maine.edu/~rhodes/SPVTut/index.html Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu WWW Home Page: http://www.usm.maine.edu/~rhodes Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 charset="koi8-r" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: Rasmol archive (idea) Date: Tue, 21 Mar 2000 02:17:15 +0300 To: Hi all! I have an idea to make web page on DPIDB server with different versions of RasMol for different OS (compiled working versions :) Please, send me working version of our RasMol with decription: a. your first name, family name (full name) b. version (variant) of your RasMol program c. for what OS is your version of Rasmol d. if you make any changes in source code, please, write about this e. any your comments :) As you understand, I can't test all programs. Please, send your variants of RasMol programs to email: rasmol@dpidb.genebee.msu.ru Thank you. Sergey Vasil'ev, Ph.D. /*----------------------------------------------- DNA-Protein Interaction DataBase project team. http://dpidb.genebee.msu.ru Department of Mathematical Methods in Biology. Belozersky Institute of Physico-Chemical Biology, Moscow State University. Vorobyevy gory, Moscow 119899, RUSSIA. email: vasil@genebee.msu.ru vasil@iab.ac.ru tel: +7-095-9395414 fax: +7-095-9390338 -----------------------------------------------*/ References: <002701bf6f13$9b4f7200$3b8506c1@chem.klte.hu> <38CCB538.275B83BF@rz.uni-sb.de> ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: Re: compiling RasMol for SuSe Linux 6.3 Date: Fri, 24 Mar 2000 22:37:24 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Dear dr Eblinger : I tryed to do the same you are trying and I founf very usefull to read the documentation I do not remember where is it so I will check my files I mail you , cheers Dr. Frank Eblinger wrote: > Hi all, > > Just recently I installed SuSe Linux 6.3. on my PC, works fine. > The software package includes RasMol 2.6, but if I try to start it I > get an > error message: No graphical display > I have no experience with compiling and I would like to have rasmol > 2.7 (for > working with cif files) installed on Linux. Is there anybody who can > give me a > detailed description how to do this?? > > thanks in advance > > Frank X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Smith Subject: Structural similarity software Date: Tue, 28 Mar 2000 16:34:37 -0500 To: rasmol list I've been searching the net for software programs which will compare the 3 dimensional surface structure of two different small molecules but have been unsuccessful. I have found programs like TOP which do 3-d protein comparisons but none for small molecules. Does any-one know of any program that can do such comparisons. Thank you in advance for your input. ++++------+------+------+------+------+------+------+------+------+------+ From: SWelte@aol.com Subject: Seeking Internship in 3D Structural Bioinformatics in the US Date: Fri, 31 Mar 2000 10:02:35 EST To: pdb-l@rcsb.org Cc: rasmol@dhcp-srv2.oit.umass.edu Dear RasMol and PDB Community, I am a Biochemistry exchange student from Germany. During the last year I continued my graduate studies at the University of Massachusetts, Amherst. I attended a macromolecular visualization class with Eric Martz at UMass using his Protein Explorer. For this class I did a tutorial about the SV 40 capsid assembly and a journal club presentation on a MHC class Ib molecule. In the meantime I am thinking about going in the direction of bioinformatics for my future professional work. Therefore I am looking for a kind of internship/summer student position in research groups in companies, universities or other institutes in the US, which work in 3D Structural Bioinformatics or in bioinformatic in general (not DNA based) in drug design, development and research. My time of interest would be from the end of May 2000 for approx. 3 months. I am fully eligible to work here in the US as long as the work is study related and I can extend my current J-1 visa up to 12 additional months. My background from Germany is more focused on Chemistry, but at Umass I attended courses in Virology, Advanced Molecular Biology, Adv Immunology and I did in both semesters independent study on gamma delta T cells and mAb on PBMC in cattle. Also I am a TA in a Biotechnology course. I would be happy to hear of some opportunities. References you may contact: Prof. Eric Martz, emartz@microbio.umass.edu, 413-545-2325 Prof. Cynthia Baldwin, cbaldwin@vasci.umass.edu, 413-545-3167 ------------------------------------------------------------------------------ ------------------------ Stefan A Welte Graduate Student in the Molecular and Cellular Biology Program University of Massachusetts, Amherst Amherst, MA 01003 USA Local Address: Permanent Address: 100 Fearing St Hopfenstrasse 23 Amherst, MA 01002 88069 Tettnang USA Germany phone: (413) 549 2758 ++49 7542 4714 e-Mail: swelte@aol.com ------------------------------------------------------------------------------ ----------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg (by way of Eric Martz ) Subject: Rasmol scripts Date: Mon, 17 Apr 2000 09:00:06 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Dear Eric, I have been using Rasmol for quite a while in solid-state physics research. In projects exploring a number of structural parameters it is often useful to have a bunch of rasmol scripts around to help in viewing and producing images. I wrote up a web page for my colleagues documenting the process. http://www.phys.uni-paderborn.de/~stern/rasmol/ I thought I drop you a note on this to share with the rasmol user community at large. Feel free to include the link in one of the lists at your site, if you see fit. Regards, Michael -- Michael Sternberg | Uni-GH Paderborn http://www.phys.uni-paderborn.de/~stern/ | FB6 Theoretische Physik phone: +49-(0)5251-60-2329 fax: -3435 | 33098 Paderborn, Germany "Who disturrrbs me at this time?" << Zaphod Beeblebrox IV >> <*> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: java applet questions Date: Tue, 18 Apr 2000 18:03:19 -0400 To: rasmol@dhcp-srv2.oit.umass.edu If there's anyone out there who has experience writing java applets, please contact me directly if you're willing to answer some questions about what they can and can't do. Thanks, -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at References: <200004182200.SAA19584@marlin.bio.umass.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: java applet questions Date: Tue, 18 Apr 2000 21:18:00 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I have _a little_ experience. What's the question? Brian Eric Martz wrote: > If there's anyone out there who has experience writing java applets, please > contact me directly if you're willing to answer some questions about what > they can and can't do. Thanks, -Eric > > - - - > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 01003-5720 > > RasMol Email List > TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. > History -- all messages sent to this list are searchable at > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Win2000 compatibility Date: Thu, 20 Apr 2000 10:35:53 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: stwining@mcw.edu I am using Windows 98. I received an inquiry and would like to know about compatibility of Windows 2000 with: 1. RasMol 2.6-beta-2a 2. RasMol 2.7.1 3. Chime 2.0.3 Does anyone have experience with any of these cases? By the way, Chime 2.0.3 does not work with Netscape Communicator 6-beta-1. It works fine with Communicator 4.08 through 4.7x. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "DALE SAMPSON" Subject: RE: Win2000 compatibility Date: Thu, 20 Apr 2000 11:16:29 -0400 To: Hi, RasMol 2.7.1 works on W2K. I haven't tried ALL features, but general file viewing seems to work OK. Dale Sampson -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz Sent: Thursday, April 20, 2000 10:36 AM From: owner-rasmol@lists.umass.edu Subject: Win2000 compatibility To: rasmol@dhcp-srv2.oit.umass.edu Cc: stwining@mcw.edu I am using Windows 98. I received an inquiry and would like to know about compatibility of Windows 2000 with: 1. RasMol 2.6-beta-2a 2. RasMol 2.7.1 3. Chime 2.0.3 Does anyone have experience with any of these cases? By the way, Chime 2.0.3 does not work with Netscape Communicator 6-beta-1. It works fine with Communicator 4.08 through 4.7x. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at References: <200004201433.KAA04974@marlin.bio.umass.edu> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: Re: Win2000 compatibility Date: Fri, 21 Apr 2000 01:41:27 +0400 To: > I am using Windows 98. I received an inquiry and would like to know about > compatibility of Windows 2000 with: http://www.dpidb.genebee.msu.ru/Archive/software.html#rasmol -- RasMol 2.6 ucb > 1. RasMol 2.6-beta-2a > 2. RasMol 2.7.1 Everything is O'k with Win2K Prof. > 3. Chime 2.0.3 stable work with IE5 and Netscape Navigator 4.08 (Win2K Prof) Sergey Vasil'ev, Ph.D. /*----------------------------------------------- DNA-Protein Interaction DataBase project team. http://www.dpidb.genebee.msu.ru Department of Mathematical Methods in Biology. Belozersky Institute of Physico-Chemical Biology, Moscow State University. Vorobyevy gory, Moscow 119899, RUSSIA. email: vasil@genebee.msu.ru vasil@iab.ac.ru tel: +7-095-9395414 fax: +7-095-9390338 -----------------------------------------------*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime (and RasMol) bug? Color group Date: Sun, 07 May 2000 12:37:55 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I would like to report the following behavior which may be a bug -- if it a feature some enlightenment from Roger Sayle would be beneficial. The questionable behavior is marked *****. The following behavior is observed identically in RasWin 2.6-beta-2a, RasWin 2.7.1, and Chime 2.0.3 for Windows: load 1d66.pdb wireframe off backbone 0.3 color group # Mostly blue due to assignment of red colors to high group numbers of water; # this feature and the solution below has been in the manual for a long time. set hetero off # Now hetero group numbers are ignored in assigning group colors. color group # protein and dna are now colored blue through red -- a good 'group' coloring result. select dna color group # Hmmm -- DNA is all blue again. ***** select protein color group # Hmmm -- protein colors change. ***** select dna color group # Hmmm -- DNA colors are reasonable but different than before. ***** select protein color group # Yikes, protein colors change again. ***** Apparently the assignment of group colors depends on existing group color assignments to other nonselected moieties in a complex way? (Never did I get the 'unable to allocate shade' message in the above sequence.) The anomalous behavior does not depend on DNA, since the same behavior can be seen by selecting one chain at a time in 1fdl.pdb (no water, all protein) and following each select command with a 'color group'. This situation raises a problem: If one assigns group colors first, then the palette is consumed and other color schemes cannot always be assigned later ('unable to allocate shade'). However, if one assigns other color schemes first, and then selects a subset of the atoms for 'color group', a valid 'group' color scheme may not result. If anyone goes about fixing this situation, here is what I suggest as desired behavior: "color group" should assign blue to the lowest *selected* residue number, and red to the highest *selected* residue number, scaling a spectral sequence to intermediate *selected* residue numbers. Although the palette problem (unable to allocate shade) may preclude using this as desired, the goal would be to allow the user to decide which of these to employ: 1. a single mapping of residue number to colors to all chains (select all, color group), so chains which begin with high residue numbers don't begin with blue, etc. (This is the current situation) or 2. independent mapping of residue numbers to colors for each chain, so each chain goes from blue to red regardless of the range of residue numbers assigned to it. (Not currently possible, I think). -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Bug in RasWin 2.7.1 Date: Sun, 07 May 2000 12:38:17 -0400 To: rasmol@dhcp-srv2.oit.umass.edu The following sequence of operations causes RasWin 2.7.1 to crash (under Windows 98), but neither RasWin 2.6-beta-2a nor Chime 2.0.3 crash: MENU OPERATIONS: File, Open, 1d66.pdb Display, Cartoon Options, Hetero Atoms (toggle off) Color, Group COMMANDS: select dna color group -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: CHIME surface files Date: Mon, 08 May 2000 13:45:30 -0400 To: rasmol@dhcp-srv2.oit.umass.edu [I forward this for James Meek to circumvent technical difficulties. -Eric Martz] >A CHIME question: > >What software package can I use to generate and save the pmesh files that >CHIME can load and display? > >CHIME can very nicely generate external surfaces, and as shown in the >MDL tutorial can load them: "load pmesh myfilename.tmesh". > >I'd like to be able to generate surfaces of cavities in another program >(e.g. GRASP) and display them in CHIME. > >Any ideas? Thanks > James L. Meek, DuPont > James.L.Meek@dupontpharma.com X-Sybari-Space: 00000000 00000000 00000000 ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Chime 2.0 and IE5 for Macintosh Date: Tue, 09 May 2000 13:48:00 -0500 To: 9. May, 2000 A Chime Question: Has anyone had a positive experience with getting Chime 2.0 to work with Microsoft's Internet Explorer v5.0 for the Macintosh? How about IE5 for Windows NT? _______________________________________________ Warren Gallagher Associate Professor Department of Chemistry University of Wisconsin-Eau Claire Eau Claire, WI 54702-4004 TEL: (715) 836-5388 FAX: (715) 836-4979 References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime 2.0 and IE5 for Macintosh Date: Tue, 09 May 2000 16:51:11 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Both the Chime installer readme file and the MDLI Web site support page state that Chime 2.0 is not compatible with IE for the Mac. No such claim is made for Win, though I've heard reports of inconsistent compatibility. A lot depends on the way Chime is used; my understanding (open to correction, of course) is that IE does not support LiveConnect, which is the way that Chime and javascript communicate. So very simple Chime pages may work fine, but more complicated interactive pages do not. My two cents only. Someone more in the know may want to substantiate or clarify my comments. -- Timothy Driscoll 60 Trapelo Road Belmont, MA 02478 617 489 0705 mvisions@speakeasy.org http://www.molvisions.com/ Warren Gallagher wrote: > 9. May, 2000 > > A Chime Question: > > Has anyone had a positive experience with getting Chime 2.0 to work with > Microsoft's Internet Explorer v5.0 for the Macintosh? How about IE5 for > Windows NT? > > _______________________________________________ > Warren Gallagher > Associate Professor > Department of Chemistry > University of Wisconsin-Eau Claire > Eau Claire, WI 54702-4004 > TEL: (715) 836-5388 > FAX: (715) 836-4979 References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Re: Chime 2.0 and IE5 for Macintosh Date: Tue, 09 May 2000 16:03:47 -0600 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu My experience with IE5 and Windows NT is very limited. I quickly became very discouraged and gave up on IE5. Anyway, it turns out that Chime 2.0 scripts written specifically for IE5 with Windows NT do run-- but poorly. By specific, I mean that you must replace the tag with for IE5. But the doesn't work in Netscape. That means you need two versions of every Chime tutorial. Nuts!!! Dave Fahrney Professor of Biochemistry Colorado State University Warren Gallagher wrote: > > 9. May, 2000 > > A Chime Question: > > Has anyone had a positive experience with getting Chime 2.0 to work with > Microsoft's Internet Explorer v5.0 for the Macintosh? How about IE5 for > Windows NT? > > _______________________________________________ > Warren Gallagher > Associate Professor > Department of Chemistry > University of Wisconsin-Eau Claire > Eau Claire, WI 54702-4004 > TEL: (715) 836-5388 > FAX: (715) 836-4979 References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Leif Johansen Subject: Re: Chime 2.0 and IE5 for Macintosh Date: Wed, 10 May 2000 09:54:48 +0200 To: rasmol@dhcp-srv2.oit.umass.edu I have no problems with explorer 5, I used Chime in a modest way. I also can display the Chime-Rasmol tutorial file. Earlier I had some problems , then I deinstall other chemical - plugins ( from Cambridge ) and the problems were over. Leif Johansen Teachers College Haderslev Denark Warren Gallagher wrote: > 9. May, 2000 > > A Chime Question: > > Has anyone had a positive experience with getting Chime 2.0 to work with > Microsoft's Internet Explorer v5.0 for the Macintosh? How about IE5 for > Windows NT? > > _______________________________________________ > Warren Gallagher > Associate Professor > Department of Chemistry > University of Wisconsin-Eau Claire > Eau Claire, WI 54702-4004 > TEL: (715) 836-5388 > FAX: (715) 836-4979 X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id KAA13909 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Chime 2.0 and IE5 for Macintosh Date: Wed, 10 May 2000 10:29:40 -0400 To: rasmol@dhcp-srv2.oit.umass.edu [Resent for Alan Wolfson to circumvent technical difficulties. -Eric Martz] ... From MDL's Technical Note T13-2000... ----------- begin included message ----------- This is a follow up on Technical Note T36-99. In T36-99, we reported the following problem: When viewing HTML pages that contain multiple Chime or Chime Pro structures (2D or 3D), clicking and dragging on the scroll bar in Microsoft Internet Explorer 5 causes the browser to crash. This happens with all Chime and Chime Pro 2.x versions (CCT-4518). Solution Microsoft has confirmed the problem is within the Microsoft Windows 95 operating system. (Please see the article on the Microsoft Web site: http://support.microsoft.com/support/kb/articles/Q255/6/20.ASP.) As a result of this, we can not support Chime/Chime Pro 2.0x on Microsoft Internet Explorer 5 and 5.01 on Microsoft Windows 95. We recommend you do one of the following: · Use Netscape Communicator 4.05, or later; · Use Microsoft Internet Explorer 4.01sp2 on Microsoft Windows 95; · Upgrade your operating system to Microsoft Windows 98 or Microsoft Windows NT for Chime. ----------- end included message ----------- This may not explain all of the IE/Chime problems, but it certainly makes me suspicious about IE5. Alan Alan Wolfson Senior Consultant MDL Information Systems alanw@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: New Protein Explorer Version Date: Mon, 22 May 2000 16:21:41 -0400 To: rasmol@dhcp-srv2.oit.umass.edu A new version of Protein Explorer is available for use and beta-testing at www.umass.edu/microbio/chime/explorer The previous version, 1.0, was released September 1999, and is offered as a structure viewing option at the Protein Data Bank and its mirrors. This new version will be installed there eventually after more thorough testing and completion. New features: I. EASE OF USE. The goal of Protein Explorer is to make visualization sufficiently easy that even occasional users can focus on the answers to their questions about molecular structure, rather than the technology needed to answer them. The most important enhancement in this new version is much-increased ease of use. A generic FirstView description of PE's default initial rendering of any molecule guides the user through the key structural features of any macromolecule, with links to detailed explanations for novices (chains and "backbones", ligands, solvent, disulfides). A new simplified interface for exploration is called QuickViews. It provides simplified yet powerful menus for SELECTION, DISPLAY, and COLORING. Every action taken by the user is explained in a new help frame. Troubleshooting is always available. Although inspired by RasMol's menu system, QuickViews menus enable novices to use more exploration tools than are available from RasMol's menus. Examples: selecting by chain, rendering of surfaces and contact surfaces, hiding portions of the structure, and automated tools for centering, distinguishing DNA from RNA, coloring by hydrophobicity or ATGCU code. QuickViews has even simpler menus than RasMol, with constantly visible context-triggered help and color keys. Basic exploration can be accomplished without ever entering a typed command. However, the command entry slot is always available and understands Chime's superset of RasMol commands. The commands employed for each menu action are visible to facilitate learning the command language for those interested. The help system for the new QuickViews interface comprises over 5,000 words including numerous graphics. In my opinion, this version of Protein Explorer is capable of superceding RasMol for Windows and Macintosh/PPC users. Here are some snapshots of FirstView and QuickViews: www.umass.edu/microbio/chime/explorer/preview.htm II. SEQUENCE TO STRUCTURE MAPPING. The second major new feature is that the sequence(s) of the molecule can be displayed. You can click on residues, or a range of residues, to highlight them in the 3D structure. The display and color scheme for such highlighting is menu-selectable. The above snapshots include one of Seq3D in action. III. MOLECULE INFORMATION WINDOW. A new 'molecule information window' is always accessible. It shows the PDB ID code, the name of the molecule (from the HEADER and COMPND records), and provides direct links for viewing the PDB file header, or for entering RCSB's Structure Explorer page. It can also produce PE's new interactive sequence displays. IV. Miscellaneous. Over a hundred small improvements have been made. Ensembles of NMR models could be played as a movie in version 1.0; now they can be played bidirectionally. Because the layers of help for novices could slow down regular users, a new preference setting for EXPERTS bypasses unnecessary help. New convenience buttons have been added to toggle Slab mode, to invoke the clickable sequence display, and to reset (reload the molecule, restoring the initial display). I will appreciate feedback, bug reports, and suggestions for improvement. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime vs. Netscape 6 Date: Fri, 26 May 2000 17:35:16 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: Koch@xray3.chem.sunysb.edu, chime-feedback@mdli.com [Resent for Stephen Koch by Eric Martz] Has anyone been able to install the Chime plugin on Netscape6.0. In my hands the chime installation program can't find Netscape6.0 Thanks Stephen A. Koch 631-632-7944 (7931) Koch@sbchem.sunysb.edu Fax 631-632-7960 Department of Chemistry, SUNY,Stony Brook, NY 11794-3400 Bioinorganic WWW Server: http://www.chem.sunysb.edu/koch/biic.html --------------- A Reply: Chime 2 does not work with Netscape 6-preview-1. MDLI has confirmed this and is aware of the problem. For now, Netscape 4.08 - 4.73 should be used with Chime-enhanced sites. I can't even figure out how to list the plugins in Nav6 (about:plugins doesn't work, neither does javascript:). -Eric Martz - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at References: <200005280403.AAA14617@dhcp-srv2.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Craig T. Martin" Subject: 3D glasses Date: Tue, 30 May 2000 15:51:55 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Does anyone have any information on 3D glasses, screens, projectors, etc, for viewing macromolecular structures? Does anyone know of a kludge to have Rasmol or CHIME talk to such a device? How about SwissPDBViewer? Other software? Opinions, experience? I'd appreciate any information... -- Craig Martin *** Chemistry *** X5-3299 References: <200005280403.AAA14617@dhcp-srv2.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: 3D glasses Date: Tue, 30 May 2000 16:38:57 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu VMD does 3d viz using LCD shutter glasses. Craig T. Martin writes: > Does anyone have any information on 3D glasses, screens, projectors, > etc, for viewing macromolecular structures? Does anyone know of a > kludge to have Rasmol or CHIME talk to such a device? How about > SwissPDBViewer? Other software? Opinions, experience? > > I'd appreciate any information... > -- > > Craig Martin *** Chemistry *** X5-3299 References: <200005280403.AAA14617@dhcp-srv2.oit.umass.edu> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Roy Fultun" Subject: Re: 3D glasses Date: Tue, 30 May 2000 23:48:05 -0700 To: Cc: "Roy Fultun" Try wfeiereisen@mail.arc.nasa.gov. Bill Feireisen is division chief at Numerical Aerospace Simulation (NAS) Systems Division, Ames Research Center, Moffet Field, CA. They've got a really sweet visualization lab and I would expect he would be either willing to answer your question directly or direct you to someone who can give you a sense of what's out there. NAS also has a Computational Astrobiology Center (NCCA) whose acting director is Andrew Pohorille. Try http://cca.arc.nasa.gov or perhaps http://astrobiology.arc.nasa.gov/index.cfm Among other great toys, NAS has a Responsive Workbench, manufactured by Fakespace Inc. The Gridpoints brochure I am reading from does not mention the other equipment. To subscribe online online to their Gridpoints magazine, visit: http://www.nas.nasa.gov/Gridpoints/subscribe.html or send an e-mail message with your mailing address, corporate affiliation and title to gridpoints@nas.nasa.gov. ----- Original Message ----- Sent: Tuesday, May 30, 2000 12:51 PM From: Craig T. Martin Subject: 3D glasses To: > Does anyone have any information on 3D glasses, screens, projectors, > etc, for viewing macromolecular structures? Does anyone know of a > kludge to have Rasmol or CHIME talk to such a device? How about > SwissPDBViewer? Other software? Opinions, experience? > > I'd appreciate any information... > -- > > Craig Martin *** Chemistry *** X5-3299 > References: <200005280403.AAA14617@dhcp-srv2.oit.umass.edu> <14644.20753.633765.528944@lrz.uni-muenchen.de> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Roy Fultun" Subject: Re: 3D glasses Date: Fri, 2 Jun 2000 01:06:34 -0700 To: An informative web site is http://www.stereographics.com/ Check out the sections on Products, Stereo-Ready Software and Stereo-Ready Hardware. ----- Original Message ----- Sent: Tuesday, May 30, 2000 4:38 PM From: Eugene Leitl Subject: 3D glasses To: Cc: > > VMD does 3d viz using LCD shutter glasses. > > Craig T. Martin writes: > > Does anyone have any information on 3D glasses, screens, projectors, > > etc, for viewing macromolecular structures? Does anyone know of a > > kludge to have Rasmol or CHIME talk to such a device? How about > > SwissPDBViewer? Other software? Opinions, experience? > > > > I'd appreciate any information... > > -- > > > > Craig Martin *** Chemistry *** X5-3299 > ++++------+------+------+------+------+------+------+------+------+------+ From: Nikesh Kotecha Subject: screen resizing and mol->gif conversion Date: Mon, 5 Jun 2000 09:59:26 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Hi, I just started using Rasmol a couple of weeks ago and find it to be very useful. However, I have run into a problem and am hoping that one of you can help me solve it. I have been going through the documentation and the email archives to find a way to convert mols to gifs through a script file. I was successful in doing that after finding the email about the -insecure feature in the latest versions of rasmol. However, the gif generated is too big. I am running rasmol on an NT machine and the gif generated is the same size as the rasmol window which is ~500x500 pixels. In order for me to generate a smaller gif I have to run rasmol and resize the screen manually before I write to a gif file. Are there any script commands or any automatic way to resize the screen or specify the size of a gif? The script I currently run is pretty simple: load testmol.mol write testmol.gif exit Thanks, Nikesh __________________________________________________ Do You Yahoo!? Yahoo! Photos -- now, 100 FREE prints! http://photos.yahoo.com charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Bulent Aydogan" Subject: Slecting atoms Date: Mon, 5 Jun 2000 13:02:04 -0400 To: When displaying I want to choose certain atom and reduce their dispaly radius. For instance, I would like to choose all H atoms in the sugar-phosphate backbone in a DNA segment. Is there any command to select certain atoms in a molucule.? Thanx Bulent boundary="----=_NextPart_000_00A5_01BFD118.3A5DA860" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Achiever" Subject: Vedic Mathematics Date: Thu, 8 Jun 2000 07:07:37 +0530 To: This is a multi-part message in MIME format. ------=_NextPart_000_00A5_01BFD118.3A5DA860 charset="iso-8859-1" Namaskar to all the group members. Want to learn Vedic Math, "Magical methods of fast calculations" to = calculate 10 times faster. visit http://www.magicalmethods.com ------=_NextPart_000_00A5_01BFD118.3A5DA860 charset="iso-8859-1"
Namaskar to all the group = members.
 
Want to learn Vedic Math, = "Magical methods=20 of fast calculations" to calculate 10 times faster. visit http://www.magicalmethods.com<= /FONT>
 
 
------=_NextPart_000_00A5_01BFD118.3A5DA860-- ++++------+------+------+------+------+------+------+------+------+------+ From: Matt Patterson Subject: display quirks Date: Tue, 13 Jun 2000 13:01:36 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Can anyone help me? I'm trying to display only the ribbon of a PDB and 4 of the residues in stick form. Whenever I try to restrict the viewing to the 4 residues, the ribbon (or cartoon) turns off. What would the command line sequence be? Mike Ford CCRC University of Georgia __________________________________________________ Do You Yahoo!? Yahoo! Photos -- now, 100 FREE prints! http://photos.yahoo.com References: <20000613200136.15665.qmail@web216.mail.yahoo.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: display quirks Date: Tue, 13 Jun 2000 16:21:05 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Matt Patterson wrote: > Can anyone help me? > > I'm trying to display only the ribbon of a PDB and 4 > of the residues in stick form. Whenever I try to > restrict the viewing to the 4 residues, the ribbon (or > cartoon) turns off. What would the command line > sequence be? > > Mike Ford > CCRC > University of Georgia Hi Matt, If it's a standard pdb file, and I understand your question correctly, try this: select res1-res4 cartoon on wireframe 0.2 If you want the entire protein in cartoon, with those residues in sticks, try instead: select all cartoon on select res1-4 wireframe 0.2 You can change "cartoon" to "ribbon" and play with the value of "wireframe" to suit your taste. Hope that helps! Tim -- Timothy Driscoll 60 Trapelo Road Belmont, MA 02478 617 489 0705 mvisions@speakeasy.org http://www.molvisions.com X-pair-Authenticated: 209.139.109.240 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: patch for XYZ and MOL2 input Date: Sat, 17 Jun 2000 12:39:45 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Roberto C. Pasianot has reported a serious problem in the handling of XYZ input by RasMol 2.7.1. The same problem has been found in handling MOL2 input. The bug is in infile.c and affects only XYZ and MOL2 formats. The displays are correct, but reported coordinates are wrong. A context patch which should fix the problem is as follows: *** infile.c 2000/06/17 15:26:37 1.9 --- infile.c 2000/06/17 15:29:29 *************** *** 1213,1221 **** ptr->xorg = (Long)(250.0*xpos); ptr->yorg = (Long)(250.0*ypos); ptr->zorg = -(Long)(250.0*zpos); ! ptr->xtrl = (10000.0*xpos*-40.*(double)ptr->xorg); ! ptr->ytrl = (10000.0*ypos*-40.*(double)ptr->yorg); ! ptr->ztrl = (-10000.0*zpos*-40.*(double)ptr->zorg); if( (count==5) || (count==8) ) { ptr->temp = (short)(100.0*charge); --- 1213,1221 ---- ptr->xorg = (Long)(250.0*xpos); ptr->yorg = (Long)(250.0*ypos); ptr->zorg = -(Long)(250.0*zpos); ! ptr->xtrl = (10000.0*xpos-40.*(double)ptr->xorg); ! ptr->ytrl = (10000.0*ypos-40.*(double)ptr->yorg); ! ptr->ztrl = (-10000.0*zpos-40.*(double)ptr->zorg); if( (count==5) || (count==8) ) { ptr->temp = (short)(100.0*charge); *************** *** 1318,1326 **** ptr->xorg = (Long)(250.0*xpos); ptr->yorg = (Long)(250.0*ypos); ptr->zorg = -(Long)(250.0*zpos); ! ptr->xtrl = (10000.0*xpos*-40.*(double)ptr->xorg); ! ptr->ytrl = (10000.0*ypos*-40.*(double)ptr->yorg); ! ptr->ztrl = (-10000.0*zpos*-40.*(double)ptr->zorg); ProcessAtom( ptr ); } --- 1318,1326 ---- ptr->xorg = (Long)(250.0*xpos); ptr->yorg = (Long)(250.0*ypos); ptr->zorg = -(Long)(250.0*zpos); ! ptr->xtrl = (10000.0*xpos-40.*(double)ptr->xorg); ! ptr->ytrl = (10000.0*ypos-40.*(double)ptr->yorg); ! ptr->ztrl = (-10000.0*zpos-40.*(double)ptr->zorg); ProcessAtom( ptr ); } I will include this fix in the next release. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== charset="iso-8859-1" ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Meredith Subject: Bug with chime and IE 5.01 Date: Mon, 19 Jun 2000 08:57:32 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dear all, If you are developing resources for delivery over the net and viewing with chime then there is a new bug. The latest version of IE (5.01) does not allow you to turn off the option "Load browser window in a new process" (apparently if your computer ahs more than 32 Mb RAM IE now turns on this option automatically) resulting in the error messages: "not enough memory to allocate frame buffer" and a rendering error. Anybody got any clues how to bypass this then I would be most grateful. Michael Content-Disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: wm0p Subject: Re: Bug with chime and IE 5.01 Date: Mon, 19 Jun 2000 10:31:17 -0400 To: rasmol@dhcp-srv2.oit.umass.edu --On Mon, Jun 19, 2000 8:57 AM +0100 Michael Meredith wrote: > The latest version of IE (5.01) does not > allow you to turn off the option "Load browser window in a new process" > (apparently if your computer ahs more than 32 Mb RAM IE now turns on this > option automatically) resulting in the error messages: "not enough memory > to allocate frame buffer" and a rendering error. > > Anybody got any clues how to bypass this then I would be most grateful. > > Michael, Use a W3-compatible browser! -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Trina Valencich Subject: Re: patch for XYZ and MOL2 input Date: Mon, 19 Jun 2000 17:36:20 -0600 To: rasmol@dhcp-srv2.oit.umass.edu thanx, trina At 12:39 PM 6/17/00 -0400, you wrote: >Roberto C. Pasianot has reported a serious problem in the handling of XYZ >input by RasMol 2.7.1. The same problem has been found in handling MOL2 >input. > > >The bug is in infile.c and affects only XYZ and MOL2 formats. The >displays are correct, but reported coordinates are wrong. A context patch >which should fix the problem is as follows: > >*** infile.c 2000/06/17 15:26:37 1.9 >--- infile.c 2000/06/17 15:29:29 >*************** >*** 1213,1221 **** > ptr->xorg = (Long)(250.0*xpos); > ptr->yorg = (Long)(250.0*ypos); > ptr->zorg = -(Long)(250.0*zpos); >! ptr->xtrl = (10000.0*xpos*-40.*(double)ptr->xorg); >! ptr->ytrl = (10000.0*ypos*-40.*(double)ptr->yorg); >! ptr->ztrl = (-10000.0*zpos*-40.*(double)ptr->zorg); > > if( (count==5) || (count==8) ) > { ptr->temp = (short)(100.0*charge); >--- 1213,1221 ---- > ptr->xorg = (Long)(250.0*xpos); > ptr->yorg = (Long)(250.0*ypos); > ptr->zorg = -(Long)(250.0*zpos); >! ptr->xtrl = (10000.0*xpos-40.*(double)ptr->xorg); >! ptr->ytrl = (10000.0*ypos-40.*(double)ptr->yorg); >! ptr->ztrl = (-10000.0*zpos-40.*(double)ptr->zorg); > > if( (count==5) || (count==8) ) > { ptr->temp = (short)(100.0*charge); >*************** >*** 1318,1326 **** > ptr->xorg = (Long)(250.0*xpos); > ptr->yorg = (Long)(250.0*ypos); > ptr->zorg = -(Long)(250.0*zpos); >! ptr->xtrl = (10000.0*xpos*-40.*(double)ptr->xorg); >! ptr->ytrl = (10000.0*ypos*-40.*(double)ptr->yorg); >! ptr->ztrl = (-10000.0*zpos*-40.*(double)ptr->zorg); > ProcessAtom( ptr ); > } > >--- 1318,1326 ---- > ptr->xorg = (Long)(250.0*xpos); > ptr->yorg = (Long)(250.0*ypos); > ptr->zorg = -(Long)(250.0*zpos); >! ptr->xtrl = (10000.0*xpos-40.*(double)ptr->xorg); >! ptr->ytrl = (10000.0*ypos-40.*(double)ptr->yorg); >! ptr->ztrl = (-10000.0*zpos-40.*(double)ptr->zorg); > ProcessAtom( ptr ); > } > >I will include this fix in the next release. > >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Herbert J. Bernstein > * *** yaya@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 >===================================================== > > > > X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: core dump:rasmol_8BIT -nodisplay Date: Tue, 20 Jun 2000 10:26:36 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Hi, trying to load a PDB file using IRIX64 (8-bit version) of RasMol 2.7.1 with the -nodisplay parameter results directly in a core dump. (The same with 32-bit and with 8-bit IRIX53 version.) Is there any patch out there? Regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: core dump:rasmol_8BIT -nodisplay Date: Tue, 20 Jun 2000 13:02:24 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu, jr Many thanks to JR for the trouble report. The following patch to x11win.c should fix this problem: 1927c1927,1929 < XStoreName(dpy,MainWin,ptr); --- > if ( Interactive ) { > XStoreName(dpy,MainWin,ptr); > } or as a context difference *** x11win.c 2000/06/20 16:49:59 1.1 --- x11win.c 2000/06/20 16:55:56 *************** *** 1924,1930 **** --- 1924,1932 ---- void SetCanvasTitle( char *ptr ) { + if ( Interactive ) { XStoreName(dpy,MainWin,ptr); + } } This patch will be in the next release. -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Tue, 20 Jun 2000, jr wrote: > Hi, > trying to load a PDB file using IRIX64 (8-bit version) of RasMol 2.7.1 > with the -nodisplay parameter results directly in a core dump. (The same > with 32-bit and with 8-bit IRIX53 version.) > > Is there any patch out there? > Regards, Jan > > -- > Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. > Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) > mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml > > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Possible service outage Date: Thu, 06 Jul 2000 09:15:49 -0400 To: rasmol@dhcp-srv2.oit.umass.edu The listproc software which supports this list will be upgraded later today by our central computer support staff. It is possible that some temporary outages of service, or other technical issues, may result. We hope to resolve any such issues quickly. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Test - Discard Date: Sat, 08 Jul 2000 20:14:02 -0400 To: rasmol@lists.umass.edu Please discard this -- it is to test the upgrade of the listproc managers software which manages this list. - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Listing found atoms in NonCovalent Bond Finder Date: Tue, 11 Jul 2000 21:19:44 -0400 To: Olga Rechkoblit Cc: rasmol@lists.umass.edu, Joel.Sussman@weizmann.ac.il At 07/07/2000, you wrote: >Dear Dr. Martz, > >I am started to use non covalent bond finder. It is a wonderful, >convenient and very useful program. >However, I could not figure out how to generate an automatic report of >found atoms on a particular distance. I could click on a found atom >manually to identify it, but it is not very convenient if you want to >explore the interactions carefully. > >Thank you so much for your help and time. > >Sincerely yours, >Olga Rechkoblit (Ph.D. student) >New York University >Chemistry Department > You are correct that I have not implemented an automated button for this. But you can already do this easily enough: Press the [Instructions] button and read "Selectable terms defined by NCBF". After finding some atoms, issue these commands in the command slot at the bottom select found show residue or show atoms Then copy the report in the message window and paste it into a word processor. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Judging Model Quality Date: Thu, 13 Jul 2000 11:34:02 -0400 To: discuspv@usm.maine.edu, rasmol@lists.umass.edu Two of my web sites might be useful to list subscribers: 1) Judging the Quality of Macromolecular Models: An Online Glossary of Terms from Crystallography, NMR, and Homology Modeling http://www.usm.maine.edu/~rhodes/ModQual/index.html 2) Learning Biochemistry with Deep View Given the state of structural biology and molecular graphics today, I believe that all biochemistry students should learn molecular graphics at the same time they are learning biomolecular structure. In this belief, I am developing graphics exercises for introductory biochemistry. In these exercises, students use Deep View (formerly Swiss-PdbViewer) to explore biomolecules and answer questions aimed at reinforcing many basic concepts in structural biology. These exercises are not like the many excellent text-like animations or push-button tutorials now available, but instead are aimed at empowering the student to explore and analyze structure with a great degree of independence, including making use of the Protein Data Bank. Deep View provides a friendly way to start this mission, but also provides advanced features that allow the student to develop true research-level skills. My students start by learning Deep View with the basic tutorial (http://www.usm.maine.edu/~rhodes/SPVTut/index.html), and then build additional skills throughout the course using these exercises. My exercises are keyed to typical course topics in a first-year biochemistry course. Topics are listed along with appropriate assignments in the biochemistry text by Voet, Voet, and Pratt, but the topics list could easily be keyed to other texts. If anyone who uses Stryer, Nelson and Cox ("Lehninger"), Mathews/van Holde, Zubay, or other texts would like to provide assignments keyed to these topics, I will be happy to include them in additional columns of the topics table. This would make the exercises useful to many students. Entry page: http://www.usm.maine.edu/~rhodes/BiochemViews/index.html Topics list: http://www.usm.maine.edu/~rhodes/Biochem/Text/Topics.html Unlike the Model Quality site, this one is under development, and may be a little rough or incomplete in spots. I will extend it and clean it up during the 2000/2001 apparition of my course. In addition, by the end of the summer, the site will look less like a part of my own course, and more like a public site for all biochemistry teachers and students. (Teachers of biochemistry may also be interested in my Learning Strategies for Biochemistry, which are also linked to the topics page.) I will appreciate comments and suggestions on these projects. Cheers! Homeopaths have dilutions of grandeur. ***************************** Gale Rhodes http://www.usm.maine.edu/~rhodes Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 Director: The Molecular Level Molecular Graphics Training for Research and Education http://www.usm.maine.edu/~rhodes/MolLevel Author: Crystallography Made Crystal Clear A Guide for Users of Macromolecular Models Academic Press, 2000, Second Edition http://www.usm.maine.edu/~rhodes/CMCC charset=us-ascii X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Judging Model Quality Date: Thu, 13 Jul 2000 12:57:30 -0400 To: rasmol@lists.umass.edu Gale Rhodes wrote: > 2) Learning Biochemistry with Deep View > > Given the state of structural biology and molecular graphics today, I > believe that all biochemistry students should learn molecular graphics at > the same time they are learning biomolecular structure. In this belief, I > am developing graphics exercises for introductory biochemistry. In these > exercises, students use Deep View (formerly Swiss-PdbViewer) to explore > biomolecules and answer questions aimed at reinforcing many basic concepts > in structural biology. These exercises are not like the many excellent > text-like animations or push-button tutorials now available, but instead > are aimed at empowering the student to explore and analyze structure with a > great degree of independence, including making use of the Protein Data > Bank. Deep View provides a friendly way to start this mission, but also > provides advanced features that allow the student to develop true > research-level skills. My students start by learning Deep View with the > basic tutorial (http://www.usm.maine.edu/~rhodes/SPVTut/index.html), and > then build additional skills throughout the course using these exercises. > > My exercises are keyed to typical course topics in a first-year > biochemistry course. Topics are listed along with appropriate assignments > in the biochemistry text by Voet, Voet, and Pratt, but the topics list > could easily be keyed to other texts. If anyone who uses Stryer, Nelson and > Cox ("Lehninger"), Mathews/van Holde, Zubay, or other texts would like to > provide assignments keyed to these topics, I will be happy to include them > in additional columns of the topics table. This would make the exercises > useful to many students. > > Entry page: http://www.usm.maine.edu/~rhodes/BiochemViews/index.html > > Topics list: http://www.usm.maine.edu/~rhodes/Biochem/Text/Topics.html > > Unlike the Model Quality site, this one is under development, and may be a > little rough or incomplete in spots. I will extend it and clean it up > during the 2000/2001 apparition of my course. In addition, by the end of > the summer, the site will look less like a part of my own course, and more > like a public site for all biochemistry teachers and students. > > (Teachers of biochemistry may also be interested in my Learning Strategies > for Biochemistry, which are also linked to the topics page.) > > I will appreciate comments and suggestions on these projects. > Hi Gale, I certainly agree that all life science students should have some exposure to molecular visualization/graphics early in their careers. To that end, I think you have a put together great set of Web pages for educators, and I hope they get the use and recognition that they deserve. You mention coordinating assignments on your Web site with various biochemistry textbooks. Educators who use the Lehninger text may want to visit the Lehninger3D Web site first (http://www.worthpublishers.com/lehninger3d). This site uses Chime to deliver detailed 3D structure tutorials on such topics as Amino Acids and Peptides, Protein Structure, Myoglobin and Hemoglobin (Protein Function) - all of which are also present on Gale's Web site. Lehninger3D also includes G Protein and Lac Repressor tutorials, with Restriction Enzymes and Nulceic Acid Structure due to be released this summer. In addition to offering the standard linear tutorial interface, Lehninger3D allows users to interact with the structures independently using a set of Control Panels, and offers helpful "Try This!" suggestions embedded within the text. An update to be released in the next few days will provide a command line interface panel for advanced users. Including assignments that combine the Lehninger3D tutorials, textbook, and Deep View exercises on Gale's Web site would represent a powerful educational package. BTW, the Lehninger3D site is not restricted to educators who use the textbook; it is a public site. Gale, you may be interested to know that I compile and annotate biochemistry-related Web sites for both Lehninger (http://www.worthpublishers.com/lehninger/con_index.htm?99bwl) and Stryer (http://www.whfreeman.com/stryer/con_index.htm?99awl) textbooks. With your permission, I'd like to list your site in these two resources. I'd also encourage you to put your site in Eric Martz's Visitor-Maintained Index (http://molvis.sdsc.edu/visres) if it isn't already posted there. In fact, I would extend the same offer to anyone who maintains a biochemistry and/or mol vis site on the Web. Any takers can email me their link(s) for either Lehninger or Stryer texts; you can enter your own information on Eric's VMI. Tim -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet mvisions@speakeasy.org http://www.molvisions.com rebecca.craft@prudential.com, csmith@sdsc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Visitor-Maintained Indices of Chime Resources Date: Mon, 17 Jul 2000 12:33:11 -0400 To: rasmol@lists.umass.edu Cc: tkramer@hampshire.edu, twoodin@nsf.gov, hlevitan@nsf.gov, If you have authored Chime-based resources on the web, please enter your URL, title, description, and cross-indexing keywords into the form at the new "Visitor-Maintained" World Index of BioMolecular Visualization Resources (http://www.umass.edu/microbio/rasmol/tutbymol.htm) -- this is the permanent URL best for bookmarking also. Resources based on RasMol, SwissPDB Viewer, or other freeware are also welcome. Cross-indexing terms should include major topics and the names of molecules featured in your resource. Most Chime resources are designed to be educational. However, if your resource contains an explicit lesson plan or suggestions on how to use it as an educational resource (separate from the presentation or tutorial on molecular structure), please include the keyword "lesson plan". Several currently indexed resources are so-marked and can be viewed as examples. If you know of a resource you did not author, but which should be entered into the system, please forward this message to its author. If the author does not get around to entering the resource, the VMI system has provision for a person other than the author to submit a resource (which could later be edited by the author if desired). The new Visitor-Maintained mechanism for the World Index has been designed to minimize the need for manual curation by an editor (me). The old World Index that I curated manually (also still available at the above URL) has fallen years behind due the time it would have taken to keep it up to date. It will be superceded and retired as soon as all of its contents are entered into the new system. The new VMI system allows any visitor to the website to submit new entries, or request a revision or deletion of an old entry. As soon as submissions are approved, the additions and changes are immediately and automatically alphabetized into the title, subject, and author index web pages. Submitters will be informed by email when their submissions are accepted. The system verifies that the URL is active and will not accept a submission with a mistyped url. It also periodically checks for dead links and informs submitters by email that their links need to be updated. The Visitor Maintained Indices (VMI) system has been designed by myself and Trevor D. Kramer and implemented as java server pages by Trevor D. Kramer, and is now in version 1. Version 2 (still under development) will enable visitors to add comments, critiques, and ratings. The implementation is completely independent of subject matter, and new sites can easily be established for different topics. For example, the journal Biochemistry & Molecular Biology Education is considering use of the VMI for an index to several categories of web-delivered biochemical educational resources, and I am planning to replace my old web-based catalog of flow cytometry software, and my website on general purpose scientific plotting software with VMI implementations. If you are interested in using the VMI system for indices on your server, please contact me. VMI development has been supported by the Division of Undergraduate Education of the US National Science Foundation. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/microbio/rasmol/emartz.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Rob Steele Subject: new rasmol user having Mac problem Date: Wed, 19 Jul 2000 17:39:55 -0700 To: rasmol@lists.umass.edu In case this issue has already been discussed ad nauseum, I offer my apologies. I am a new rasmol user who is trying to view structures using rasmol on a Mac G3 with OS 8.5.1 and 192 MB of RAM. While I can view the sample structures that come with rasmol 2.6, my attempt to view a downloaded pdb file have been unsuccessful. Attempts to open the file result in rasmol freezing up and requiring a forced quit. Subsequent to the forced quit, pull-down menus fail to stay open when single-clicked. I've given rasmol what seems to me should be ample memory (10 MB). I get a similar result using rasmol 2.7.1. Any suggestions as to the nature of the problem and how to solve it would be greatly appreciated. Thanks, ====================================================================== ========== Rob Steele Associate Professor Department of Biological Chemistry 240 D Medical Sciences I University of California, Irvine Irvine, CA 92697-1700 office phone: 949-824-7341 lab phone: 949-824-4343 fax: 949-824-2688 e-mail: resteele@uci.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Authentication-warning: cube.aptamer.com: slaton owned process doing -bs ++++------+------+------+------+------+------+------+------+------+------+ From: Slaton Lipscomb Subject: Re: new rasmol user having Mac problem Date: Wed, 19 Jul 2000 21:27:00 -0700 (PDT) To: rasmol@lists.umass.edu Rob, Could this be a CR/LF problem? If you are downloading the structures using FTP, make sure you use ascii mode instead of binary or "auto" mode. Most FTP clients (Fetch included) assume that files other than .TXT should be downloaded as binary. Downloading in ascii mode will convert the carriage returns and linefeeds to the proper Mac format. Another (though less likely) possibility is that the structures you are downloading are compressed with GNU Zip, for use with Chime. Rasmol does not support the use of GZip compressed structures. Good luck, Slaton Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://c4.cabrillo.cc.ca.us On Wed, 19 Jul 2000, Rob Steele wrote: > In case this issue has already been discussed ad nauseum, I offer my > apologies. I am a new rasmol user who is trying to view structures > using rasmol on a Mac G3 with OS 8.5.1 and 192 MB of RAM. While I can > view the sample structures that come with rasmol 2.6, my attempt to > view a downloaded pdb file have been unsuccessful. Attempts to open > the file result in rasmol freezing up and requiring a forced quit. > Subsequent to the forced quit, pull-down menus fail to stay open when > single-clicked. I've given rasmol what seems to me should be ample > memory (10 MB). I get a similar result using rasmol 2.7.1. Any > suggestions as to the nature of the problem and how to solve it would > be greatly appreciated. > > Thanks, > ====================================================================== > ========== > Rob Steele ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Loren Williams Subject: Re: new rasmol user having Mac problem Date: Thu, 20 Jul 2000 12:38:28 -0400 To: rasmol@lists.umass.edu Sometimes the downloading goofs things up in the file datafork, or can even convert it to binary. Try opening a pdb file with a text editor or word processor to see what it looks like. If it looks ok, save the file as 'text only'. >In case this issue has already been discussed ad nauseum, I offer my >apologies. I am a new rasmol user who is trying to view structures >using rasmol on a Mac G3 with OS 8.5.1 and 192 MB of RAM. While I >can view the sample structures that come with rasmol 2.6, my attempt >to view a downloaded pdb file have been unsuccessful. Attempts to >open the file result in rasmol freezing up and requiring a forced >quit. Subsequent to the forced quit, pull-down menus fail to stay >open when single-clicked. I've given rasmol what seems to me should >be ample memory (10 MB). I get a similar result using rasmol 2.7.1. >Any suggestions as to the nature of the problem and how to solve it >would be greatly appreciated. > >Thanks, >====================================================================== >========== >Rob Steele >Associate Professor >Department of Biological Chemistry >240 D Medical Sciences I >University of California, Irvine >Irvine, CA 92697-1700 > >office phone: 949-824-7341 >lab phone: 949-824-4343 >fax: 949-824-2688 >e-mail: resteele@uci.edu > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: new rasmol user having Mac problem Date: Thu, 20 Jul 2000 08:51:48 -0700 To: rasmol@lists.umass.edu Cc: resteele@e4e.oac.uci.edu I've been using Rasmol 2.5x and 2.6 on Macs for a while now and haven't had any of the problems you've encountered, even with OS 9. The only apparent freezing that I've seen is while Rasmol is opening a particularly large file (say, greater than 600 KB) or if it has to do many calculations, such as when displaying dot surfaces. But it always comes back to life eventually. Have you had this problem with small molecules? Dave Hurley University of Washington Biology Program 318 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-685-1728 >In case this issue has already been discussed ad nauseum, I offer my >apologies. I am a new rasmol user who is trying to view structures >using rasmol on a Mac G3 with OS 8.5.1 and 192 MB of RAM. While I >can view the sample structures that come with rasmol 2.6, my attempt >to view a downloaded pdb file have been unsuccessful. Attempts to >open the file result in rasmol freezing up and requiring a forced >quit. Subsequent to the forced quit, pull-down menus fail to stay >open when single-clicked. I've given rasmol what seems to me should >be ample memory (10 MB). I get a similar result using rasmol 2.7.1. >Any suggestions as to the nature of the problem and how to solve it >would be greatly appreciated. > >Thanks, >====================================================================== >========== >Rob Steele >Associate Professor >Department of Biological Chemistry >240 D Medical Sciences I >University of California, Irvine >Irvine, CA 92697-1700 > >office phone: 949-824-7341 >lab phone: 949-824-4343 >fax: 949-824-2688 >e-mail: resteele@uci.edu > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Rob Steele Subject: Re: new rasmol user having Mac problem (solved by Dave Hurley) Date: Thu, 20 Jul 2000 15:27:23 -0700 To: Dave Hurley Cc: rasmol@lists.umass.edu Dear Dave, You solved my problem. I got the file from "Molecules R Us" and it opened perfectly. Thanks much for your help and for everyone else who offered advice. -- Rob >Rob, > > The file you sent was in CIF format (a new one on me, but maybe >it's a good one for other purposes) and therefore Rasmol is choking >on it. Fortunately, you can open such files in Word or a text editor >and in the first section will be the name of the pdb file that you >can download from such sources as "Molecules R Us" >(http://webasaurus.dcrt.nih.gov/cgi-bin/pdb). In fact, your source >seems to have named the file using the same naming scheme that the >NIH database uses. I just entered "1EJ1" in the search field on the >above web page and it brought up the right file. > >Let me know if you have other questions. > >Cheers, > >Dave ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jake@ncsa.uiuc.edu, radkins@bio.umass.edu, ssdonova@students.wisc.edu, ricky.cox@murraystate.edu, adepass@liu.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PE 1.48: MSA3D, cation-pi, salt bridges Date: Tue, 01 Aug 2000 19:52:05 -0400 To: rasmol@lists.umass.edu Cc: Joel.Sussman@weizmann.ac.il, bourne@sdsc.edu, ravagepositronic@v-wave.com, I have upgraded Protein Explorer (PE) to version 1.48-beta at http://www.umass.edu/microbio/chime/explorer It has been tested on both Windows and Macintosh. It is downloadable. This version has the following major changes since version 1.46-beta previously there: NEW FEATURES MSA3D: color a molecule by mutation/conservation based on a multiple protein sequence alignment. This feature has a tutorial with built-in examples so it is easy to try. The most difficult part of using it is creating the multiple sequence alignment (done at an external site such as Biology Workbench -- instructions are provided). Once that is done, pasting it into PE and generating the colors is easy! Detection of most errors is automatic. (MSA3D is much more mature than it was in PE version 1.47-alpha.) Cation-Pi Display: One of the least appreciated kinds of noncovalent bonds contributing significantly to protein stability is binding of the cationic sidechains of Lys or Arg to the pi orbital faces of aromatic rings in Trp, Phe or Tyr. PE can now display these automatically in a single click (in QuickViews). Advanced Explorer has a form that can include ligands in the detection and display. Salt Bridges can be displayed in one click in QuickViews. In Advanced Explorer, a form enables ligand ions to be included in detection and display. You might be surprised at how many salt bridges are in your favorite proteins (I was!). ---------------------- Please report bugs to me, especially any sequence alignments that are not handled correctly by MSA3D. I would also appreciate emailed copies of sequence alignments that give pretty results in MSA3D! This version will not replace version 1.0 at the Protein Data Bank until more debugging and some documentation revisions are completed. If you haven't seen Protein Explorer since version 1.0, it is now enormously easier to use, and has a clickable sequence-to-structure interface. It is much easier to use than RasMol, and much more powerful. Version 1.47-alpha debuted in June at the ASBMB, and at workshops at Boston University and the Weizmann Institute, Israel. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,pdf References: <0FYN007LG0F0VY@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Hogue Subject: PE 1.48b? What about RasMol 2.7! Date: Wed, 02 Aug 2000 11:52:24 -0400 To: rasmol@lists.umass.edu Hi Eric, It seems to me that your interests no longer lie in supporting RasMol. I know you take great pride in counting the huge number of hits you get on your web site, but you know very well that you have not updated since 2.6, and it it torturous for people to find the links to the current, maintained version of RasMol 2.7x excecutables from your site. I think you need to seriously consider redirecting your current RasMol home page more clearly towards the Bernstein-plus-sons site (i.e. that should be the first thing people see). Eric, you are using the rasmol discussion list to flog PE betas. It looks like you are in a conflict of interest to me doing this and keeping people away from the most recent RasMol. I am quietly advising you that you need to yield your hold on RasMol to the www.bernstein-plus-sons site. You need to extract yourself from this situation both on the discussion list and on the web site. Find another moderator for the discussion list, break off your own PE discussion list if that makes sense, or simply dissolve it. Above all, play fair. Best regards, Christopher Hogue. --------------------------------------- Christopher W.V. Hogue, Ph.D. Samuel Lunenfeld Research Institute Mt. Sinai Hospital 600 University Ave. Toronto Ontario Canada M5G 1X5 (416) 586-4800 xt2866 fax (416) 586-8857 hogue@mshri.on.ca http://bioinfo.mshri.on.ca Eric Martz wrote: > > I have upgraded Protein Explorer (PE) to version 1.48-beta at > http://www.umass.edu/microbio/chime/explorer > It has been tested on both Windows and Macintosh. It is downloadable. > > This version has the following major changes since version 1.46-beta > previously there: > > NEW FEATURES > > MSA3D: color a molecule by mutation/conservation based on a multiple > protein sequence alignment. This feature has a tutorial with built-in > examples so it is easy to try. The most difficult part of using it is > creating the multiple sequence alignment (done at an external site such as > Biology Workbench -- instructions are provided). Once that is done, pasting > it into PE and generating the colors is easy! Detection of most errors is > automatic. (MSA3D is much more mature than it was in PE version 1.47-alpha.) > > Cation-Pi Display: One of the least appreciated kinds of noncovalent bonds > contributing significantly to protein stability is binding of the cationic > sidechains of Lys or Arg to the pi orbital faces of aromatic rings in Trp, > Phe or Tyr. PE can now display these automatically in a single click (in > QuickViews). Advanced Explorer has a form that can include ligands in the > detection and display. > > Salt Bridges can be displayed in one click in QuickViews. In Advanced > Explorer, a form enables ligand ions to be included in detection and > display. You might be surprised at how many salt bridges are in your > favorite proteins (I was!). > > ---------------------- > > Please report bugs to me, especially any sequence alignments that are not > handled correctly by MSA3D. > > I would also appreciate emailed copies of sequence alignments that give > pretty results in MSA3D! > > This version will not replace version 1.0 at the Protein Data Bank until > more debugging and some documentation revisions are completed. > > If you haven't seen Protein Explorer since version 1.0, it is now > enormously easier to use, and has a clickable sequence-to-structure > interface. It is much easier to use than RasMol, and much more powerful. > Version 1.47-alpha debuted in June at the ASBMB, and at workshops at Boston > University and the Weizmann Institute, Israel. > > -Eric Martz > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: www.umass.edu/microbio/chime/explorer > World Index of Chime Resources: http://molvis.sdsc.edu/visres > PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > 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: Frieda Reichsman Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Wed, 02 Aug 2000 15:12:57 -0400 To: rasmol@lists.umass.edu I cannot disagree more strongly with the sentiments expressed in the email below, and I find the tone of it offensive. Posting a note such as this to an email listserv and then saying that you are "quietly advising" Eric, while incidentally berating him publicly, is preposterous. "Play fair," indeed! If you feel that the links to 2.7.1 are too lengthy, why are you posting this thought to the list in such a rude and obstreperous manner, rather than starting a discussion of this in a normal, logical manner? Your post sounds like you have boiled over--why would you do that in a public venue, particularly without even publicly simmering first? You do yourself and your cause a disservice by this attack. It will be harder to convince me that you have legitimate complaints if this is the style that you adopt when expressing them. Sincerely, Frieda Reichsman, Ph.D. >Hi Eric, > >It seems to me that your interests no longer lie in supporting RasMol. I >know you take great pride in counting the huge number of hits you get on >your web site, but you know very well that you have not updated since >2.6, and it it torturous for people to find the links to the current, >maintained version of RasMol 2.7x excecutables from your site. > >I think you need to seriously consider redirecting your current RasMol >home page more clearly towards the Bernstein-plus-sons site (i.e. that >should be the first thing people see). Eric, you are using the rasmol >discussion list to flog PE betas. It looks like you are in a conflict >of interest to me doing this and keeping people away from the most >recent RasMol. > >I am quietly advising you that you need to yield your hold on RasMol to >the www.bernstein-plus-sons site. You need to extract yourself from this >situation both on the discussion list and on the web site. Find another >moderator for the discussion list, break off your own PE discussion list >if that makes sense, or simply dissolve it. > >Above all, play fair. > > >Best regards, >Christopher Hogue. > >--------------------------------------- >Christopher W.V. Hogue, Ph.D. >Samuel Lunenfeld Research Institute >Mt. Sinai Hospital 600 University Ave. >Toronto Ontario Canada M5G 1X5 >(416) 586-4800 xt2866 >fax (416) 586-8857 > >hogue@mshri.on.ca > >http://bioinfo.mshri.on.ca > > > >Eric Martz wrote: >> >> I have upgraded Protein Explorer (PE) to version 1.48-beta at >> http://www.umass.edu/microbio/chime/explorer >> It has been tested on both Windows and Macintosh. It is downloadable. >> >> This version has the following major changes since version 1.46-beta >> previously there: >> >> NEW FEATURES >> >> MSA3D: color a molecule by mutation/conservation based on a multiple >> protein sequence alignment. This feature has a tutorial with built-in >> examples so it is easy to try. The most difficult part of using it is >> creating the multiple sequence alignment (done at an external site such as >> Biology Workbench -- instructions are provided). Once that is done, pasting >> it into PE and generating the colors is easy! Detection of most errors is >> automatic. (MSA3D is much more mature than it was in PE version 1.47-alpha.) >> >> Cation-Pi Display: One of the least appreciated kinds of noncovalent bonds >> contributing significantly to protein stability is binding of the cationic >> sidechains of Lys or Arg to the pi orbital faces of aromatic rings in Trp, >> Phe or Tyr. PE can now display these automatically in a single click (in >> QuickViews). Advanced Explorer has a form that can include ligands in the >> detection and display. >> >> Salt Bridges can be displayed in one click in QuickViews. In Advanced >> Explorer, a form enables ligand ions to be included in detection and >> display. You might be surprised at how many salt bridges are in your >> favorite proteins (I was!). >> >> ---------------------- >> >> Please report bugs to me, especially any sequence alignments that are not >> handled correctly by MSA3D. >> >> I would also appreciate emailed copies of sequence alignments that give > > pretty results in MSA3D! >> >> This version will not replace version 1.0 at the Protein Data Bank until >> more debugging and some documentation revisions are completed. >> >> If you haven't seen Protein Explorer since version 1.0, it is now >> enormously easier to use, and has a clickable sequence-to-structure >> interface. It is much easier to use than RasMol, and much more powerful. >> Version 1.47-alpha debuted in June at the ASBMB, and at workshops at Boston >> University and the Weizmann Institute, Israel. >> >> -Eric Martz >> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - >> The Protein Explorer: www.umass.edu/microbio/chime/explorer >> World Index of Chime Resources: http://molvis.sdsc.edu/visres >> PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm >> >> Eric Martz, Professor (Immunology), Dept Microbiology >> U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 >> www.umass.edu/molvis/martz >> - - - - - - - - - - - - - - - - - - - - - - - - - - - */ >> > -- Frieda Reichsman, Ph.D. 30 South Whitney Street MoleculesInMotion! Amherst MA 01002 USA Interactive Molecular Structures Voice: (413) 253-2405 http://www.MoleculesInMotion.com Fax: (612) 397-9975 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en References: <0FYN007LG0F0VY@supai.oit.umass.edu> <398843B8.FB5AD191@mshri.on.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Wed, 02 Aug 2000 15:23:56 -0400 To: rasmol@lists.umass.edu Christopher, Thanks for sharing your opinion, but your tone and content are offensive. First of all, it is hardly "torturous" to access the Bernstein-and-sons site from the Rasmol Home Page - I found it two clicks and about 20 seconds. Click the giant "Rasmol" link on the home page, then the "getting and installing Rasmol" link on the next one. The resulting page provides hyperlinks to both the 2.6b version and the Bernstein-and-sons site, in big type and standard blue color. It does require that you read some of the text on each page, and hit the scrollbar a few times, but it wasn't too taxing. In no way does Eric's site keep people away from the most recent version of RasMol. As for your "quiet" suggestion to Eric to release control of RasMol, you would have been well advised to send him an email directly instead of broadcasting to the list - that's hardly quiet, and invites responses from people like me. Secondly, as far as I know (as someone outside the loop), RasMol 2.6 is the latest version in the public domain and I see no "conflict of interest" with offering it for download. Thirdly, RasMol is freely available from a number of sites; when did Eric gain "control" over it? In my opinion, he provides a valuable service in compiling a lot of helpful information on molvis in general, including RasMol, Chime, and other programs, to say nothing of his Chime projects. There are many other such sites; have you emailed these people as well, requesting they relinquish control over their RasMol materials? Regarding the RasMol list, I consider it a normally good place to hear from other people developing molvis software of all types, RasMol and otherwise. I applaud Eric for maintaining it faithfully and impartially, especially in the face of the ocassional shortsighted criticism. There are also other email lists that discuss RasMol and molvis; would you like these lists to dedicate themselves to the Bernstein-and-sons' efforts in molvis as well? Perhaps we should all just redirect our own sites and lists to the Bernstein-and-sons site and find something else to do with our time. Bernstein-and-sons are developing RasMol in their own direction; more power to them, I honestly wish them great success. However, they are not the only ones involved in RasMol and RasMol-like software development. I find it offensive for you to suggest that any of us should defer to them simply because they call their product RasMol 2.7 - especially Eric, who has done more for the advancement of molvis than most of the rest of us combined. I won't stop my own efforts in developing molvis resources, and I hope that Eric won't stop, either. -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet mvisions@speakeasy.org Christopher Hogue wrote: > Hi Eric, > > It seems to me that your interests no longer lie in supporting RasMol. I > know you take great pride in counting the huge number of hits you get on > your web site, but you know very well that you have not updated since > 2.6, and it it torturous for people to find the links to the current, > maintained version of RasMol 2.7x excecutables from your site. > > I think you need to seriously consider redirecting your current RasMol > home page more clearly towards the Bernstein-plus-sons site (i.e. that > should be the first thing people see). Eric, you are using the rasmol > discussion list to flog PE betas. It looks like you are in a conflict > of interest to me doing this and keeping people away from the most > recent RasMol. > > I am quietly advising you that you need to yield your hold on RasMol to > the www.bernstein-plus-sons site. You need to extract yourself from this > situation both on the discussion list and on the web site. Find another > moderator for the discussion list, break off your own PE discussion list > if that makes sense, or simply dissolve it. > > Above all, play fair. > > Best regards, > Christopher Hogue. > > --------------------------------------- > Christopher W.V. Hogue, Ph.D. > Samuel Lunenfeld Research Institute > Mt. Sinai Hospital 600 University Ave. > Toronto Ontario Canada M5G 1X5 > (416) 586-4800 xt2866 > fax (416) 586-8857 > > hogue@mshri.on.ca > > http://bioinfo.mshri.on.ca > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Herbert J. Bernstein" Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Wed, 02 Aug 2000 18:27:26 -0400 (EDT) To: rasmol@lists.umass.edu > I will not comment on the issues of how Eric manages his site, but the > recent interchange included some comments by Timothy Driscoll that seem > in need of a bit of clarification about the RasMol 2.7 series. First, the reason that the RasMol 2.7 series is called the RasMol 2.7 series is because Roger and I agree that it was most appropriate to call it that. Since Roger is the primary developer of RasMol, I think it appropriate to lend considerable weight to his opinion as to how to name versions of his program. I am trying to keep the 2.7 series an upwards compatible extension of the 2.6 series. This is somethimes difficult. For example UCB provided their mods for integration just this past month, and I face some difficult design choices in maintaining compatibility with the non-ucb variants while incorporating the very useful ucb functionality. I rely on this community to help keep me on the right track with your comments so that the RasMol 2.7 series be an appropriate successor to the RasMol 2.6 series. Second, there seems to be some misunderstanding about the conditions on use of RasMol 2.7. If you are an ordinary user or an "open-source" software developer, you should not find the new "open-source" conditions at all restrictive. We had to impose these new conditions to be sure of being able to keep source code available for all future releases in this series. I understand that some "closed-source" software developers would prefer not to have to release source of their visualization code. They will have to work from the 2.6 version and miss out on the most recent changes. That is their choice to make but, for most users, the RasMol 2.7 series, which is supported, may be a better choice than using 2.6, which apparently is no longer supported and does not include all the useful features included in 2.7. The bugs that 2.7 users find and the comments they send in are helping the main line of development of RasMol to continue at a healthy pace. Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: dank@hq.lindsayelec.com (Dan Kolis) Subject: Rasmol 2.7 and the homepage Date: Thu, 03 Aug 2000 21:13:42 -0400 To: rasmol@lists.umass.edu Greetings, I have Rasmol 2.5 on my computers and have successfully compiled some custom versions (amazingly enough and horribly) in Microsoft C++. That compile was of Rasmol 2.6 I find the scripting especially brilliant in Rasmol, and allthough I think I'm a good programmer, Roger S is a *very* talented man. I freely admit he is a better programmer than I am. *any* version of Rasmol is great, and having the source completely makes it a gift to humanity. Glaxo has done a noble thing to support this, I assume, financially. I don't know specifically how much sweat of the brow has been contributed by Univ of Mass but I assume 'enough' as the web presence is at least, very very good, and the term 'pretty great' does come to mind. The concept that the latest version is hard to find is I think inaccurate. I think I looged this sequence correctly: http://www.umass.edu/microbio/rasmol/ Is the Homepage: 'You can download RasMol here.' {CLICK} 'RasMol 2.7 and its full documentation' Source Code and Binaries. {CLICK} All the goodies are here. Anyway it certainly takes only a negligable amount of time to find the source, compiled .exe's and so on. ----------------------------------------- Eric M s page at: http://www.umass.edu/microbio/rasmol/getras.htm says: "... Eric Martz, at the University of Massachusetts does not document the changes in RasMol 2.7. For two and a half years (November 1995 through April 1998) I actively developed the RasMol branch of my website. However, the documentation at my site will remain largely frozen at RasMol 2.6-beta-2a. This is because my efforts are now focused largely on Chime, notably the Protein Explorer, an alternative to RasMol which is easier to use and more powerful (though, unlike RasMol, limited to Windows and Macintosh PPC users since Chime is not supported on unix/linux)." So I think that represents Eric's forward focus in time is going to be Protein Explorer. I'd guess without the amazing reality of Rasmol, it would have been hard to visualize where to start on PE. The Bernstein RasMol 2.7 site. is only one page from the home page. It right away presents material on Rasmol 2.7, and is at: http://www.bernstein-plus-sons.com/software/rasmol/ Any deep pockets institution / company needing to modify Rasmol would realize the Berstein thing is a resource to be explored. Before committing to some big project any diligence at all would make this possibility apparent. I guess I don't grasp even the essence of the complaints. Since the source is there, anything you want to do, if you know how, you can do. A commercial site adding value to the Rasmol concept is clearly there; (the Bernstein site). Things change, things differentiate. Rasmol and all these programs have different roles. For me, for instance "easy to use" means little. I don't care if its easy to use, undoubtably lots of people do. There are a zillion reasons to prefer or require a Linux viewer or a Microsoft one, there are reasons to LOVE having the source, etc. Running in a browser is perhaps essential to do some things. I hope I haven't wasted the readers time; (I fear I have). I am suggesting the status quo is pretty good. Regards, Dan Kolis ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: PE 1.48b? What about RasMol 2.7! Date: Thu, 10 Aug 2000 14:54:36 -0400 To: rasmol@lists.umass.edu I'd like to explain my plans regarding some of the important issues brought up by Chris Hogue in his message of August 2. (For those of you who don't know, Dr. Hogue is the original author of the CN3D visualization software featured by the NCBI.) MY WEBSITE VS. THE RASMOL 2.7 WEBSITE - DIFFERENT GOALS RasMol's importance in bringing macromolecular visualization to the general scientific pubic is huge. The team of volunteers led by Herb Bernstein who are continuing to develop it are to be congratulated. The website for RasMol 2.7 is aimed at experienced users, emphasizing RasMol's newest features and source code. In contrast, my site has always emphasized detailed help for beginners, including students in high school and above, educators, and even researchers who need macromolecular visualization on an occasional basis. For the three years from 1995 through 1997, development of help, documentation, and templates for RasMol was my main effort. Since then, as Chris Hoge correctly points out (and I have stated explicitly on my RasMol site over a year ago), my interests have shifted to Chime and Protein Explorer because they better meet the needs of beginners and occasional users. I strongly believe it is the documentation for beginners that is responsible for the traffic at my site (8,000 people/week during spring 2000). Because the focus of the RasMol 2.7 website is quite different, the majority of the visitors to my site would not be well served by being sent to the RasMol 2.7 site as a place to start. (It has not a single link my site nor to any of the dozens of RasMol reference documents at my site for which it offers no equivalents.) At this point, Protein Explorer has superceded RasMol in ease of use and power. Therefore, soon I plan to change my site to feature Protein Explorer instead of RasMol. In 1995, my site was named the "RasMol Home Page" with the blessing of Roger Sayle. I renamed my site to "RasMol & Chime: Molecular Visualization Freeware" in 1997. Henceforth, Chime-based Protein Explorer will better serve the majority of those who can benefit from molecular visualization, namely students, educators, and researchers who need visualization on an occasional basis. Of course I'll continue to provide RasMol 2.6-beta-2a, links to RasMol 2.7, and RasMol documentation for those interested (especially the growing number of linux users). My site has had a prominent link to RasMol 2.7 since June, 1999. But RasMol will no longer be featured as the place to start for novices using Windows or Macintosh systems. It is of course unfortunate that MDL has not been convinced to open the source code for Chime. This prevents a number of serious limitations of Chime from being addressed by the user community, following the excellent model set by Bernstein and the other RasMol volunteers. Nevertheless, Chime as it stands is sufficiently powerful that I have put all of my work into it for the past few years, and plan to continue to do so indefinitely. The goal of my website continues to be, as it always has been, to make molecular visualization as accessible as possible. Until summer 2000, RasMol has been the best mechanism, but that is no longer the case. I do not see this transition as a conflict of interest, but a necessary evolution towards achieving this goal. RASMOL EMAIL LIST While my website will indeed reflect my opinions about what best serves beginners and occasional users, this email list serves a very different function and shall remain an open forum for all opinions. Originally called the "RasMol list", in fact it became a general discussion of molecular visualization freeware years ago, a fact reflected in its description at its website, http://www.umass.edu/microbio/rasmol/raslist.htm. You, as one of its more than 500 subscribers, will help to decide the topics of interest. I expect RasMol (both 2.6 and 2.7) and its support on linux and other unix systems to remain of great interest, as well as Chime, Protein Explorer, and related topics. (SwissPDB Viewer has a separate discussion, see http://www.usm.maine.edu/~rhodes/SPVTut/text/DiscuSPV.html). In my view, the community is best-served by continuing to discuss all these resources (including sometimes their relation to SwissPDB Viewer) in a single email list, given the low volume of traffic, and the intimate relationships between RasMol, Chime, and Protein Explorer. As founder and maintainer of this list, my role is primarily in the technical capacity of keeping the list operating smoothly, a task that requires daily attention. I certainly have never blocked any messages or intentionally discouraged any viewpoints from being expressed. Others are free to initiate competing or overlapping lists, as indeed the SwissPDB Viewer group did recently -- an initiative that has worked out well. RASMOL'S DIFFICULTY INSPIRED PROTEIN EXPLORER'S EASE OF USE It is my experiences with RasMol and Chime that have inspired the design of Protein Explorer. Below I have summarized these experiences and given some illustrations concerning 'ease of use' and 'power'. Between 1996 and 1999 I worked to help realize RasMol's potential in education by teaching workshops on RasMol and Chime for college professors. In a series of five 3-day workshops held in Amherst MA and Long Island Univ, New York City (supported by NSF), nearly 100 college educators from 11 states and over 60 colleges participated. To support these workshops I developed extensive documents to help people use RasMol. The main thing I learned from these workshops is that RasMol is too difficult for the majority of students and educators who could benefit from molecular visualization. For this majority, even after having been taught how to use RasMol and provided with detailed reference documents, there are too many commands or technical tricks needed to use the software effectively. The typical biochemistry professor or student may need to visualize macromolecules only one or a few times per year. Between uses, the tricks are forgotten and the result is that RasMol is used ineffectively if at all by most. (Of course some do have the talent or persistence needed and become quite effective users of RasMol. But I estimate that these are less than 10% of the scientists and students who could benefit and would use visualization software were it sufficiently easy to use.) My proposed solution to this problem is Protein Explorer. I am working to make it possible to achieve relatively powerful visualizations without needing to know any of the teletype-style typed command language necessary to use RasMol effectively. As an example, it takes several hours to teach a new user, looking at a molecule for the first time, how to find out the number of chains present, whether they are protein, DNA, or RNA, whether water is present, whether disulfide bonds are present, and whether any ligands are present. Also, whether more than one model is present. I have taught several classes of students to do this. Even after such teaching, when quizzed with a new molecule, most fail to answer these questions within the first hour of exploration due to the difficulty of remembering the questions, and how to answer them. My solution: by default, the first image in Protein Explorer shows the answers to most of these questions (and the answers to the remainder are only a click or two away). The "FirstView" description that accompanies the initial image lists these questions and provides help on how to interpret the image to answer them. (Experienced users can check "Expert" in the Preferences, after which the FirstView description is shown only when requested.) Roger Sayle's design for RasMol's menus was excellent. However, RasMol itself provides no guidance on how to use these menus or how to interpret the results. Protein Explorer's QuickViews menus are similar to RasMol's, but have more power, including the ability to select subsets of atoms for differential rendering or coloring, rendering of surfaces, contact surfaces, cation-pi interactions, salt bridges, color schemes for hydrophobic vs. polar, ATGCU, etc. Most importantly, each and every one of the dozens of QuickViews menu options automatically displays help targeted to novices, including color keys where appropriate. Even most experienced RasMol users are hard pressed to tell DNA from RNA, or to realize when they have encountered a multiple-model NMR PDB file. Protein Explorer answers the first question in one click, and automatically informs users when the second situation is encountered. There are a number of questions that it is possible to answer in RasMol, but the difficulty is sufficient that only the most expert, willing to spend many hours, could do so. An example is locating residues that contact a moiety of interest in a series of distinct shells of increasing distance. True, an expert can create scripts to help, but running these scripts is cumbersome at best, especially for someone else. The Noncovalent Bond Finder (now part of Protein Explorer) makes it possible to do this smoothly and easily, without knowing the command language (beyond selecting the initial target moiety). It produces images of a clarity and simplicity that only highly experienced RasMol users might achieve. Most importantly, it makes the process of answering the questions so easy that the process can be repeated at will on different portions of the same structure, or on different structures, all in a single session. Hundreds of detailed, technical commands are generated automatically by an intelligent interface. Similar sections of Protein Explorer deal with selection or animation of multiple-model NMR files, solvent-accessible surfaces, cation-pi interactions, salt bridges, sequence to structure mapping, and coloring a molecule according to conservation/mutation in multiple sequence alignment. Imagine trying to do these things all in the same day, in the same session, with RasMol! Yet this has become possible with Protein Explorer. I thank Chris Hogue for expressing his opinions and welcome the opinions of others. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 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: "Herbert J. Bernstein" Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Thu, 10 Aug 2000 21:42:54 -0400 (EDT) To: rasmol@lists.umass.edu In his recent message, Eric Martz said: " ...The website for RasMol 2.7 is aimed at experienced users, emphasizing RasMol's newest features and source code." Eric Martz is mistaken. The RasMol 2.7 web site is intended for users at all levels who wish to have the latest release of RasMol. I would be happy to hear suggestions for improvements to make the site more accessible to all users and accept contributions of materials which are available for release as part of an open source site. We appreciate the contributions that have been made by many members of the community. For example, the version of the manual on the site is the result not only of Roger Sayle's original fine document, but of changes made by Margaret Wong, Eric Martz and William McClure. To produce that manual, we worked from Roger Sayle's manual for version 2.6.4 and William McClure's manual. The manual is, I think, reasonably complete and tries to cover all features in the current version. If something important is missing, please tell me. To avoid cluttering the list, if your comments are not intended for the whole community, please send your message to: rasmol@bernstein-plus-sons.com Eric Martz goes on to say: " ... Because the focus of the RasMol 2.7 website is quite different, the majority of the visitors to my site would not be well served by being sent to the RasMol 2.7 site as a place to start. (It has not a single link my site nor to any of the dozens of RasMol reference documents at my site for which it offers no equivalents.)" Clearly, with Eric Martz moving on to focus on other programs, we will have to enrich the RasMol 2.7 site from simply being a site from which to obtain the latest release of RasMol to being a more complete site. I will be happy to consider adding links to documents and sites which are relevant to the current release and which don't create confusion about the open source status of the 2.7 release. Better, if you have an appropriate and useful RasMol-related document you are willing to have included directly on the site under our open-source release conditions, I will be happy to consider it for inclusion and to handle the necessary updates as the program evolves. -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: German/Germany, de-DE, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Fri, 11 Aug 2000 11:31:20 +0200 To: rasmol@lists.umass.edu RasMol and Chime are powerful programs which should coexist in peace :-) I, myself prefer RasMol, may be, it is because I have no choice on unix systems. But the students, proud owners of laptops with W9x software often intend to install Chime first, because installation of a plugin is easier. After demonstrating the power of RasMol, they liked to use RasMol alternatively. This shouldn't be a problem, because e.g. The RCSB PDB ( http://www.rcsb.org/index.html ) provides coordinate for RasMol as chemical/x-ras and for Chime as chemical/x-pdb and for PE as I don't know. The NDB ( http://ndbserver.rutgers.edu/NDB/index.html ) for remote RasMol coordinate display uses application/x-rasmol The OCA ( http://bioinfo.weizmann.ac.il:8500/oca-docs/ ) uses for coordinate to be displayed in RasMol application/x-rasmol and for Chime chemical/x-pdb The IMB Jena Image Library of Biological Macromolecules ( http://www.imb-jena.de/IMAGE.html ) provides RasMol as application/x-rasmol and Chime scripts as application/x-spt and coordinates as chemical/x-pdb so in principle RasMol and Chime should be able to coexist, but after installing Chime it claims all mime types and I have no idea how to reassign only application/x-rasmol back to RasMol. If this is possible, I think it should be part of the installation instructions: Installing RasMol v2.7.1 MS Windows it has been some time ago, that I have tried this by my own and I read (I don't remember where) that I have to assign this in the Windows Explorer file type assignment, and tried to do so, but failed. If no coexistence is possible, Chime should be altered to make it possible. With kind regards, and thanks to all who made this wonderful programs, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Andy Tucker Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Fri, 11 Aug 2000 13:37:30 -0500 (EST) To: rasmol@lists.umass.edu I've been using rasmol for research and teaching purposes for about 7 years, and would like to make some comments on the current discussion. 1. Concerning Eric, Rasmol, PE, and the list: First of all, I have been very impressed with the work Eric has with his website and this list over the years. I routinely use modified versions of scripts from his pages in my classes. My impression has been that Eric did a lot of work with very little support at first. I am extremely grateful for all the work he has done to support the use of the program. Now he is focussing his attention on Chime and Protein Explorer, and I don't feel that I, as a user, have any right to complain. I suspect (and hope) that he still feels some obligation to maintain links to the most current rasmol version, 2.7.1, due to the fact that his page has been the official home of rasmol for some time. However, I think we should all respect his desire to move in a different direction. Thanks for all the help, Eric, and keep up the good work! I suspect that there are a few of us who are disappointed with the fact that there seems to be less emphasis on rasmol on the net these days. Most likely the solution will be, as Bernstein has said, to expand the Rasmol 2.7.1 site. 2. Why I still like rasmol: I started using rasmol because it was the only free program of its type available. I was amazed that I could view proteins on my desktop computer (a 486), and rotate them with a performance that was nearly as good as Biosym software on an SGI Personal Iris (remember those?). Today there are several free programs available, and most of those have been built on top of the rasmol code base (I've used Chime, MolMol, and SwissPDBViewer, and Protein explorer). One of the problems I've observed are that some of the programs built on rasmol sacrifice the speed of molecular movement at the expense of adding new features. This doesn't seem to be too much of an issue with Chime and PE, but they require loading a bloated web browser to use. I prefer to use a smaller stand-alone program. I still feel that rasmol is easy to use for novices, if they are given a little hands-on instruction. I think teaching the command line interface to students is very useful to those who will later use other molecular modelling packages. 3. How I use Rasmol in teaching Biochemistry: I use rasmol to present various molecular structures in all of my chemistry classes. In my biochemistry class, I make brief presentations of several different proteins in class, then teach the students to use the software in a subsequent lab. I give them a handout with an introduction to the software and the PDB, a hands-on tutorial exercise, and a quick reference to commands and mouse operation for the program. The goal of the lab is for the students to prepare a 5 min. presentation to the class for a protein of their choice(usually 2 weeks later). I spend that one lab period with the students helping them out. In my experience, about 2/3 of the students never go beyond using the simple commands that they have on their handouts, but the remainder of the students will really get involved and sometimes use other software packages or advanced scripting and labelling. All students are able to highlight the important features of their proteins, and I am always satisfied with the results. 4. On keeping Rasmol accessible for Novice users: Rasmol 2.7.1 is a wonderful combination of the work of many people. However, I feel that some work needs to be done to make it more user- friendly to new users. My personal philosophy is that all scientists need to be adept at using computers, but we all know that is not always the case. Several times I have tried to interest a colleague in using rasmol, but they were intimidated by the perceived difficulty of installation. People who use Windows and Mac computers are used to being able to download self- installing programs from the internet, and installing rasmol has never really been trivial. While I (and many readers of this list) may be comfortable with compiling programs from source on a linux box, and fighting with compiler errors, most would rather have their software in a more accessible format. One really simple thing that could be done on the Bernstein site would be to provide .zip files with the executable and help files in one place, perhaps with an example .pdb file, as Roger once packaged the program. As recently as last week I found that there were still problems with some of the windows files on the page (help files labelled as .gz, but were really uncompressed, an uncompressed .exe file that was corrupt). Even better would be a self-installing executable that would install the files in their own directory. Finally, there are two small issues in Rasmol 2.7.1 which keep it from being as user friendly as possible. First of all, the current help is comprehensive, but clicking on "user manual" immediately shows some copyright info, instead of the menu, which is on the next page. I would bet that many new users wouldn't even bother to hit "Page Down" to find the menu. I think the copyright info should be placed elsewhere, so the user can get to the help menu immediately. The other problem originates with the earliest versions of rasmol. When clicking on an individual atom, the information is displayed as follows: "Atom: CE2 2548 Group:PHE36 Chain C" Unfortunately, if the user wants to select said atom (or residue), he or she must remember the format for specifying an atom which, in this case, would be " phe36:C.CE2". If you don't remember the format, it becomes difficult to select the atom that was just picked, because the information given isn't even in the same order in which it is needed in the specifier. Since I use several modelling programs, I always forget and have to look at the online help or my own notes to remember. Thanks to those who have read this far. I hope this list continues to discuss all of the freely available molecular presentation programs. andy Dr. W. Andrew Tucker Queens College Chem. Dept. tuckera@queens.edu 1900 Selwyn Ave. (704)337-2317 Charlotte, NC 28274 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: dank@hq.lindsayelec.com (Dan Kolis) Subject: Rasmol and students Date: Fri, 11 Aug 2000 15:20:56 -0400 To: rasmol@lists.umass.edu Interesting stuff. It took me a weekend of waking hours to learn Rasmol scripting which I think is a pretty amazing program. I am surprised students have trouble with it. Consider for instance learning a new human language (Ex: Spanish). Nobody expects to master it suddenly. But upon getting to know it, you enable a vast set of new possibilities. I guess I was privately wondering, if they can't 'get' that, what chance do they have doing science, really? I feel guilty to assert it that way. Ok, Here I stand, feeling guilty. Just suggesting no matter how many pulldown menu's you have to make things obvious and easy, the new matter will usually be only revealed by things no program author would include. That's why the scripting and programmibility is so pivotal for new work. I am sure we all agree there's lots of roles for different programs, interface styles and ease of use levels versus power. Agreed. I'm just suggesting sometimes things are not easy, for a reason; (not just an omission in design). Regards to all Dan Kolis ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <200008111731.NAA23711@jazz.ncren.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Fri, 11 Aug 2000 17:32:52 -0700 (PDT) To: rasmol@lists.umass.edu Andy Tucker writes: > 2. Why I still like rasmol: > I started using rasmol because it was the only free program of its type > available. I was amazed that I could view proteins on my desktop computer > (a 486), and rotate them with a performance that was nearly as good as > Biosym software on an SGI Personal Iris (remember those?). Today there > are several free programs available, and most of those have been built on top > of the rasmol code base (I've used Chime, MolMol, and SwissPDBViewer, > and Protein explorer). One of the problems I've observed are that some of Have a look at VMD: http://www.ks.uiuc.edu/Research/vmd/ It works much better with OpenGL hardware acceleration, of course. There are things like Spock: http://quorum.tamu.edu/spock/ Rasmol is nice, because it's minimal, and uses smart CPU sphere rendering, which can beat even the best 3d acceleration hardware for special uses. > the programs built on rasmol sacrifice the speed of molecular movement at > the expense of adding new features. This doesn't seem to be too much of an > issue with Chime and PE, but they require loading a bloated web browser to > use. I prefer to use a smaller stand-alone program. I still feel that rasmol is > easy to use for novices, if they are given a little hands-on instruction. I think > teaching the command line interface to students is very useful to those who > will later use other molecular modelling packages. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Erik Helmerhorst Subject: rasmol for students Date: Mon, 14 Aug 2000 11:27:27 +0800 To: rasmol@lists.umass.edu We have been using rasmol in second year biochemisty classes for several years and find that most students find it extremely valuable. They only need to be guided through some of the most basic type of commands to begin learning about protein structure. We have designed tutorials to guide them on rasmol use and to reinforce lecture material. You can view these at: http://wbiomed.curtin.edu.au/teach/biochem/tutorials/tutorials.html More recently we have turned towards using Chime for second year students but have preserved the command line interactivity by creating a 'command line' text box in which you can send commands to the Chime Plug-in much the same way you do for Rasmol (thanks go to Eric Martz for providing useful JavaScript examples which showed us how to do this). These tutorials are listed as the "three exercises using chime" at the above location. In third year, students build their knowledge of Rasmol by doing some scripting exercises and advanced Rasmol functions. After just a few sessions, students are given an assignment that requires them to use Rasmol to explore the structure of a DNA - DNA binding protein interaction. They are expected to learn more advanced functions by reading the manual and to try to work it out for themselves! If they can't work it out, only then do they come to me for help. They present their assignment as a movie script with the text appropriate to the movie appearing in the command line window. They are assessed on the knowledge they portray in their movie with marks also given for the quality of the scripting & movie - this is heaps easier to mark than reading and assessing essays and its lots more fun!!!! Our students find this approach to be FUN - and they learn heaps. Some of the movie scripts generated are fantastic and exceed my own level of competence with Rasmol and scripting! But perhaps more importantly and interestingly, even the most computer phobic person becomes quite computer literate by the time they finish the exercise - and it gives them the confidence they need around computers. It is rare that any student performs so poorly as to fail the assignment (usually this is just thru lack of effort). So - I do not believe that given some guidance, Rasmol presents any real difficulty for students to use. They just need some basic guidance in the first place. Erik This e-mail message and any accompanying documents may be privileged and may contain confidential information intended only for the person named above. Any other distribution, copying or disclosure is strictly prohibited. If you have received this e-mail message in error, please notify me immediately by return e-mail or telephone. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Associate Professor Erik Helmerhorst | ihelmerh@info.curtin.edu.au School of Biomedical Sciences | Phone: (08) 9266 7378 Building 308 Room 201C | Fax: (08) 9266 2342 Curtin University of Technology | For International GPO Box U1987, Perth, | FAX 618 9266 2342 Western Australia 6001 | _--_|\ / \ >>>----->\_.-- ._ / ^ -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: David Crout Subject: Heatley Medal Date: Mon, 14 Aug 2000 09:50:10 -0700 To: rasmol@lists.umass.edu Amidst all of the flurry of e-mails about RasMol that have been flying around in recent days, it is a great pleasure to be able to inform folk that Roger Sayle has been awarded the Heatley Medal. The Heatley Medal is awarded by Unilever plc to an individual who has made a contribution to biochemistry by developing a tool that is widely used and which confers great benefits on the scientific community in general. I understand that Roger has accepted the award and will be giving the Heatley Lecture here at the University of Warwick, UK on November 3 2000. I will be happy to put anyone interested in attending in touch with the organisers at Unilever Research, Colworth House, Sharnbrook, Bedford, UK, if they care to send me an e-mail. David Crout -- Professor D.H.G. Crout Department of Chemistry University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 76523961 FAX: +44 (0)24 76524429 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: dank@hq.lindsayelec.com (Dan Kolis) Subject: Heatley Medal congrats Date: Mon, 14 Aug 2000 13:17:10 -0400 To: rasmol@lists.umass.edu >Professor D.H.G. Crout >Department of Chemistry >University of Warwick >Coventry CV4 7AL Posted Roger S is receiving an announced award and presentation is late in this year... Maybe it would have more impact to post the address for congratulations for both paper and email closer to that date. Either way if the best address comes to mind I suggest posting it here. Thanks, Dan K Dan Kolis - Lindsay Electronics Ltd dank@hq.lindsayelec.com 50 Mary Street West, Lindsay Ontario Canada K9V 2S7 (705) 324-2196 Phone (705) 324-5474 Fax (888) 326-5654 Pager Anywhere (888) DANKOLIS {Same #) An ISO 9001 Company; SCTE Member ISM-127194 /Document end ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: segmentation fault: nodisplay Date: Tue, 15 Aug 2000 22:04:56 -0400 To: rasmol@lists.umass.edu [Message from Arne Mueller, redirected to the list by Eric Martz to circumvent technical difficulties.] ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: segmentation fault: nodisplay Date: Mon, 14 Aug 2000 17:57:52 +0100 To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com Dear RasMol developers, I came a cross a problem that was probably introduced in version RasMol 2.7.1 (since it does not occure in 2.7.0.1) under unix (irix 6.5 and linux RadHat 6.2). Wehn starting rasmol -nodisplay and then loading a pdb file failes because RasMol tries to set the canvas title although there's no display due to '-nodisplay'. This causes a segmentation fault. Here's some debugging information: mueller@cedar:/bmm/scratch/mueller/RasMol-2.7.1/src> make -f Makefile.in gcc -c -g -O rasmol.c gcc -c -g -O x11win.c gcc -c -g -O abstree.c gcc -c -g -O cmndline.c gcc -c -g -O command.c gcc -c -g -O infile.c gcc -c -g -O molecule.c gcc -c -g -O outfile.c gcc -c -g -O pixutils.c gcc -c -g -O render.c gcc -c -g -O repres.c gcc -c -g -O script.c gcc -c -g -O transfor.c gcc -c -g -O tokens.c gcc -c -g -O cif_fract.c gcc -c -g -O cif.c gcc -c -g -O cif_ctonum.c gcc -c -g -O cif_stx.c gcc -o rasmol -L/usr/X11R6/lib rasmol.o x11win.o abstree.o cmndline.o command.o infile.o molecule.o outfile.o pixutils.o render.o repres.o script.o transfor.o tokens.o cif_fract.o cif.o cif_ctonum.o cif_stx.o -lX11 -lXext -lm chmod 755 rasmol mueller@cedar:/bmm/scratch/mueller/RasMol-2.7.1/src> gdb ./rasmol GNU gdb 19991004 Copyright 1998 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i386-redhat-linux"... (gdb) run -nodisplay Starting program: /bmm/scratch/mueller/RasMol-2.7.1/src/./rasmol -nodisplay RasMol Molecular Renderer Roger Sayle, August 1995 Copyright (C) Roger Sayle 1992-1999 Version 2.7.1 June 1999 Copyright (C) Herbert J. Bernstein 1998-1999 *** See "help notice" for further notices *** [8-bit version] Display window disabled! RasMol> load '/bmm/data/pdb/pdb1opc.ent' Program received signal SIGSEGV, Segmentation fault. 0x40030d28 in XChangeProperty () from /usr/X11R6/lib/libX11.so.6 (gdb) where #0 0x40030d28 in XChangeProperty () from /usr/X11R6/lib/libX11.so.6 #1 0x40049c49 in XStoreName () from /usr/X11R6/lib/libX11.so.6 #2 0x804eeef in SetCanvasTitle (ptr=0xbffff6ac "1OPC X-RAY DIFFRACTION") at x11win.c:1927 #3 0x8063be6 in ReviseTitle () at molecule.c:183 #4 0x8053932 in ProcessFile (format=1, info=1, fp=0x80c3430) at command.c:496 #5 0x8053c71 in FetchFile (format=1, info=1, name=0x80abdb9 "") at command.c:666 #6 0x80556dd in ExecuteLoadCommand () at command.c:1687 #7 0x8057c15 in ExecuteCommand () at command.c:2910 #8 0x804b4b8 in ProcessCommand () at rasmol.c:1109 #9 0x804bf4a in main (argc=2, argv=0xbffff844) at rasmol.c:1473 (gdb) in command.c line 496 change ReviseTitle() to if ( Interactive ) ReviseTitle(); to fix the bug. thanks for RasMol developement and maintenance, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534 email : a.mueller@icrf.icnet.uk | http://www.bmm.icnet.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: PE 1.48b? What about RasMol 2.7! Date: Wed, 16 Aug 2000 11:31:58 -0400 To: rasmol@lists.umass.edu At 08/10/2000, Herbert Bernstein wrote: >In his recent message, Eric Martz said: > >" ...The website for RasMol 2.7 is aimed at experienced users, >emphasizing RasMol's newest features and source code." > >Eric Martz is mistaken. The RasMol 2.7 web site is intended for >users at all levels who wish to have the latest release of RasMol. Of course beginners can download RasMol binaries from Herb's site. My point is that the 2.7 site offers no help to get a beginner started. The vast majority of people who come to my site are beginners or occasional users. Herb added: >I would be happy to hear suggestions for improvements to make the >site more accessible to all users and accept contributions of >materials which are available for release as part of an open >source site. >I will be happy to consider adding links to documents and sites >which are relevant to the current release and which don't >create confusion about the open source status of the 2.7 release. >Better, if you have an appropriate and useful RasMol-related >document you are willing to have included directly on the site >under our open-source release conditions, I will be happy to >consider it for inclusion and to handle the necessary updates as >the program evolves. A good start would be to put at least this single link on the RasMol 2.7 site: "Help for beginners is available at the Martz RasMol Site." Better would be explicitly to list the titles of the most important help documents, including links to: -RasMol Quick-Start -What can you learn about a protein/DNA molecule with RasMol? -Where to find over 1,000 micromolecules and several thousand macromolecules on the web. -Gallery of RasMol images, including some by Roger Sayle. -Frequently asked questions (FAQ) for RasMol, many by Roger Sayle. -Select Commands in RasMol -- a Comprehensive Overview. -Tutorials on How to Use RasMol, e.g. by Andrew Coulson, the crystallographer mentor of Roger Sayle. -How RasMol places covalent bonds, the van der Waals radii it uses, hiding and showing arbitrary bonds. -History of molecular visualization, including RasMol. -Author Roger Sayle's personal story of RasMol. -How To Make Your Own Educational BioMolecular Structure Presentaions with RasMol. -The RasMol EMail List. -RasMol Bibliography. -The RasMol Reference Manual in Spanish, and other NonEnglish RasMol resources." (Herb, I'll be happy to provide you with the html including all the above-mentioned links which you can revise as you see fit.) Among the documents above, perhaps only the guide to Select Commands and the Spanish translation of the RasMol Reference Manual need revision to reflect enhancements in RasMol 2.7. Herb Bernstein or any other volunteer hereby has my permission to adapt this, or any other documents I've authored and made available at the RasMol Home Page, to reflect changes in RasMol 2.7, and place the adapted version on the RasMol 2.7 site, provided my coauthorship is recognized (where appropriate), and a link to my site is included. All software and documentation I've developed are freely available and all software is open source. Herb, if you find anything in any of the above documents that you think might create confusion about the open-source status of the 2.7 release, you are free to revise the document and place the revised version on your site subject to the above-stated provisions. (At the one place on my site where I have a link to the RasMol 2.7 site, an explicit notice that the status of 2.7 is different from that of 2.6, with a link to http://www.bernstein-plus-sons.com/software/rasmol/, has been there since the link was installed over a year ago.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Mozilla (open-source Netscape) vs. Chime? Date: Wed, 16 Aug 2000 12:32:18 -0400 To: rasmol@lists.umass.edu In February, 1998, Netscape made the source code for its version 5 browser open source (http://home.netscape.com/newsref/pr/newsrelease577.html). There is now an active project to develop it (http://www.mozilla.org). Has anyone tested the current Mozilla browser release (Milestone build 17, http://www.mozilla.org/binaries.html) with Chime? -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 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: Alan Wolfson Subject: RE: Mozilla (open-source Netscape) vs. Chime? Date: Wed, 16 Aug 2000 15:35:45 -0400 To: "'rasmol@lists.umass.edu'" Cc: "'emartz@microbio.umass.edu'" Eric, I downloaded the second preview release of Netscape 6 the other day and have just now put the Chime .dll into the plugin directory. All I did was to copy npchime.dll from my Netscape 4.74 plugin directory to the plugin directory for Netscape 6. It seems to do the basic things you would expect of Chime, but I have not exhaustively tested it. Please note that this is a personal post, and does not reflect official MDL support for the unreleased Netscape 6 browser. Alan Alan Wolfson Senior Consultant MDL Information Systems alanw@mdli.com -----Original Message----- Sent: Wednesday, August 16, 2000 12:32 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Mozilla (open-source Netscape) vs. Chime? To: rasmol@lists.umass.edu In February, 1998, Netscape made the source code for its version 5 browser open source (http://home.netscape.com/newsref/pr/newsrelease577.html). There is now an active project to develop it (http://www.mozilla.org). Has anyone tested the current Mozilla browser release (Milestone build 17, http://www.mozilla.org/binaries.html) with Chime? -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 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: "Herbert J. Bernstein" Subject: Re: PE 1.48b? What about RasMol 2.7! Date: Wed, 16 Aug 2000 21:23:07 -0400 (EDT) To: rasmol@lists.umass.edu Eric Martz is to be congratulated on his public-spirited contribution of so much useful material on RasMol to the common good. I will start including links and material (updated for 2.7 series) in my next release. If Eric is agreeable, I will provide the major documents not only as web pages but also as rtf and pdf documents. This should be helpful to those making course handouts and those who wish to have printed reference copies. We'll keep you posted on the progress of this effort. Our thanks again to Eric Martz. -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Wed, 16 Aug 2000, Eric Martz wrote: .... > (Herb, I'll be happy to provide you with the html including all the > above-mentioned links which you can revise as you see fit.) > > Among the documents above, perhaps only the guide to Select Commands and > the Spanish translation of the RasMol Reference Manual need revision to > reflect enhancements in RasMol 2.7. > > Herb Bernstein or any other volunteer hereby has my permission to adapt > this, or any other documents I've authored and made available at the RasMol > Home Page, to reflect changes in RasMol 2.7, and place the adapted version > on the RasMol 2.7 site, provided my coauthorship is recognized (where > appropriate), and a link to my site is included. > > All software and documentation I've developed are freely available and all > software is open source. Herb, if you find anything in any of the above > documents that you think might create confusion about the open-source > status of the 2.7 release, you are free to revise the document and place > the revised version on your site subject to the above-stated provisions. .... ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Movie of knot in 1yve Date: Sat, 26 Aug 2000 17:37:01 -0400 To: pdb-l@rcsb.org, rasmol@lists.umass.edu, edmolvis@lists.umass.edu In the Aug 24 issue of Nature, William R. Taylor describes an algorithm for detecting knots. He found a knot more complex than those previously recognized, and deeply embedded (far from the ends), in 1yve. Dr. Taylor has kindly provided me with his data files, and I have made a movie in Chime of the shrinking process, starting with the knot-containing domain and ending with a smoothed backbone displaying the irreducible knot. There is also a control movie for an unknotted protein. This process is analogous to grasping the ends of the backbone and pulling it out straight to determine whether or not is is knotted. The reference to Taylor's paper, and convenience links to RCSB's Structure Explorer page for each PDB file, and to Protein Explorer etc. are at the site. Go to http://www.umass.edu/microbio/chime and click on "Knots in Proteins". To see the movies, you'll need to be using Windows or Macintosh with Netscape Communicator, and have Chime 2 installed. Links for downloading these required components are at the site. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 12.79.21.234 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Testers for RasMol 2.7.2 Date: Wed, 30 Aug 2000 10:17:54 -0400 To: rasmol@lists.umass.edu Many of you have asked when the UCB mods will be incorporated into the RasMol 2.7 series. Thanks to the generous cooperation of Eileen Lewis and Marco Molinaro at Berkeley, we have had access to source from UCB Enhanced RasMol since July. We need help from adventurous volunteers who would be willing to experiment and test version 2.7.2 of RasMol which is beginning to incorporate a version of the UCB code. If you can help us, please take a look at: http://www.bernstein-plus-sons.com/software/RasMol_2.7.2 You should find source code, documentation and compiled binaries for Windows, Mac, and i386 Mandrake Linux. As always, contributions of additional compiled binaries would be appreciated, but at this point the most important thing is a critical eye for the functionality and correctness of the code. Please send your comments, suggestions and criticisms to: rasmol@bernstein-plus-sons.com My apologies to those who have provided fixes for problems in 2.7.1 who find their code is not yet incorporated. The UCB mods required extensive changes, and each pending mod has to be reviewed and reintegrated. If you find a problem you reported against 2.7.1 you are welcome to tell us again, but you need not do so. Again, our apologies. If you decide to help, you won't find the familiar UCB toolbar in this version. We hope to incorporate a toolbar in a future release, but for now you will have to use the command line and the new "Settings" menu for access to the new features. You may load multiple molecules. You may pick bonds and rotate around them. There are some problems with color assignments and we're working on that issue. Please use this version with great caution. It is _not_ ready for production use. We would appreciate whatever testing people can do in the near future, and would hope to be able to incorporate their comments into creation of a stable production release near the end of the year. Our thanks again to the fine folks in the MultiChem Facility at UCB for this very useful contribution to RasMol. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Leif Johansen Subject: Rasmol 2.7 for Windows Date: Wed, 30 Aug 2000 20:11:56 +0200 To: rasmol@lists.umass.edu Dear members ! Please help an amateur. I have used 2.6 often and I would like to try 2.7. I have downloaded RASWIN.EXE and the two helpfiles, but when I tried to run/open the exe file I got the answer " This program can not be run in DOS mode " and the program realy tried to open the DOS box in my WIN 95. But I have not asked for DOS mode. I used Netscape 4.7. With greetings from Denmark Leif Johansen Teachers College Haderslev ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <39AD4E6B.FD736B66@udd.haderslevsem.dk> ++++------+------+------+------+------+------+------+------+------+------+ From: Leif Johansen Subject: Re: Rasmol 2.7 for Windows Date: Wed, 30 Aug 2000 20:27:41 +0200 To: rasmol@lists.umass.edu Dear members again ! I found the solution - use Explore. ( I don't like it, but ... ). Netscape tried to make a text file for direct reading, in this way the files were smashed. Leif Johansen again Leif Johansen wrote: > Dear members ! > > Please help an amateur. I have used 2.6 often and I would like to try > 2.7. I have downloaded RASWIN.EXE and the two helpfiles, but when I > tried to run/open the exe file I got the answer " This program can not > be run in DOS mode " and the program realy tried to open the DOS box in > my WIN 95. But I have not asked for DOS mode. I used Netscape 4.7. > > With greetings from Denmark > > Leif Johansen > Teachers College Haderslev > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Herbert J. Bernstein" Subject: Re: Rasmol 2.7 for Windows Date: Wed, 30 Aug 2000 14:35:36 -0400 (EDT) To: rasmol@lists.umass.edu The problem raised is a common one -- Internet Explorer tries to download the file as ASCII, not binary. The cure on most windows systems is to hold down the shift key while clicking on the download link. However, some systems are so stubborn about assigning the wrong file type, you have to download the gzipped file with ftp and then unzip it on the target system. -- HJB ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Wed, 30 Aug 2000, Leif Johansen wrote: > Dear members ! > > Please help an amateur. I have used 2.6 often and I would like to try > 2.7. I have downloaded RASWIN.EXE and the two helpfiles, but when I > tried to run/open the exe file I got the answer " This program can not > be run in DOS mode " and the program realy tried to open the DOS box in > my WIN 95. But I have not asked for DOS mode. I used Netscape 4.7. > > With greetings from Denmark > > Leif Johansen > Teachers College Haderslev > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: select problem Date: Wed, 30 Aug 2000 15:01:04 -0400 To: rasmol@lists.umass.edu Michael Dooley says: Hmmm, I am having problems with this type of expression with select select 167-182:a.ca ^ syntax error in expression! I've checked in: http://www.umass.edu/microbio/rasmol/seleccmd.htm#serial and this syntax seens to be correct. It certainly works with something like select :a.ca or select phe176:a.ca, etc but hten that's not what I want. I'm using Rasmol 2.6 on a mac. Is there a workaround to this command? Cheers Michael ------------------------------ Reply from Eric Martz: I also cannot get syntax such as 5-10:a.ca to work. Hmmm, maybe that part of seleccmd.htm is incorrect (in which case mea culpa). Workaround: select 167-182 and :a.ca or select 167-182 and :a and *.ca ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Windows under linux Date: Wed, 06 Sep 2000 10:43:37 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Cc: sturaga@student.umass.edu, tkramer@hampshire.edu, joshuap@sdsc.edu With a view towards enabling linux users to run Protein Explorer, I'd like to know whether anyone has experience with a Windows under linux system, including http://www.vmware.com VMware http://www.trelos.com Win4Lin or WINE (I don't know its website) particulary regarding the performance of Netscape, Chime, and Protein Explorer. I don't know of any packages to run Windows under other unix flavors but I'd be interested in finding out. I do know about http://www.citrix.com Citrix Metaframe. It puts a WinNT session (from a remote WinNT server) in a window on any OS. It is expensive and tricky to install, but performs very well (e.g. you can rotate a molecule effectively with the mouse in Protein Explorer on e.g. SGI/Irix). It is good solution for institutions with good support staff. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <0G0G00J8VYUXZW@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ignacio Valdes Subject: Re: Windows under linux Date: Wed, 06 Sep 2000 09:44:46 -0500 To: rasmol@lists.umass.edu Read my recent review of Win4Lin and the others at http://www.linuxmednews.com a site exclusively devoted to news about open source software in medicine. The review can be found at: http://www.linuxmednews.com/linuxmednews/967526746/index_html Thanks, -- IV Eric Martz wrote: > > With a view towards enabling linux users to run Protein Explorer, I'd like > to know whether anyone has experience with a Windows under linux system, > including > > http://www.vmware.com VMware > > http://www.trelos.com Win4Lin > > or WINE (I don't know its website) > > particulary regarding the performance of Netscape, Chime, and Protein > Explorer. > > I don't know of any packages to run Windows under other unix flavors but > I'd be interested in finding out. > > I do know about http://www.citrix.com Citrix Metaframe. It puts a WinNT > session (from a remote WinNT server) in a window on any OS. It is expensive > and tricky to install, but performs very well (e.g. you can rotate a > molecule effectively with the mouse in Protein Explorer on e.g. SGI/Irix). > It is good solution for institutions with good support staff. > > Thanks, -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: www.umass.edu/microbio/chime/explorer > World Index of Chime Resources: http://molvis.sdsc.edu/visres > PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > 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-- 2000 at 09:44:46AM -0500 Content-disposition: inline User-Agent: Mutt/1.2.5i References: <0G0G00J8VYUXZW@supai.oit.umass.edu> <39B6585E.40A0C673@csi.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Bianciotto Subject: Re: Windows under linux Date: Thu, 07 Sep 2000 13:54:51 +0200 To: rasmol@lists.umass.edu See too the discussion on slashdot (http://slashdot.org/article.pl?sid=00/09/06/0123216&mode=thread ) about this review for more and more advices. Marco Je cite Ignacio Valdes, le Wed, Sep 06, 2000 at 09:44:46AM -0500 : -) Read my recent review of Win4Lin and the others at http://www.linuxmednews.com -) a site exclusively devoted to news about open source software in medicine. -) -) The review can be found at: -) http://www.linuxmednews.com/linuxmednews/967526746/index_html -) -) Thanks, -) -) -- IV -) -) Eric Martz wrote: -) -) > -) > With a view towards enabling linux users to run Protein Explorer, I'd like -) > to know whether anyone has experience with a Windows under linux system, -) > including -) > -) > http://www.vmware.com VMware -) > -) > http://www.trelos.com Win4Lin -) > -) > or WINE (I don't know its website) -) > -) > particulary regarding the performance of Netscape, Chime, and Protein -) > Explorer. -) > -) > I don't know of any packages to run Windows under other unix flavors but -) > I'd be interested in finding out. -) > -) > I do know about http://www.citrix.com Citrix Metaframe. It puts a WinNT -) > session (from a remote WinNT server) in a window on any OS. It is expensive -) > and tricky to install, but performs very well (e.g. you can rotate a -) > molecule effectively with the mouse in Protein Explorer on e.g. SGI/Irix). -) > It is good solution for institutions with good support staff. -) > -) > Thanks, -Eric -) > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - -) > The Protein Explorer: www.umass.edu/microbio/chime/explorer -) > World Index of Chime Resources: http://molvis.sdsc.edu/visres -) > PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm -) > -) > Eric Martz, Professor (Immunology), Dept Microbiology -) > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 -) > www.umass.edu/molvis/martz -) > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ -) > -) --- dixit --- -- Marc Bianciotto Université Paul Sabatier L.S.P.C.M.I.B. /L.P.Q.(I.R.S.A.M.C) 118, route de Narbonne 31062 Toulouse 05.61.55.62.97 biancio@irsamc1.ups-tlse.fr ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Mojgan Rostaie Gerylow Subject: Not working Commands! Date: Mon, 11 Sep 2000 19:36:39 +0200 (MET DST) To: rasmol@lists.umass.edu Dear List Subscribers, I'm new to this discussion group but I'm sure you all can help an amateur! I've installed Rasmol 2.6 on our computers ( Win NT) but few commands (such as copy, paste etc..... ) are not working. Could it be an installing problem ( or it's probably my mistake in the operation?!) Thanks a lot for your help, With greetings from Kiel/Germany Mojgan R. Gerylow ============================================== Mojgan Rostaie Gerylow Department of Pharmaceutical Chemistry University of Kiel Gutenbergstr. 76 24118 Kiel / Germany Tel: (49) 431-880-1425 Fax: (49) 431-880-1352 ============================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- sbrewer@bio.umass.edu, tkramer@hampshire.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime and Protein Explorer under linux Date: Wed, 13 Sep 2000 22:10:17 -0400 To: rasmol@lists.umass.edu Cc: sturaga@student.umass.edu, bourne@sdsc.edu, net@bio.umass.edu, Today Srinivas Turaga and I tested Protein Explorer in Win98 running with Win4Lin (www.trelos.com) under linux on a PC. Win4Lin installed easily following their instructions. We then installed Win98 with Win4Lin. There is no significant speed degradation in performance of Protein Explorer in this mode vs. native Win98. Win98 boots in under 15 sec under linux vs. 1.5 min in native mode on the same hardware. It is possible to backup the Win98 system as a single tar.gz file, and restore it to a linux/Win4Lin system because Win98 exists as a linux file tree in this mode. When the molecule is rotated rapidly with the mouse, there are slight screen update delays that cause the molecule to become disconnected into multiple segments with different degrees of rotation. With the slower rotations one would normally use, these are quite tolerable. A similar phenomenon is seen when running Chime under WinNT via Citrix Metaframe to a window at a remote workstation, such as SGI; also tolerable. Phil Bourne reports that Protein Explorer also works under linux in Windows with VMware (www.vmware.com). VMware costs $300; Win4Lin currently costs $35 (and will go to $50 in future). Both have free trials. In both cases, you need a windows license to install Windows under linux. So the Win4Lin solution to make Chime accessible for linux users seems workable and reasonably affordable. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0G0U00B57TB1F2@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Chime and Protein Explorer under linux Date: Thu, 14 Sep 2000 03:38:59 -0700 (PDT) To: rasmol@lists.umass.edu Eric Martz writes: > So the Win4Lin solution to make Chime accessible for linux users seems > workable and reasonably affordable. Thank you for your concern, but this is not really viable (I almost never reboot my machine, and only if this means losing a lot of state). Only crossplatform software (which is not that difficult nowadays, see VMD, gOpenMol) will manage to insert itself into multiple niches. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: es ++++------+------+------+------+------+------+------+------+------+------+ From: agc Subject: water/other pdbs Date: Fri, 15 Sep 2000 13:50:37 -0500 To: rasmol@lists.umass.edu where can I find a good gallery of pdb files, among otheres the file for the water, please!!!! molecules for basic biochem teaching, cheers ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <39C26F7D.75B7A135@accefyn.org.co> ++++------+------+------+------+------+------+------+------+------+------+ From: "William F. Coleman" Subject: Re: water/other pdbs Date: Fri, 15 Sep 2000 14:48:18 -0500 To: rasmol@lists.umass.edu rasmol@lists.umass.edu writes: >where can I find a good gallery of pdb files, among otheres the file for >the water, please!!!! molecules for basic biochem teaching, cheers > I am sure that there are many sources of such. I have a moderate sized collection at http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html http://www.wellesley.edu/Chemistry/chem120/aacids.html with other molecules scattered throughout my course pages http://www.wellesley.edu/Chemistry/chem120/12000home.html http://www.wellesley.edu/Chemistry/chem341/341home.html My colleague Paul Reisberg (a biochemist, unlike me) has many molecules in his course pages. These can be reached through our departmental home page http://www.wellesley.edu/Chemistry/chem.html going to Course Web Pages and looking at Paul's courses. Other places to check would be the "Molecule of the Month" pages at the various British Universities: http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm http://www.ch.ic.ac.uk/motm/ http://www.chem.ox.ac.uk/mom/ and places such a Liz Dorland's pages: http://www.mc.maricopa.edu/academic/phy_sci/Chemistry/faculty/dorland/chime.html Flick Coleman Flick Coleman William F. Coleman (a.k.a. Flick Coleman) Professor of Chemistry Wellesley College Wellesley, MA 02481 voice: 781-283-3129 email: wcoleman@wellesley.edu fax: 781-283-3642 web: www.wellesley.edu/Chemistry/colemanw.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: water/other pdbs Date: Fri, 15 Sep 2000 16:01:44 -0400 To: rasmol@lists.umass.edu Cc: acad@accefyn.org.co At 09/15/2000, acad@accefyn.org.co wrote: >where can I find a good gallery of pdb files, among otheres the file for >the water, please!!!! molecules for basic biochem teaching, cheers You can find water in many NMR files. In Protein Explorer, click on the QuickStart for Lac Repressor:DNA Complex (1lcd), then click Explore More to get to the QuickViews menus, and SELECT Solvent, DISPLAY Only Or for your convenience, I have put one, two, and five water molecules (hbonded together) at http://www.umass.edu/microbio/chime/pdb/h2o.pdb http://www.umass.edu/microbio/chime/pdb/2h2o.pdb http://www.umass.edu/microbio/chime/pdb/5h2o.pdb Or to bring these up directly in Protein Explorer http://www.umass.edu/microbio/chime/explorer/pe.htm?id=../pdb/5h2o.pdb& A nice display is obtained in either PE or RasMol with DISPLAY menu, Ball+Stick (type command) dots 500 ATP, Hemoglobin, Gal4 protein bound to DNA (nice double helix), and Gramicidin in a lipid bilayer are packaged up at http://www.umass.edu/microbio/rasmol/distrib/fourmols.exe Many sources of molecules, including small (micro) molecules, are listed at the Molecular Visualization Freeware site http://www.umass.edu/microbio/rasmol/ click on Molecules A gallery of snapshots is at http://www.umass.edu/microbio/rasmol/gallery.htm Some of these images are linked to the PDB files. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0G0U00B57TB1F2@ponzi.oit.umass.edu> <0G0U00B57TB1F2@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime and Protein Explorer under linux Date: Fri, 15 Sep 2000 16:12:15 -0400 To: rasmol@lists.umass.edu At 09/14/2000, Eugene Leitl wrote: >Eric Martz writes: > > > So the Win4Lin solution to make Chime accessible for linux users seems > > workable and reasonably affordable. > >Thank you for your concern, but this is not really viable (I almost >never reboot my machine, and only if this means losing a lot of >state). Only crossplatform software (which is not that difficult >nowadays, see VMD, gOpenMol) will manage to insert itself into >multiple niches. My linux guru Srinivas Turaga informs me that it is necessary to reboot linux ONCE during installation of Win4Lin because Win4Lin requires a kernel provided by TreLOS (www.trelos.com). Only a single reboot is needed. After that, booting Windows98 as a subprocess under Win4Lin, or shutting down Windows, leaves linux intact. So you have to decide whether being able to use Protein Explorer is worth the single reboot. I would be interested to hear from linux users who have installed Win4Lin regarding whether Win4Lin has caused any problems for linux. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 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: Gale Rhodes Subject: Re: water/other pdbs Date: Fri, 15 Sep 2000 16:40:42 -0400 To: rasmol@lists.umass.edu Dave Woodcock's site, mentioned in Eric Martz's Micromolecules list, is now up to 2500 small molecules, including our friend water. Seems like I can always find the small molecule I want here: http://www.sci.ouc.bc.ca/chem/molecule/molecule.html Cheers! ***************************** Gale Rhodes Chemistry Department University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Originator-info: login-token=Mulberry:01sy14qSqaqBnFmwAv+q6oBkaN89Y+YfEgoqYO6a0=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: wm0p Subject: Re: water/other pdbs Date: Fri, 15 Sep 2000 17:51:33 -0400 To: rasmol@lists.umass.edu > At 09/15/2000, acad@accefyn.org.co wrote: > where can I find a good gallery of pdb files, among otheres the file for > the water, please!!!! molecules for basic biochem teaching, cheers Yet another water display for a Biochem course: http://www.bio.cmu.edu/courses/03231/LecF00/Lec02/water.html This is a cluster showing H-Bonds and a single H2O with the lone pair electrons highlighted using "fake atoms". -Will McClure ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Herbert J. Bernstein" Subject: OpenRasMol Date: Tue, 19 Sep 2000 16:41:28 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org We are pleased to announce the availability of the OpenRasMol web page at: http://www.OpenRasMol.org This site was established in mid-September 2000 to provide a home for Open Source versions of RasMol. RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in 1992. RasMol is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Science is best served when the tools we use are fully understood by those who wield those tools and by those who make used of results obtained with those tools. When a scientific tool exists as software, access to source code is an important element in achieving full understanding of that tool. As our field evolves and new versions of software are required, access to source allows us to adapt our tools quickly and effectively. There has always been free access to the source of the main line of RasMol development. With the creation of the RasMol 2.7 series of releases starting in 1999, RasMol formally became an open source program. There is some confusion about the meaning of the phrase "open source". In the early days of software development, most scientific software source code was freely and openly shared with a minimum of formalities. These days, it appears that carefully drawn legal documents are necessary to protect free access to the source code of scientific software. We are all deeply indebted to Richard Stallman for showing us how a creative combination of copyrights and seemingly restrictive licenses could give us truly unfettered freedom to use programs, to read their source code and to develop new versions. The GNU project and the Linux project have shown that an open source approach works. We do not use the GNU General Public License (the "GPL") for OpenRasMol, but the OpenRasMol conditions for use have correctly been called "GPL-like". You can find a complete explanation of the OpenRasMol conditions in the page on the Copying and Distribution web page http://www.OpenRasMol.org/Copyright.html. If you are a user of OpenRasMol programs, you will find that the copyrights and notices ask little more of you than that you avoid mistakes by others by keeping the notices with copies, display scientific integrity by citing your sources properly and treating this like other shared scientific developments by not inferring a warranty. If you are a software developer and wish to incorporate what you find here into new code, or to pick up bits and pieces and used them in another context, the situation becomes more complex. Read the copyrights and notices carefully. You will find that they are "infectious". Whatever you make from our Open Source code must itself be offered as Open Source code. In addition, in order to allow users to understand what has changed and to ensure orderly development you have to describe your changes. There is a lot still to be done before this site is fully functional. Many links and features need to be added. With your help, with your comments, suggestions and corrections, and with contributions of new Open Source RasMol code and documentation, hopefully this site will evolve into an increasingly useful tool for the community. Please direct your comments and suggestions to: webmaster@OpenRasMol.org -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Welcome to OpenRasMol Date: Tue, 19 Sep 2000 21:11:29 -0400 To: rasmol@lists.umass.edu I would like to thank Herb Bernstein for setting up the OpenRasMol Home Page. Those of you who have visited my Molecular Visualization Freeware website (formerly the "RasMol Home Page") since August 28 have noticed that it now features Protein Explorer. RasMol and all the old RasMol Home Page documents, files, and resources also remain available and will remain available indefinitely. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 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: valadon@ix.netcom.com Subject: RasTop Date: Wed, 20 Sep 2000 01:26:13 -0400 (EDT) To: rasmol@lists.umass.edu Hello everybody, This is to announce the release of RasTop 1.3, an interactive interface to RasMol adapted for Windows 95, Windows 98, and Windows NT platforms. RasTop combines the drawing capabilities and the speed of RasMol with a powerful interface using menus, dialogs, and command panel. The interface allows multiple windows to be opened at the same time. Care has been given to allow rapid and complex atom selections to be performed directly on screen and the possibility to save and restore a work session. RasTop 1.3 derives from RasMol 2.7.1, and like RasMol 2.7.1 it is open source. Many thanks to Roger Sayle, Anne Muller, and Herbert J. Bernstein for giving RasMol freely to the community. Special thanks to Herbert Bernstein whose help was particularly crucial to achieve this release. You can obtain a preliminary package including binary, complete source code, and user documentation on Herbert Bernstein's site at the following address: http://www.bernstein-plus-sons.com/software/rastop Your input, suggestions, comments, and corrections are very welcome. You can send them directly to me (valadon@ix.netcom.com). More general comments or comments relevant to RasMol as open source are also welcome by Herbert Bernstein (rasmol@bernstein-plus-sons.com) or directly to the RasMol list. As is customary, we must say that this is a preliminary release with a lot of new code; caution is required! Thanks, Philippe ---------------------------------------- Philippe Valadon, M.D.-Ph.D. P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: 3D Flash format? Date: Mon, 25 Sep 2000 19:40:09 -0400 To: rasmol@lists.umass.edu [Forwarded at Susana Halpine's request] >I assume that Rasmol, Chime and Protein Explorer are all based on raster >display of the images. Is this still true? > >Is there anyone out there exploring the integration of vector-based >technology, such as 3D Flash-format, with Molecular Visualization? The >small file size, scalability, and the interactivity of the .fla format >make it an ideal partner. > >I'd love to hear back from anyone investigating this approach (I >apologize if I've missed prior discussion on this topic). > >Best regards, > >Susana (Flash-Nut) Halpine > >Susana Maria Halpine >Artist-Biochemist > Playa del Rey, CA >shalpine@earthlink.net >http://home.earthlink.net/~shalpine/vita.htm > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0G1G00C3QU9WB3@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paz Padilla Subject: unsubscribe Date: Tue, 26 Sep 2000 13:10:40 +0200 To: rasmol@lists.umass.edu Eric Martz skrev: > [Forwarded at Susana Halpine's request] > > >I assume that Rasmol, Chime and Protein Explorer are all based on raster > >display of the images. Is this still true? > > > >Is there anyone out there exploring the integration of vector-based > >technology, such as 3D Flash-format, with Molecular Visualization? The > >small file size, scalability, and the interactivity of the .fla format > >make it an ideal partner. > > > >I'd love to hear back from anyone investigating this approach (I > >apologize if I've missed prior discussion on this topic). > > > >Best regards, > > > >Susana (Flash-Nut) Halpine > > > >Susana Maria Halpine > >Artist-Biochemist > > Playa del Rey, CA > >shalpine@earthlink.net > >http://home.earthlink.net/~shalpine/vita.htm > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: IBM Employee Subject: unsubscribe Date: Tue, 26 Sep 2000 16:01:40 -0700 To: rasmol@lists.umass.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: unsubscribe Date: Tue, 26 Sep 2000 21:28:40 -0400 To: rasmol@lists.umass.edu Please do not send subscription/removal requests to the list in general; I doubt they will be processed correctly. >From http://www.umass.edu/microbio/rasmol/listsub.htm#unsubscribing " Unsubscribing To unsubscribe, from the address you wish to unsubscribe send to listproc@lists.umass.edu this message: unsubscribe rasmol " -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet Waltham, MA USA driscoll@molvisions.com http://www.molvisions.com voice 781 899 3873 fax 781 899 4108 > From: IBM Employee > Reply-To: rasmol@lists.umass.edu > Date: Tue, 26 Sep 2000 16:01:40 -0700 > To: rasmol@lists.umass.edu > Subject: unsubscribe > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- (by way of Eric Martz ) ++++------+------+------+------+------+------+------+------+------+------+ From: David Crout Subject: Heatley Medal Symposium Date: Wed, 27 Sep 2000 15:53:55 -0400 To: rasmol@lists.umass.edu Dear Eric, There is now a web site for the Symposium at which Roger Sayle will be presented with the Heatley Medal of the Biochemical Society. I would be most grateful if you would circulate this to subscribers of the Rasmol e-mail list. http://www.warwick.ac.uk/fac/sci/Chemistry/conferences/Heatley/Heatley.html Kind regards David Crout -- Professor D.H.G. Crout Department of Chemistry University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 76523961 FAX: +44 (0)24 76524429 e-mail: msrky@csv.warwick.ac.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Post Doctoral Position Available in Toronto Date: Thu, 28 Sep 2000 10:26:33 -0400 To: rasmol@lists.umass.edu Cc: suresh@ems.ncl.res.in, howell@sickkids.on.ca POSTDOCTORAL FELLOWSHIP AVAILABLE IN TORONTO, ONTARIO A postdoctoral position in Protein Crystallography is available at the Hospital for Sick Children/University of Toronto. Knowledge of crystallographic techniques including data processing, phase determination and improvement, model building, and protein structure refinement is preferable but candidates having strong skills in molecular biology and protein biochemistry, with an interest in learning techniques for structural biology will also be considered. A recent Ph.D. in chemistry, biochemistry, biophysics, or a closely related field is required. Current goals of the laboratory include the elucidation of catalytic mechanisms and structure-based drug design. Projects include enzymes involved in the N-glycan biosynthesis, methylation and methionine recycling and the arginine-citrulline cycle. For more information about ongoing projects please go to our web site: http://www.sickkids.on.ca/structuralbiology/default.asp. The position is available December 1 2000 for a minimum of at least two years and renewable for at least an additional year. Applications will be accepted until the position is filled and the salary will be commensurate with qualifications and experience. Candidates should forward a cover letter with curriculum vita and contact information for three references to Dr. P. Lynne Howell, Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, M5G 1X8 (Phone: 416-813-5378, Fax: 416-813-5022) or via Email to: howell@sickkids.on.ca -- P. Lynne Howell *************************************************** Senior Scientist (HSC) and Assoc. Prof. (University of Toronto) Structural Biology and Biochemistry Hospital for Sick Children, 555 University Avenue, Toronto, M5G 1X8, CANADA Phone: 416-813-5378 Fax: 416-813-5022 Email: howell@sickkids.on.ca ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-Outlook-Express-Macintosh-Edition/5.02.2022 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id e8U1YxN29015 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Standardized Color Schemes at DRuMS Web Site Date: Fri, 29 Sep 2000 21:39:41 -0400 To: RasMol List Greetings! This message is to announce the release of DRuMS, a set of standardized color schemes for macromolecules. DRuMS is now available for preview in an interactive Chime-based Web site (http://www.umass.edu/molvis/drums), and offered free for adoption in other Web sites. * * * * * * * * * * * * * * * THE WEB SITE DRuMS is a set of seven intuitive color schemes applicable to macromolecular structures and specifically designed for use on the Web. The DRuMS Web site (http://www.umass.edu/molvis/drums) uses Chemscape Chime to display macromolecular structures in 3D. Interactive control panels allow you to preview DRuMS applied to different molecules, including the ability to: € Choose from among a number of sample molecules to display. € Select subsets of atoms (protein, solvent, ligand, and more). € Apply any of the DRuMS color schemes to the selection. € Interact with the molecule-change the view, rotation, zoom, and more. € Obtain DRuMS (html code and Chime scripts) FREE for your own use. [Access to the DRuMS Web site requires Win 95/98/2000/NT or Mac OS, and Netscape Communicator 4.5 or higher with Chime 2.x installed. Both Communicator and Chime are FREE and can be downloaded from the DRuMS Web site home page.] * * * * * * * * * * * * * * * AVAILABILITY FOR DOWNLOAD AND USE DRuMS is also available from the Web site as a downloadable package (for Mac and Win platforms). This package contain all of the files needed to integrate the color schemes into your own resources, including Chime scripts, Cascading Style Sheets, hex and rgb values, and detailed instructions with example code. THESE FILES ARE OFFERED TO NONCOMMERCIAL AND COMMERCIAL USERS ALIKE WITH NO RESTRICTIONS ON THEIR USE OR MODIFICATION. You are invited and encouraged to use or adapt DRuMS for your own online resources. * * * * * * * * * * * * * * * CONTRIBUTORS AND ADOPTIONS The color schemes were developed by Timothy Driscoll (MolVisions; http://www.molvisions.com), Frieda Reichsman (Molecules in Motion; http://www.moleculesinmotion.com), and Eric Martz (UMass Amherst; http://www.umass.edu/molvis/martz). They are based loosely on several RasMol color schemes devised by Roger Sayle. The DRuMS Color Schemes have been adopted for use already in: € (http://www.umass.edu/microbio/chime/explorer) Protein Explorer; € (http://www.worthpublishers.com/lehninger3d) Biochemistry in 3D, a set of online 3D structure tutorials that accompany Lehninger Principles of Biochemistry, Third Edition. * * * * * * * * * * * * * * * HELP AND MORE INFORMATION If you have suggestions for improving DRuMS, or questions regarding its use, please contact Timothy Driscoll at driscoll@molvisions.com. Please also let us know if you have found the DRuMS color schemes useful. Thank you! -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet Waltham, MA USA driscoll@molvisions.com http://www.molvisions.com voice 781 899 3873 fax 781 899 4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Downloading DRuMS Date: Sat, 30 Sep 2000 13:49:23 -0400 To: Robert Lynch , RasMol List Thanks to Bob Lynch for catching a Mac user's mistake; the DRuMS package for Windows is now available as an .exe file, which should decompress automatically. Please email if there are any other problems. Thanks! Tim -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet Waltham, MA USA driscoll@molvisions.com http://www.molvisions.com voice 781 899 3873 fax 781 899 4108 > From: "Robert Lynch" > Date: Sat, 30 Sep 2000 11:20:08 -0400 > To: > > Timothy, > > I have not succeeded in downloading DRuMS from the web-site. When I click > on "download DRuMS" a box opens showing me a bunch of machine language, + a > few words, among them "stuffit". I have downloaded the Aladdin software, > but that doesn't seem to help. (I am on a relatively new PC (800Mhz AMD > processor, lots of memory etc. running windows 98). I have Chime, PE etc > installed > > Any suggestions? > > Bob Lynch > Professor & Chair > Department of Biological Sciences > University of Massachusetts Lowell > One University Avenue > Lowell, MA 01854 > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- RasMol List User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id e8UJY6N04637 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Standardized Color Schemes at DRuMS Web Site Date: Sat, 30 Sep 2000 15:38:45 -0400 To: Philippe Valadon , Hi Philippe, You raise a good point; the DRuMS site is not useful to IE users at the moment because of Chime (and javascript), and that's not really fair. If you want the files themselves, you can download them from the DRuMS home page directly and bypass the preview. However, the current packages do not work with RasMol because they use hex codes for the color definitions (RasMol uses RGB). I will add RasMol-friendly packages to the site as soon as possible. As far as "generic" previews that work on all browsers, I am working on a number of still images showing the DRuMS color schemes in action; I will post the URL to the RasMol list once they are complete. Thanks for the input, Tim -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet Waltham, MA USA driscoll@molvisions.com http://www.molvisions.com voice 781 899 3873 fax 781 899 4108 > From: "Philippe Valadon" > Organization: Personal > Date: Fri, 29 Sep 2000 16:17:00 -0700 > To: > Subject: Re: Standardized Color Schemes at DRuMS Web Site > > Hi Timothy, > > This looks like an interesting idea. I'd love to have a look on the result > and see the files. It would be nice to offer some previews without chime > and info on a web compatible with internet explorer. My Netscape scratched > on opening the link preview in the url you gave. > > Look forward to see the work. > Regards, > Philippe > > ------------------------------------------------------------ > *** RasTop *** > ------------------------------------------------------------ > Philippe Valadon > P.O. Box 13014, La Jolla, CA 92039, USA. > valadon@ix.netcom.com > > > ----- Original Message ----- > From: "Timothy Driscoll" > To: "RasMol List" > Sent: Friday, September 29, 2000 6:39 PM > Subject: Standardized Color Schemes at DRuMS Web Site > > > Greetings! > > This message is to announce the release of DRuMS, a set of standardized > color schemes for macromolecules. DRuMS is now available for preview in an > interactive Chime-based Web site (http://www.umass.edu/molvis/drums), and > offered free for adoption in other Web sites. > > > * * * * * * * * * * * * * * * > THE WEB SITE > > DRuMS is a set of seven intuitive color schemes applicable to macromolecular > structures and specifically designed for use on the Web. The DRuMS Web site > (http://www.umass.edu/molvis/drums) uses Chemscape Chime to display > macromolecular structures in 3D. Interactive control panels allow you to > preview DRuMS applied to different molecules, including the ability to: > > € Choose from among a number of sample molecules to display. > € Select subsets of atoms (protein, solvent, ligand, and more). > € Apply any of the DRuMS color schemes to the selection. > € Interact with the molecule-change the view, rotation, zoom, and more. > € Obtain DRuMS (html code and Chime scripts) FREE for your own use. > > [Access to the DRuMS Web site requires Win 95/98/2000/NT or Mac OS, and > Netscape Communicator 4.5 or higher with Chime 2.x installed. Both > Communicator and Chime are FREE and can be downloaded from the DRuMS Web > site home page.] > > > * * * * * * * * * * * * * * * > AVAILABILITY FOR DOWNLOAD AND USE > > DRuMS is also available from the Web site as a downloadable package (for Mac > and Win platforms). This package contain all of the files needed to > integrate the color schemes into your own resources, including Chime > scripts, Cascading Style Sheets, hex and rgb values, and detailed > instructions with example code. THESE FILES ARE OFFERED TO NONCOMMERCIAL > AND COMMERCIAL USERS ALIKE WITH NO RESTRICTIONS ON THEIR USE OR > MODIFICATION. You are invited and encouraged to use or adapt DRuMS for your > own online resources. > > > * * * * * * * * * * * * * * * > CONTRIBUTORS AND ADOPTIONS > > The color schemes were developed by Timothy Driscoll (MolVisions; > http://www.molvisions.com), Frieda Reichsman (Molecules in Motion; > http://www.moleculesinmotion.com), and Eric Martz (UMass Amherst; > http://www.umass.edu/molvis/martz). They are based loosely on several > RasMol color schemes devised by Roger Sayle. > > The DRuMS Color Schemes have been adopted for use already in: > € (http://www.umass.edu/microbio/chime/explorer) Protein Explorer; > € (http://www.worthpublishers.com/lehninger3d) Biochemistry in 3D, a set > of online 3D structure tutorials that accompany Lehninger Principles of > Biochemistry, Third Edition. > > > * * * * * * * * * * * * * * * > HELP AND MORE INFORMATION > > If you have suggestions for improving DRuMS, or questions regarding its use, > please contact Timothy Driscoll at driscoll@molvisions.com. Please also let > us know if you have found the DRuMS color schemes useful. > > Thank you! > > -- > Timothy Driscoll > MolVisions - Molecular Visualization on the Internet > Waltham, MA USA > driscoll@molvisions.com > http://www.molvisions.com > voice 781 899 3873 > fax 781 899 4108 > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Laurence Hall Subject: Can I change the background color from black to white? Date: Mon, 02 Oct 2000 11:05:11 -0700 To: rasmol@lists.umass.edu Hi all, It looks easy on a Unix version, but I am running on Windows NT. Any help would be appreciated. Laurence Laurence K. Hall Developer and Architect (650) 463-3979 ClickAction, Inc. mailto:lhall@clickaction.com www.clickaction.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.7-beta available Date: Fri, 02 Mar 2001 19:01:57 -0500 To: rasmol@lists.umass.edu Cc: rphillis@bio.umass.edu I have upgraded Protein Explorer (PE) to version 1.7-beta at http://www.proteinexplorer.org It has been tested on both Windows and Macintosh. It is downloadable. Since the previous release September 7, 2000, PE's QuickViews menu system has new options to modify the logic of selections and displays. For example, one can select the backbone atoms of a particular chain, then render them both as ball and stick and as a backbone trace, all without entering a single command manually. (It is less cumbersome for these tasks than is Chime's built-in menu, and it offers help including color keys for each action the user takes.) The tutorial has been completely revised to take advantage of the new features since version 1.0. It is not necessary to look at the tutorial in order to use PE; the tutorial offers an overview of PE's capabilities for those interested. It is the basis for a course that I teach (http://www.bio.umass.edu/micro/courses/molvis.html) If you haven't seen Protein Explorer since version 1.0 (the version currently at the Protein Data Bank), it is now enormously easier to use, and has a clickable sequence-to-structure interface, detects and displays cation-pi interactions and salt bridges. It is much easier to use than RasMol, and much more powerful. The new version debuted in June at the ASBMB, and was featured at workshops at Boston University and the Weizmann Institute, Israel, and at Chemistry and the Internet 2000 (Wasington DC, September). PE's ability to color a molecule from a multiple protein sequence alignment (MSA3D) was mentioned in Science's Netwatch, September 1 issue. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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: Juan Alexander Padron Garcia Subject: Under Linux? Date: Tue, 03 Oct 2000 08:47:46 -0400 To: rasmol@lists.umass.edu Dear all: I have tested the protein explorer and I have to congratulate the authors for the high end quality of the program. Nevertheless I would like to know when it will be (or it is already?) aviable (and operational!) for linux user. My distribution is Red Hat 6.2. Best Regards, Juan Alexander Padorn Molecular Modeling Lab Pharmaceutical Chemistry Center La Havana, Cuba ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Jeffrey Atkinson Subject: Re: Accessing Protein Explorer 1.7-beta Date: Tue, 03 Oct 2000 08:53:38 -0400 To: rasmol@lists.umass.edu To all; Since getting the message this morning about PE 1.7 I went to the page and tried to download but have been caught up on the registration page (which happened some time ago when I registered fro CHime resources). It flashes this error message when I try to submit: 'Javascript error: Type "Javascript" into location for details". Can someone offer some advice? Sorry if its trivial. Jeffrey >I have upgraded Protein Explorer (PE) to version 1.7-beta at > >http://www.proteinexplorer.org It has been tested on both Windows and >Macintosh. It is downloadable. -- Dr. Jeffrey Atkinson Associate Professor Department of Chemistry Brock University St. Catharines, Ontario Canada L2S 3A1 jatkin@spartan.ac.BrockU.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ phone: 905 688-5550 ext 3967 fax: 905 682-9020 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: reissner@papa.uncp.edu Subject: Re: Accessing Protein Explorer 1.7-beta Date: Tue, 03 Oct 2000 09:17:22 -0400 To: rasmol@lists.umass.edu > From: MX%"rasmol@lists.umass.edu" 3-OCT-2000 09:02:24.73 > To: MX%"rasmol@lists.umass.edu" > CC: Interestingly (?) or trivially (?) I get the same message when I try to run PE locally. Would appreciate an advice on that, indeed! John > X-Listprocessor-Version: 8.2.09/990901/11:28 -- ListProc(tm) by CREN > this error message when I try to > submit: 'Javascript error: Type "Javascript" into location for reissner@papa.uncp.edu http://www.uncp.edu/home/reissner vox: (910)521-6425 fax: (910)521-6649 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Diana Irwin Subject: Protein Explorer download Date: Tue, 03 Oct 2000 09:57:44 -0400 To: rasmol@lists.umass.edu Dear Eric, I tried to download Protein Explorer and after filling out the registration form I get a message that says "javascript error, type javascript in location" at the bottom. All that did was do a web search for javascript. I have an IMac, OS9. Javascript was enabled. Also I don't see any "comments box". I have tried to download before with no luck. Do you have any suggestions? Thank you. Diana Irwin ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Under Linux? Date: Tue, 03 Oct 2000 11:16:17 -0400 To: rasmol@lists.umass.edu Cc: padrongj@cqf.co.cu Chime is not going to be available for linux. The best solution is: http://www.trelos.com With their inexpensive Win4Lin, you can install Windows under linux, run Netscape and Protein Explorer. We have tested it and it is OK! Installation of Win4Lin requires that you reboot your linux. A more expensive alternative is VMWare (http://www.vmware.com). We have not tested it but others report that it works well with Protein Explorer. At 10/03/2000, you wrote: >Dear all: > >I have tested the protein explorer and I have to congratulate the >authors for the high end quality of the program. Nevertheless I would >like to know when it will be (or it is already?) aviable (and >operational!) for linux user. My distribution is Red Hat 6.2. > >Best Regards, >Juan Alexander Padorn >Molecular Modeling Lab >Pharmaceutical Chemistry Center >La Havana, Cuba /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Help for downloading or installing Protein Explorer Date: Tue, 03 Oct 2000 11:36:53 -0400 To: rasmol@lists.umass.edu 1. Downloading problems: I apologize for the occasional problems with the existing registration and downloading system. We are working very hard at top priority on a new system that will replace it very soon. Meanwhile, about one out of 40 people registering can't get the old system to work, usually because they have not set up their browser to send email. Anyone having difficulty downloading should send me the information requested in the registration form by email. I will reply with instructions for downloading. 2. Installation problems: Despite an average of over 30 downloads/day, I get very few complaints that Protein Explorer doesn't work when downloaded. The most common reason for failure is that the installation instructions were not followed. On Macintoshes, it is occasionally necessary to reinstall Netscape and Chime. This only takes a few minutes so it is a good thing to try. Those who have installed the Chem3D plugin may have a conflict for chemical/x-pdb, also needed by Chime. What usually works easily is simply to reinstall Chime. This does not disable Chem3D, which uses a different MIME type as its major one. If you are having trouble getting a downloaded copy of Protein Explorer to work, I will try to help, but am unable to diagnose the problem unless you give me a VERY DETAILED description of what you did and what happened. This must include: Windows or Macintosh Netscape version (Help, About Communicator) Chime version (Help, About Plugins) Are the chemical/x-pdb and application/x-spt MIME types enabled in the above About Plugins report? Is Chime working at all? http://www.umass.edu/microbio/chime/atp.pdb (should see wireframe of ATP) Can you get molecular images in a simple Chime/javascript site? http://www.umass.edu/microbio/chime/hemoglob Whether or not you rechecked the installation instructions to be sure you followed them exactly. Did you try reinstalling Netscape and Chime? What error message you get, and at what stage in startup of PE. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael H. Patrick" Subject: Re: Protein Explorer download Date: Tue, 03 Oct 2000 09:43:44 -0500 To: rasmol@lists.umass.edu I had the same problem with my G3 Mac powerbook. It was eventually resolved by reinstalling Netscape and Chime. Very frustrating time spent trying to find this out, but Eric and Tim Driscoll were very helpful! Good luck. >Dear Eric, > >I tried to download Protein Explorer and after filling out the registration >form I get a message that says "javascript error, type javascript in >location" at the bottom. All that did was do a web search for javascript. > >I have an IMac, OS9. Javascript was enabled. Also I don't see any >"comments box". I have tried to download before with no luck. Do you >have any suggestions? > >Thank you. > >Diana Irwin > -- Michael H. Patrick, Ph.D. Department of Medical Genetics University of Wisconsin-Madison 104 Genetics 445 Henry Mall Madison, WI. 53706 Ph. (608) 265-4564 Fx. (608) 262-2976 email: mpatrick@facstaff.wisc.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Alignment Diversity Date: Tue, 03 Oct 2000 19:13:32 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_MN6ZqFQhaEH1i/JhkPqx7A) RasMollusks and Chimeleons, This is not an attempt at one-upmanship with Protein Explorer, but instead to let you know other tools that might be of interest to this group. Like Protein Explorer, Swiss-PdbViewer (Deep View) allows coloring of proteins according to alignment diversity. You can do the structural alignment within the program. For proteins of known structure, you load them all and superimpose them to get the best structural alignment. For homologous sequences with unknown structure, you homology model the sequence on known structures to get the best alignment, all within the Deep View program. After alignments are complete, the menu command Color: Alignment Diversity colors residues with the spectrum of colors, blue to red for most conserved to most diverse. I'm attaching a picture (convergent stereo) of four cytochrome c's aligned and colored. Took me only a couple of minutes from starting the program, through alignment, to finished images. (I already had the cytochrome-c PDB files). You can save alignments in a variety of formats as text files. One type is attached. View it in text editor/word processor. Be sure to use a monospaced font like Courier or Monaco to see the residues aligned properly. By the way, I just added a new section to the Swiss-PdbViewer tutorial on producing images for publication. I'll expand it soon to include the basics of making scenes for POV-Ray and rendering them. I hope to add tutorial sections on surfaces, homology modeling, and sequence alignments during the coming months. http://www.usm.maine.edu/~rhodes/SPVTut/index.html Happy modeling. Cheers! ***************************** Gale Rhodes Chemistry Department University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes --Boundary_(ID_MN6ZqFQhaEH1i/JhkPqx7A)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Juan Alexander Padron Garcia Subject: Installing Rasmol under linux Date: Wed, 04 Oct 2000 10:50:18 -0400 To: rasmol@lists.umass.edu Dear all: Sorry for the FAQ, but I am having troubles to compile rasmol. I follow the install instructions, but when I compile I get the following message gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o rasmol.c:46: sys/termio.h: No such file or directory make: *** [rasmol.o] Error 1 I am using a Pentium 166 with RedHat 5.2 and X window. The header of my rasmol.h is: /*===========================*/ /* User Definable Options! */ /*===========================*/ /* #define IBMPC */ /* #define APPLEMAC */ /* #define DIALBOX */ #define TERMIOS /* #define SOCKETS */ #define MITSHM /* #define MMIOLIB */ /* #define OMLCOMMS */ /* #define CEXIOLIB */ /* Use Default Depth! */ /* #define THIRTYTWOBIT */ /* #define EIGHTBIT */ Thanks for your time ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert P. Grosso Jr." Subject: Calling rasmol from Visual Basic Date: Wed, 04 Oct 2000 12:42:54 +0100 To: "rasmol@lists.umass.edu" To any who can help: I have written a program in Visual Basic that calls up rasmol to display molecules and unit cells. I've managed to use script files so that when Visual Basic opens the pdb files, they open as I would like them to. I am having a problem turning it off. When exiting Visual Basic the rasmol window doesn't exit automatically. I have tried using DDE, but the commands aren't recognized by Visual Basic. Does anyone know how to use Visual Basic to close the rasmol window, or, better yet, does anyone know how to use API to communicate with rasmol through Visual Basic? Any help on this subject would be appreciated. Rob Grosso ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.71 (bug fixes) Date: Wed, 04 Oct 2000 17:05:47 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org The recently announced Protein Explorer 1.7 had two bugs that (gasp) made it unable to load PDB files via Internet from the Protein Data Bank. It spuriously complained that Chime 2.0.3 was not installed (when it was). My apologies!! Version 1.71, now at proteinexplorer.org, appears to me to fix these bugs and works properly on both Windows and Macintosh. The downloadable EXE packages have been upgraded to 1.71. If you downloaded 1.7, please follow the instructions at the download site for upgrading to 1.71. Sorry for the bother! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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: sadhna Subject: visual display not detected. Date: Thu, 05 Oct 2000 14:35:46 +0530 (IST) To: "rasmol@lists.umass.edu" hi everyone! I have installed rasmol 2.6 on Redhat Linux(PC) 6.2.(Gnome). It compiled but it didnt give the display. Though Rasmol windows was displayed on Sun machine with Red hat linux ver 5.2. Is version 2.6 of rasmol compatible with the gnome. Your suggestions are welcome. thanks sadhna ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Dr. Don Harden" Subject: Re: visual display not detected. Date: Thu, 05 Oct 2000 10:42:08 -0400 (EDT) To: "rasmol@lists.umass.edu" On Thu, 5 Oct 2000, sadhna wrote: > > hi everyone! > I have installed rasmol 2.6 on Redhat Linux(PC) 6.2.(Gnome). > It compiled but it didnt give the display. Though Rasmol windows was > displayed on Sun machine with Red hat linux ver 5.2. > Is version 2.6 of rasmol compatible with the gnome. > Your suggestions are welcome. > > thanks > sadhna > > > Sadhna, It sounds like an incompatibilty between X and RasMol. The visual (display) depth for both have to be the same (i.e.; 8, 16, 32 bit). When you start RasMol you should see something like RasMol Molecular Renderer Roger Sayle, August 1995 Copyright (C) Roger Sayle 1992-1999 Version 2.7.0.1 April 1999 Copyright (C) Herbert J. Bernstein 1998-1999 *** See "help notice" for further notices *** [32-bit version] ^^^^^ ||||| This needs to match display depth of your X server. One way to determine the visual depth of your xserver is to open an xterm and type xwininfo then click on any window (e.g; the xterm from which you are running xwininfo will do) and look for a line such as Depth: 16 To get RasMol and X at the same depth you can either (1) recopile RasMol to with the default depth of your X server or (2) start X with the depth that matches RasMol. (1) edit rasmol.h in the src directory so that your X server's display depth is explicityln defined. Under "User Definable Options!" change the following section #if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT) /* #define THIRTYTWOBIT */ /* #define SIXTEENBIT */ /* #define EIGHTBIT */ #endif to (assuming you are using a 16 bit display). /* #if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT) /* /* #define THIRTYTWOBIT */ #define SIXTEENBIT /* #define EIGHTBIT */ /* #endif */ and recomplie. Note: all I did above was to coment out the if and endif statements and uncomment the #define SIXTEENBIT statement. Also, you can type xdpyinfo in an xterm to see what display depths your X server supports. (2) to start X with different depth try startx -- -bpp 32 Check Roger Sayle's FAQ http://www.umass.edu/microbio/rasmol/faq_ras.htm and the Eric's email list http://www.umass.edu/microbio/rasmol/raslist.htm for more (perhaps better info) Good Luck, Don ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry 547 NSC Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30302 fax: (404) 651-1416 http://chemistry.Gsu.EDU/glactone ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Angel Herraez Subject: file association Date: Fri, 06 Oct 2000 11:04:32 +0200 To: rasmol@lists.umass.edu Hi everybody I have file extension .pdb associated to RasMol (both 2.6 and 2.7.1, running on an PC with Windows NT 4). When I double-click on a file in the explorer, Rasmol window pops up but with no molecule in it. On the Rasmol command-line window this message appears: Error: File 'C:\MY' not found Clearly, RasMol cannot cope with the space in 'My documents' folder name. Anybody knows how to solve this? ------------------------------------------------------------- Angel Herraez (Mr., Dr.) angel.herraez@uah.es Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain fax: +34-91 885 45 85 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Porter Subject: Re: file association Date: Fri, 06 Oct 2000 10:11:25 +0100 To: rasmol@lists.umass.edu At 11:04 06/10/00 +0200, you wrote: >Hi everybody >I have file extension .pdb associated to RasMol (both 2.6 and 2.7.1, >running on an PC with Windows NT 4). When I double-click on a file >in the explorer, Rasmol window pops up but with no molecule in it. >On the Rasmol command-line window this message appears: >Error: File 'C:\MY' not found >Clearly, RasMol cannot cope with the space in 'My documents' >folder name. >Anybody knows how to solve this? > >------------------------------------------------------------- > Angel Herraez (Mr., Dr.) angel.herraez@uah.es Dear Angel, I have encountered the same problem. One solution, albeit a not very elegant one, is to open your .pdb files by dragging them onto the RasMol icon (or a shortcut to RasMol) instead of by double-clicking. Hope this helps. Mike Dr M J Porter Lecturer in Organic Chemistry Department of Chemistry Email: m.j.porter@ucl.ac.uk UCL (University College London) Tel: +44 20 7679 4710 20 Gordon Street Fax: +44 20 7679 7463 London WC1H 0AJ, UK http://www.chem.ucl.ac.uk/people/porter/index.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: Re: file association Date: Fri, 06 Oct 2000 14:58:10 +0400 To: rasmol@lists.umass.edu On 6 Oct 2000, at 11:04, Angel Herraez wrote: > Hi everybody > I have file extension .pdb associated to RasMol (both 2.6 and 2.7.1, > running on an PC with Windows NT 4). When I double-click on a file > in the explorer, Rasmol window pops up but with no molecule in it. > On the Rasmol command-line window this message appears: > Error: File 'C:\MY' not found > Clearly, RasMol cannot cope with the space in 'My documents' > folder name. > Anybody knows how to solve this? Hi, As I know, RasMol can't open PDB files, if found them in the folder with space symbol " " in it's name. Sergey /*------------------------------------------------ Sergey Vasil'ev, Ph.D. DNA-Protein Interaction DataBase project team. http://www.dpidb.genebee.msu.ru Department of Math. Methods in Biology, Belozersky Institute of Physico-Chemical Biology, Moscow State University, Korpus "A", Vorobyevi gori, Moscow, 119899, RUSSIA. email vasil@genebee.msu.ru vasil@scientist.com tel: +7-095-9395414 fax: +7-095-9393181 ------------------------------------------------*/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Jeffrey Atkinson Subject: Re: Protein Explorer 1.7-beta available Date: Fri, 06 Oct 2000 08:22:14 -0400 To: rasmol@lists.umass.edu To Eric and others who might help; I've retrieved the new fixed Protein Explorer 1.71, expanded it, renamed the appropriate folders and put it into the same folder as my Chime resources. After using my Netscape (v. 4.75) to open index.htm, I successfully see the "front door" of Explorer. However, after typing in a pdb code in the fetch box (1aua or 1AUA for Sec14p) I get the message that "The Protein Explorer should appear automatically in a few moments, if you are using a compatible browser.", where I have sat for some time clearly waiting for nothing as Netscape was not working at communicating with anyone. I have reloaded Netscape (prior to getting 1.71, after 1.7 didn't work) and Chemchime 2.0a, to no avail. I'm on a G4 Mac, OS 9.0.2. I do not have the Chem3D plugin on my computer. Any hints or suggestions? Jeffrey -- Dr. Jeffrey Atkinson Associate Professor Department of Chemistry Brock University St. Catharines, Ontario Canada L2S 3A1 jatkin@spartan.ac.BrockU.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ phone: 905 688-5550 ext 3967 fax: 905 682-9020 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Suzanne W. Slayden" Subject: Re: file association Date: Fri, 06 Oct 2000 08:39:19 -0400 (EDT) To: rasmol@lists.umass.edu This will work with Windows95, so try it with your system: Right-click on the shortcut icon to RasMol on the desktop; click on Properties; click the Shortcut tab; in the box labeled Start in: type the complete path to the location of the file you want to open. (Run: box should show normal or maximized window). Now when you click on the file, it should open with the molecule loaded as a wireframe. If you have several subdirectories that contain files you might want to open at different times, make several shortcut icons to RasMol, labeled appropriately. Suzanne Slayden ----------------------------- Angel Herraez wrote: > > Hi everybody > I have file extension .pdb associated to RasMol (both 2.6 and 2.7.1, > running on an PC with Windows NT 4). When I double-click on a file > in the explorer, Rasmol window pops up but with no molecule in it. > On the Rasmol command-line window this message appears: > Error: File 'C:\MY' not found > Clearly, RasMol cannot cope with the space in 'My documents' > folder name. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Suzanne W. Slayden sslayden@gmu.edu Chemistry Department MSN 3E2 George Mason University (703) 993-1071 Fairfax, Va. 22030 (703) 993-1055 (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-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Protein Explorer 1.7-beta available Date: Fri, 06 Oct 2000 11:59:32 -0400 To: rasmol@lists.umass.edu, jatkin@spartan.ac.brocku.ca Dear Jeffrey: I've reverified that a downloaded local copy of PE 1.71 works fine on my G4 Mac. My guess is that you forgot to rename the 'shared' folder (from 'shared.exe Folder', the default name given to it by Stuffit Expander, to 'shared') or else you didn't put it 'next to' the protexpl folder. I can duplicate your report with this condition. The instructions for installing a local PE are, I hope, very clear about the necessity of placing and naming the folders correctly. If this is not the problem, please give more details, as requested in my earlier message to this list in the past few days. -Eric At 10/06/2000, you wrote: >To Eric and others who might help; > > I've retrieved the new fixed Protein Explorer 1.71, expanded >it, renamed the appropriate folders and put it into the same folder >as my Chime resources. After using my Netscape (v. 4.75) to open >index.htm, I successfully see the "front door" of Explorer. However, >after typing in a pdb code in the fetch box (1aua or 1AUA for >Sec14p) I get the message that "The Protein Explorer should appear >automatically in a few moments, if you are using a compatible >browser.", where I have sat for some time clearly waiting for nothing >as Netscape was not working at communicating with anyone. I have >reloaded Netscape (prior to getting 1.71, after 1.7 didn't work) and >Chemchime 2.0a, to no avail. I'm on a G4 Mac, OS 9.0.2. I do not >have the Chem3D plugin on my computer. > > Any hints or suggestions? > > Jeffrey >-- > > >Dr. Jeffrey Atkinson >Associate Professor >Department of Chemistry >Brock University >St. Catharines, Ontario >Canada L2S 3A1 > >jatkin@spartan.ac.BrockU.ca >http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ >phone: 905 688-5550 ext 3967 >fax: 905 682-9020 > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id e96IwJN09714 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Preview DRuMS colors with or without Chime Date: Fri, 06 Oct 2000 15:02:40 -0400 To: RasMol List Thanks to suggestions by Philippe Valadon and others, several changes have been made to the DRuMS Web site at http://www.umass.edu/molvis/drums/ (if you missed the initial explanation of DRuMS, it's at the bottom of this message): € A DRuMS mirror site is now operational, hosted by MolVisions (http://www.molvisions.com/umassmolvis/drums/). € The site now includes a "Chime-free" preview of the DRuMS color schemes. This preview contains ten still images showing how the DRuMS schemes can be combined to render complex macromolecules more understandable. Full text explanations of the schemes, as well as color codes and downloadable packages remain available to all users. (Note: The "Chimed" version is still available for users with the required software.) € DRuMS-RGB packages were added to the download page. These packages contain script files that allow you to use DRuMS in RasMol (unlike Chime and html, RasMol uses rgb color codes). € A DRuMS logo is available for you to add to your own Web site, plus sample html to link the logo back to the DRuMS Preview page. (You are invited to use the logo whether you link to our site or not.) Please feel free to email me with any questions, comments, or feedback about DRuMS. Thank you! -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet Waltham, MA USA driscoll@molvisions.com http://www.molvisions.com voice 781 899 3873 fax 781 899 4108 [Original message] Greetings! This message is to announce the release of DRuMS, a set of standardized color schemes for macromolecules. DRuMS is now available for preview in an interactive Chime-based Web site (http://www.umass.edu/molvis/drums), and offered free for adoption in other Web sites. * * * * * * * * * * * * * * * THE WEB SITE DRuMS is a set of seven intuitive color schemes applicable to macromolecular structures and specifically designed for use on the Web. The DRuMS Web site (http://www.umass.edu/molvis/drums) uses Chemscape Chime to display macromolecular structures in 3D. Interactive control panels allow you to preview DRuMS applied to different molecules, including the ability to: € Choose from among a number of sample molecules to display. € Select subsets of atoms (protein, solvent, ligand, and more). € Apply any of the DRuMS color schemes to the selection. € Interact with the molecule-change the view, rotation, zoom, and more. € Obtain DRuMS (html code and Chime scripts) FREE for your own use. [Access to the DRuMS Web site requires Win 95/98/2000/NT or Mac OS, and Netscape Communicator 4.5 or higher with Chime 2.x installed. Both Communicator and Chime are FREE and can be downloaded from the DRuMS Web site home page.] * * * * * * * * * * * * * * * AVAILABILITY FOR DOWNLOAD AND USE DRuMS is also available from the Web site as a downloadable package (for Mac and Win platforms). This package contain all of the files needed to integrate the color schemes into your own resources, including Chime scripts, Cascading Style Sheets, hex and rgb values, and detailed instructions with example code. THESE FILES ARE OFFERED TO NONCOMMERCIAL AND COMMERCIAL USERS ALIKE WITH NO RESTRICTIONS ON THEIR USE OR MODIFICATION. You are invited and encouraged to use or adapt DRuMS for your own online resources. * * * * * * * * * * * * * * * CONTRIBUTORS AND ADOPTIONS The color schemes were developed by Timothy Driscoll (MolVisions; http://www.molvisions.com), Frieda Reichsman (Molecules in Motion; http://www.moleculesinmotion.com), and Eric Martz (UMass Amherst; http://www.umass.edu/molvis/martz). They are based loosely on several RasMol color schemes devised by Roger Sayle. The DRuMS Color Schemes have been adopted for use already in: € (http://www.umass.edu/microbio/chime/explorer) Protein Explorer; € (http://www.worthpublishers.com/lehninger3d) Biochemistry in 3D, a set of online 3D structure tutorials that accompany Lehninger Principles of Biochemistry, Third Edition. * * * * * * * * * * * * * * * HELP AND MORE INFORMATION If you have suggestions for improving DRuMS, or questions regarding its use, please contact Timothy Driscoll at driscoll@molvisions.com. Please also let us know if you have found the DRuMS color schemes useful. -- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-ZSender: rowland.geoff@zetnet.co.uk ++++------+------+------+------+------+------+------+------+------+------+ From: Geoffrey Rowland Subject: Re: Calling rasmol from Visual Basic/DDE Date: Sun, 08 Oct 2000 15:41:41 +0100 To: "rasmol@lists.umass.edu" Edited from the message <39DB17BE.B2C6AD04@soulcatcher.chem.umass.edu> from "Robert P. Grosso Jr." > ...I have tried using DDE, but the commands aren't recognized by Visual Basic. > Does anyone know how to use Visual Basic to close the rasmol window, or, better yet, does > anyone know how to use API to communicate with rasmol through Visual Basic? > Any help on this subject would be appreciated. I have also just started playing with RasMol and Visual Basic/DDE. I think this has considerable potential for designing Rasmol interfaces which are simpler (eg for pre-university education), or more specialised (eg displaying inorganic structures) and for providing exemplar or project material for VB programming, Bioinformatics courses etc. A Visual Basic (ver. 3?) interface for RasMol already exists as RasMenu. However I believe this only works with 16 bit Windows (3.1) versions of Rasmol (e.g 2.5) As I understand it, further development of RasMenu ceased because of problems with the implementation of DDE in Windows 95 (32 bit) and with the the arrival of Chime. RasMenu/Rasmol2.5 can still be downloaded from the Edinbrough RasMol ftp site. In my hands DDE now works under Windows 95 with Visual Basic 5 and RasMol 2.7.1 (but apparently not for RasMol 2.6?). Having launched RasMol with a Visual Basic Shell command such as Dim RetVal RetVal = Shell("C:\Program Files\Rasmol\Raswin.exe", 4) You can establish a DDE link between a source textbox (Text1) and the target application RasWin with Text1.LinkTopic = "RasWin|System" Text1.LinkMode = vbLinkManual The Rasmol manual states that any Topic name can be used with RasWin but "System" and/or "RemoteControl" are recommended You can then type RasMol commands into Text1 and send/execute them by clicking, say, a command button attached to the code Text1.LinkExecute Text1.Text You can also attach controls to specific RasMol commands such as Text1.LinkExecute "set menus false" 'hides RasMol menus Text1.LinkExecute "load " & CommonDialog1.filename 'Loads pdb file selected in CommonDialog1 Text1.LinkExecute "zap" 'close currently loaded molecule Text1.LinkExecute "quit" 'exits Rasmol Text1.LinkExecute "spacefill true" 'spacefill display etc. You can also use DDE to display info derived from RasMol 'Items' as the source. For example the following code, if attached to a command button which loads a pdb file into rasmol will return the molecule's name to the Label lblName. lblName.LinkMode = 0 lblName.LinkTopic = "Raswin|System" lblName.LinkItem = "Name" lblName.LinkMode = 1 I have got this to work for LinkItems "Count" and "Pick" but have as yet no luck with linking "Image" to a Picture box. (see Inter-Process Communication section in RasMol manual). Also, I have not worked out how to return distances (from set picking distance) or angles (from set picking angle) to a Visual Basic Label - has anyone any ideas? It should be possible as the original RasMenu can do it! Similarly does anyone know how to run the RasMol Display and/or Command line interfaces as "child" windows to a Visual Basic interface rather than separately launched windows? Regards Geoff Rowland ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-MSMail-priority: Normal References: <2000100815414176239@zetnet.co.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Pat McGreevy Subject: Re: Calling rasmol from Visual Basic/DDE Date: Sun, 08 Oct 2000 08:22:12 -0700 To: rasmol@lists.umass.edu At DataAspects Corporation (www.dataaspects.com), we are creating a DDE interface between 'ChemBio', a 'C based' chemical information system, and RasMol. Similar to the experience of Robert Grosso, our DDE interface works with RasMol 2.7.1 on Win98, but not with RasMol 2.6. ...Pat McGreevy > Edited from the message <39DB17BE.B2C6AD04@soulcatcher.chem.umass.edu> > from "Robert P. Grosso Jr." > > > ...I have tried using DDE, but the commands aren't recognized by Visual Basic. > > Does anyone know how to use Visual Basic to close the rasmol window, or, better yet, does > > anyone know how to use API to communicate with rasmol through Visual Basic? > > Any help on this subject would be appreciated. > > I have also just started playing with RasMol and Visual Basic/DDE. I > think this has considerable potential for designing Rasmol interfaces > which are simpler (eg for pre-university education), or more > specialised (eg displaying inorganic structures) and for providing > exemplar or project material for VB programming, Bioinformatics courses etc. > > A Visual Basic (ver. 3?) interface for RasMol already exists as > RasMenu. However I believe this only works with 16 bit Windows (3.1) > versions of Rasmol (e.g 2.5) As I understand it, further development > of RasMenu ceased because of problems with the implementation of DDE > in Windows 95 (32 bit) and with the the arrival of Chime. > RasMenu/Rasmol2.5 can still be downloaded from the Edinbrough RasMol ftp site. > > In my hands DDE now works under Windows 95 with Visual Basic 5 and > RasMol 2.7.1 (but apparently not for RasMol 2.6?). > > Having launched RasMol with a Visual Basic Shell command such as > > Dim RetVal > RetVal = Shell("C:\Program Files\Rasmol\Raswin.exe", 4) > > You can establish a DDE link between a source textbox (Text1) and the > target application RasWin with > > Text1.LinkTopic = "RasWin|System" > Text1.LinkMode = vbLinkManual > > The Rasmol manual states that any Topic name can be used with RasWin > but "System" and/or "RemoteControl" are recommended > > You can then type RasMol commands into Text1 and send/execute them by > clicking, say, a command button attached to the code > > Text1.LinkExecute Text1.Text > > You can also attach controls to specific RasMol commands such as > > Text1.LinkExecute "set menus false" 'hides RasMol menus > Text1.LinkExecute "load " & CommonDialog1.filename 'Loads pdb > file selected > in CommonDialog1 > Text1.LinkExecute "zap" 'close currently loaded molecule > Text1.LinkExecute "quit" 'exits Rasmol > Text1.LinkExecute "spacefill true" 'spacefill display > > etc. > > You can also use DDE to display info derived from RasMol 'Items' as the source. > For example the following code, if attached to a command button which > loads a pdb file into rasmol will return the molecule's name to the > Label lblName. > > lblName.LinkMode = 0 > lblName.LinkTopic = "Raswin|System" > lblName.LinkItem = "Name" > lblName.LinkMode = 1 > > I have got this to work for LinkItems "Count" and "Pick" but have as > yet no luck with linking "Image" to a Picture box. (see Inter-Process > Communication section in RasMol manual). > > Also, I have not worked out how to return distances (from set picking > distance) or angles (from set picking angle) to a Visual Basic Label > - has anyone any ideas? It should be possible as the original RasMenu > can do it! > > Similarly does anyone know how to run the RasMol Display and/or > Command line interfaces as "child" windows to a Visual Basic > interface rather than separately launched windows? > > Regards > > Geoff Rowland ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id e99AWHN03104 ++++------+------+------+------+------+------+------+------+------+------+ From: Gerard Pujadas Subject: Changing default display in RasMol Date: Mon, 09 Oct 2000 12:35:11 +0100 To: rasmol@lists.umass.edu Dear Rasmol people, I wonder if it is possible to change the default visualization format (wireframe display and CPK colour) to cartoons display and colored by secondary structure. I have to examine a large amount of PDB files and this will save me a lot of time. With many thanks in advances for your help. Yours sincerly, Gerard. =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Angel Herraez Subject: file association fixed Date: Mon, 09 Oct 2000 15:03:25 +0200 To: rasmol@lists.umass.edu I have found how to solve the file association problem, at least for RasMol 2.7.1 (seems not to work with 2.6, can't figure out why): 1) Go to PC explorer 2) open menus for View / Options... / File types 3) look for "Brookhaven Protein Databank File" or whatever is called in your system the file definition for extension "pdb" and MIME type "chemical/x-pdb" 4) click on Edit 5) choose from the "Actions:" list the entry that says "Open" (default), and click on "Edit" for it. 6) add a space and "%1" (with the quotes) after the RasMol command line Now, double-clicking on a pdb file opens it in Rasmol nicely, as it should be. ------------------------------------------------------------- Angel Herraez (Mr., Dr.) angel.herraez@uah.es Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain fax: +34-91 885 45 85 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_qaFm0lTZZ9ZmhFv/pS67kA)" User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; m17) Gecko/20000807 Netscape6/6.0b2 X-Accept-Language: en References: <2000100815414176239@zetnet.co.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: alex garcia Subject: Re: Calling rasmol from Visual Basic/DDE Date: Mon, 09 Oct 2000 15:08:40 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_qaFm0lTZZ9ZmhFv/pS67kA) I have develkoped some VB windows that send the commands to rasmiol., if you want I can send you the source code, cheers Geoffrey Rowland wrote: > > Edited from the message <39DB17BE.B2C6AD04@soulcatcher.chem.umass.edu> > from "Robert P. Grosso Jr." > > > ...I have tried using DDE, but the commands aren't recognized by Visual Basic. > > Does anyone know how to use Visual Basic to close the rasmol window, or, better yet, does > > anyone know how to use API to communicate with rasmol through Visual Basic? > > Any help on this subject would be appreciated. > > I have also just started playing with RasMol and Visual Basic/DDE. I > think this has considerable potential for designing Rasmol interfaces > which are simpler (eg for pre-university education), or more > specialised (eg displaying inorganic structures) and for providing > exemplar or project material for VB programming, Bioinformatics courses etc. > > A Visual Basic (ver. 3?) interface for RasMol already exists as > RasMenu. However I believe this only works with 16 bit Windows (3.1) > versions of Rasmol (e.g 2.5) As I understand it, further development > of RasMenu ceased because of problems with the implementation of DDE > in Windows 95 (32 bit) and with the the arrival of Chime. > RasMenu/Rasmol2.5 can still be downloaded from the Edinbrough RasMol ftp site. > > In my hands DDE now works under Windows 95 with Visual Basic 5 and > RasMol 2.7.1 (but apparently not for RasMol 2.6?). > > Having launched RasMol with a Visual Basic Shell command such as > > Dim RetVal > RetVal = Shell("C:\Program Files\Rasmol\Raswin.exe", 4) > > You can establish a DDE link between a source textbox (Text1) and the > target application RasWin with > > Text1.LinkTopic = "RasWin|System" > Text1.LinkMode = vbLinkManual > > The Rasmol manual states that any Topic name can be used with RasWin > but "System" and/or "RemoteControl" are recommended > > You can then type RasMol commands into Text1 and send/execute them by > clicking, say, a command button attached to the code > > Text1.LinkExecute Text1.Text > > You can also attach controls to specific RasMol commands such as > > Text1.LinkExecute "set menus false" 'hides RasMol menus > Text1.LinkExecute "load " & CommonDialog1.filename 'Loads pdb > file selected > in CommonDialog1 > Text1.LinkExecute "zap" 'close currently loaded molecule > Text1.LinkExecute "quit" 'exits Rasmol > Text1.LinkExecute "spacefill true" 'spacefill display > > etc. > > You can also use DDE to display info derived from RasMol 'Items' as the source. > For example the following code, if attached to a command button which > loads a pdb file into rasmol will return the molecule's name to the > Label lblName. > > lblName.LinkMode = 0 > lblName.LinkTopic = "Raswin|System" > lblName.LinkItem = "Name" > lblName.LinkMode = 1 > > I have got this to work for LinkItems "Count" and "Pick" but have as > yet no luck with linking "Image" to a Picture box. (see Inter-Process > Communication section in RasMol manual). > > Also, I have not worked out how to return distances (from set picking > distance) or angles (from set picking angle) to a Visual Basic Label > - has anyone any ideas? It should be possible as the original RasMenu > can do it! > > Similarly does anyone know how to run the RasMol Display and/or > Command line interfaces as "child" windows to a Visual Basic > interface rather than separately launched windows? > > Regards > > Geoff Rowland > > > > > > > > > > > > --Boundary_(ID_qaFm0lTZZ9ZmhFv/pS67kA) I have develkoped some VB windows that send the commands to rasmiol., if you want I can send you the source code, cheers

Geoffrey Rowland wrote:
Edited from the message <39DB17BE.B2C6AD04@soulcatcher.chem.umass.edu>
  from  "Robert P. Grosso Jr." <grosso@soulcatcher.chem.umass.edu>

> ...I have tried using DDE, but the commands aren't recognized by Visual Basic. 
> Does anyone know how to use Visual Basic to close the rasmol window, or, better yet, does 
> anyone know how to use API to communicate with rasmol through Visual Basic? 
> Any help on this subject would be appreciated.

I have also just started playing with RasMol and Visual Basic/DDE. I 
think this has considerable potential for designing Rasmol interfaces 
which are simpler (eg for pre-university education), or more 
specialised (eg displaying inorganic structures) and for providing 
exemplar or project material for VB programming, Bioinformatics courses etc.

A Visual Basic (ver. 3?) interface for RasMol already exists as 
RasMenu. However I believe this only works with 16 bit Windows (3.1) 
versions of Rasmol (e.g 2.5) As I understand it, further development 
of RasMenu ceased because of problems with the implementation of DDE 
in Windows 95 (32 bit) and with the the arrival of Chime. 
RasMenu/Rasmol2.5 can still be downloaded from the Edinbrough RasMol ftp site.

In my hands DDE now works under Windows 95 with Visual Basic 5 and 
RasMol 2.7.1 (but apparently not for RasMol 2.6?).
 
Having launched RasMol with a Visual Basic Shell command such as

     Dim RetVal
     RetVal = Shell("C:\Program Files\Rasmol\Raswin.exe", 4)

You can establish a DDE link between a source textbox (Text1) and the 
target application RasWin with

     Text1.LinkTopic = "RasWin|System"
     Text1.LinkMode = vbLinkManual

The Rasmol manual states that any Topic name can be used with RasWin 
but "System" and/or "RemoteControl" are recommended 

You can then type RasMol commands into Text1 and send/execute them by 
clicking, say, a command button attached to the code

     Text1.LinkExecute Text1.Text

You can also attach controls to specific RasMol commands such as

     Text1.LinkExecute "set menus false"  'hides RasMol menus
     Text1.LinkExecute "load " & CommonDialog1.filename  'Loads pdb 
file selected
                                                         in CommonDialog1
     Text1.LinkExecute "zap"   'close currently loaded molecule
     Text1.LinkExecute "quit"  'exits Rasmol
     Text1.LinkExecute "spacefill true"   'spacefill display
    
     etc.

You can also use DDE to display info derived from RasMol 'Items' as the source.
For example the following code, if attached to a command button which 
loads a pdb file into rasmol will return the molecule's name to the 
Label lblName.    

     lblName.LinkMode = 0
     lblName.LinkTopic = "Raswin|System"
     lblName.LinkItem = "Name"
     lblName.LinkMode = 1

I have got this to work for LinkItems "Count" and "Pick" but have as 
yet no luck with linking "Image" to a Picture box. (see Inter-Process 
Communication section in RasMol manual).

Also, I have not worked out how to return distances (from set picking 
distance) or angles (from set picking angle) to a Visual Basic Label 
- has anyone any ideas? It should be possible as the original RasMenu 
can do it!

Similarly does anyone know how to run the RasMol Display and/or 
Command line interfaces as "child" windows to a Visual Basic 
interface rather than separately launched windows?

Regards

Geoff Rowland
--Boundary_(ID_qaFm0lTZZ9ZmhFv/pS67kA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol 2.7 web site stats for 99-00 Date: Fri, 13 Oct 2000 00:25:17 -0400 (EDT) To: rasmol@lists.umass.edu This is a report on visits to the RasMol 2.7 series web pages (now a major portion of the www.OpenRasMol.org web pages) at www.bernstein-plus-sons.com during the 99-00 Academic Year (September 1999 through August 2000), the first full Academic Year during which the new open source versions of RasMol have been available. Since we allow multiple mirror sites and encourage redistribution, these statistics provide only a partial picture of activity for this software. In particular, these numbers do not include distribution via the IUCr web site mirrors. During the 99-00 Academic Year, there were visits from over 30,000 distinct hosts, from approximately 100 domains. The domains with more than 1% percent in bytes, prorating for unresolved addresses were: 22.9% from the USA .edu domain, 1.7% from the USA .gov domain, .7% from the USA .org domain, 9.1% from the .com commercial domain 9.6% from the .jp domain (Japan) 9.5% from the .de domain (Germany) 4.5% from the .uk domain (United Kingdom) 4.2% from the .fr domain (France) 2.4% from the .it domain (Italy) 2.4% from the .ca domain (Canada) 1.9% from the .se domain (Sweden) 1.6% from the .nl domain (Netherlands) 1.6% from the .au domain (Australia) 1.5% from the .dk domain (Denmark) 1.5% from the .es domain (Spain) 1.2% from the .ch domain (Switzerland) 23.7% from other domains No slight is intended to such other domains as .fo (Faroe Islands), .pr (Puerto Rico), .bn (Brunei Darussalam), .cy (Cyprus), and .nu (Niue) which made occasional visits to the site. Their interest is appreciated. A total of 34.6 GB were downloaded (96.8 MB per day). The site provides more than 2000 distinct files, but we assume most people are interested in the choices in downloading RasMol source and binary versions. The source kit was downloaded more than 8,700 times. There were approximately 58,000 downloads of binary versions: ~ 29,000 (50%) MS windows version ~ 11,000 (19%) Mac versions ~ 9,500 (16%) Linux versions ~ 4,800 (8%) SGI versions ~ 3,100 (5%) DEC versions (incl. 1,100 DUNIX) ~ 600 (1%) AIX version The html version of the manual was viewed more than 11,000 times. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Laurence Hall Subject: RE: Protein Explorer 1.7-beta available Date: Fri, 20 Oct 2000 11:54:59 -0700 To: rasmol@lists.umass.edu Hi all, I am leaving ClickAction and new email is lkhall@pacbell.net. What is the list admin address? Sorry for the inconvenience. Laurence Laurence K. Hall Developer and Architect ClickAction, Inc. 2197 E. Bayshore Road Palo Alto, CA 94306 (650) 463-3979 (650) 473-3641 mailto:lhall@clickaction.com www.clickaction.com -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz Sent: Friday, October 06, 2000 9:00 AM From: owner-rasmol@lists.umass.edu Subject: Re: Protein Explorer 1.7-beta available To: rasmol@lists.umass.edu; jatkin@spartan.ac.brocku.ca Dear Jeffrey: I've reverified that a downloaded local copy of PE 1.71 works fine on my G4 Mac. My guess is that you forgot to rename the 'shared' folder (from 'shared.exe Folder', the default name given to it by Stuffit Expander, to 'shared') or else you didn't put it 'next to' the protexpl folder. I can duplicate your report with this condition. The instructions for installing a local PE are, I hope, very clear about the necessity of placing and naming the folders correctly. If this is not the problem, please give more details, as requested in my earlier message to this list in the past few days. -Eric At 10/06/2000, you wrote: >To Eric and others who might help; > > I've retrieved the new fixed Protein Explorer 1.71, expanded >it, renamed the appropriate folders and put it into the same folder >as my Chime resources. After using my Netscape (v. 4.75) to open >index.htm, I successfully see the "front door" of Explorer. However, >after typing in a pdb code in the fetch box (1aua or 1AUA for >Sec14p) I get the message that "The Protein Explorer should appear >automatically in a few moments, if you are using a compatible >browser.", where I have sat for some time clearly waiting for nothing >as Netscape was not working at communicating with anyone. I have >reloaded Netscape (prior to getting 1.71, after 1.7 didn't work) and >Chemchime 2.0a, to no avail. I'm on a G4 Mac, OS 9.0.2. I do not >have the Chem3D plugin on my computer. > > Any hints or suggestions? > > Jeffrey >-- > > >Dr. Jeffrey Atkinson >Associate Professor >Department of Chemistry >Brock University >St. Catharines, Ontario >Canada L2S 3A1 > >jatkin@spartan.ac.BrockU.ca >http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ >phone: 905 688-5550 ext 3967 >fax: 905 682-9020 > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Karen Ocorr Subject: Image superimposition Date: Tue, 24 Oct 2000 14:15:51 -0700 To: rasmol@lists.umass.edu Hello all, I am trying to do a structural comparison between different forms of cyclin-dependent kinase to be used for teaching. I am using the templates provided by Dr. Martz for displaying RasMol-saved scripts with the chime plug-in in Netscape. I would like to be able to display both cyclin bound and cyclin-unbound forms superimposed in the same frame or displayed side by side in two frames Might it possible to use protein Explorer for this rather than Chime? Is it possible to turn off the rotation BEFORE the scripts are loaded so that they come up stationary rather than rotating? I thank you all in advance for your input, any suggestions are welcome! Sincerely, Karen Ocorr _________________________________________________________________________ Karen Ocorr, Ph.D. Biology Department University of Michigan Ann Arbor, MI. 48109-1048 Phone: 734/ 647-2470 Fax: 734/ 647-0884 E-mail: kocorr@umich.edu Home Page: http://biology.lsa.umich/~www/bio310/kohome.html Web Sites: http://biology.lsa.umich.edu/~www/bio310 http://biology.lsa.umich.edu/~www/bio225 http://biology.lsa.umich.edu/~www/bio100 _________________________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3.0.5.32.20001024141551.0140f400@biology.lsa.umich.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Image superimposition Date: Tue, 24 Oct 2000 11:50:21 -0700 To: rasmol@lists.umass.edu You can overlay two structures and have them aligned in SwissPDBViewer and then save the project as a pdb file for either Chime or Rasmol to open. Dave Hurley Senior Computer Specialist (a biologist in disguise) University of Washington Biology Program 318 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-685-1728 >Hello all, > I am trying to do a structural comparison between different forms of >cyclin-dependent kinase to be used for teaching. I am using the templates >provided by Dr. Martz for displaying RasMol-saved scripts with the chime >plug-in in Netscape. > I would like to be able to display both cyclin bound and cyclin-unbound >forms superimposed in the same frame or displayed side by side in two >frames > Might it possible to use protein Explorer for this rather than Chime? > Is it possible to turn off the rotation BEFORE the scripts are loaded so >that they come up stationary rather than rotating? > I thank you all in advance for your input, any suggestions are welcome! >Sincerely, >Karen Ocorr > >_________________________________________________________________________ >Karen Ocorr, Ph.D. >Biology Department >University of Michigan >Ann Arbor, MI. 48109-1048 >Phone: 734/ 647-2470 >Fax: 734/ 647-0884 >E-mail: kocorr@umich.edu > >Home Page: http://biology.lsa.umich/~www/bio310/kohome.html >Web Sites: http://biology.lsa.umich.edu/~www/bio310 > http://biology.lsa.umich.edu/~www/bio225 > http://biology.lsa.umich.edu/~www/bio100 > >_________________________________________________________________________ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: Image superimposition Date: Tue, 24 Oct 2000 15:29:28 -0400 To: "'rasmol@lists.umass.edu'" Karen, I second Dave's idea... use Swiss PDBViewer to calculate the best alignment, save it as a PDB (each structure will be saved as a separate chain) then display with CHIME. For one example of the result of this procedure take a look at my pages dealing with RAS (http://webhost.bridgew.edu/fgorga/ras/default.htm), specifically the link titled "Conformational Changed in RAS". One caveat, Swiss PDB viewer only seems to be able to align single polypeptides. If anyone knows how to get this procedure to work with multisubunit proteins (hemoglobin, for example!) I would love to hear the details. It would be wonderful to be able to show students the difference between oxyHb and deoxHb with "real" molecules rather than using the same old textbook pictures! Hope that this helps, --- Frank P.S. I should remember to point out that Gale Rhodes first pointed out this idea to me via this list over a year ago. ------------------------------------------ Frank R. Gorga, Ph.D. Dept. of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 508-531-1785 (fax) fgorga@bridgew.edu http://webhost.bridgew.edu/fgorga -----Original Message----- Sent: Tuesday, October 24, 2000 1:50 PM From: Dave Hurley [mailto:dhurl@u.washington.edu] Subject: Re: Image superimposition To: rasmol@lists.umass.edu You can overlay two structures and have them aligned in SwissPDBViewer and then save the project as a pdb file for either Chime or Rasmol to open. Dave Hurley Senior Computer Specialist (a biologist in disguise) University of Washington Biology Program 318 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-685-1728 >Hello all, > I am trying to do a structural comparison between different forms of >cyclin-dependent kinase to be used for teaching. I am using the templates >provided by Dr. Martz for displaying RasMol-saved scripts with the chime >plug-in in Netscape. > I would like to be able to display both cyclin bound and cyclin-unbound >forms superimposed in the same frame or displayed side by side in two >frames > Might it possible to use protein Explorer for this rather than Chime? > Is it possible to turn off the rotation BEFORE the scripts are loaded so >that they come up stationary rather than rotating? > I thank you all in advance for your input, any suggestions are welcome! >Sincerely, >Karen Ocorr > >_________________________________________________________________________ >Karen Ocorr, Ph.D. >Biology Department >University of Michigan >Ann Arbor, MI. 48109-1048 >Phone: 734/ 647-2470 >Fax: 734/ 647-0884 >E-mail: kocorr@umich.edu > >Home Page: http://biology.lsa.umich/~www/bio310/kohome.html >Web Sites: http://biology.lsa.umich.edu/~www/bio310 > http://biology.lsa.umich.edu/~www/bio225 > http://biology.lsa.umich.edu/~www/bio100 > >_________________________________________________________________________ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: RE: Image superimposition Date: Tue, 24 Oct 2000 15:00:45 -0500 To: rasmol@lists.umass.edu > >One caveat, Swiss PDB viewer only seems to be able to align single >polypeptides. If anyone knows how to get this procedure to work with >multisubunit proteins (hemoglobin, for example!) I would love to hear the >details. It would be wonderful to be able to show students the difference >between oxyHb and deoxHb with "real" molecules rather than using the same >old textbook pictures! There are several kinemages floating around that are good animations between oxyHb and deoxyHb. One is available on the kinemage ftp site, one in Exploring Molecular Structures and one with "Biochemistry" by Voet, Voet and Pratt. I just got through using them in my biochemistry course. Eric used to have one of these animations on a kinemage description page somewhere on the Rasmol website. I seem to have lost the link, though, so I cannot point you to it. Bob Bateman ___________________________________________ Robert C. Bateman, Jr. Associate Professor and Graduate Coordinator Department of Chemistry and Biochemistry University of Southern Mississippi Hattiesburg, MS 39406-5043 601-266-4707 (office), 6075 (fax), 5305 (lab), 5394 (secretary) Robert.Bateman@usm.edu http://ocean.otr.usm.edu/~rbateman ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-MSMail-priority: Normal References: <5.0.0.25.1.20001024145347.009ec8d0@ocean.otr.usm.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Image superimposition Date: Tue, 24 Oct 2000 16:15:16 -0400 To: rasmol@lists.umass.edu Cc: "Frieda S. Reichsman" There is also a great Chime tutorial on Oxygen-Binding Proteins at http://www.worthpublishers.com/lehninger3d/ (accompanies the Lehninger Principles of Biochemistry textbook). It includes a number of different Hb alignments, single and multiple subunits, and a lot more. It's authored by Frieda Reichsman, who will know more about the gory details of aligning Hb subunits... (I think that she used Swiss-PDB Viewer, but I'm not certain.) -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA 508 864 6516 voice 781 899 4108 fax ----- Original Message ----- Sent: Tuesday, October 24, 2000 4:00 PM From: "Robert Bateman" Subject: RE: Image superimposition To: > > > > >One caveat, Swiss PDB viewer only seems to be able to align single > >polypeptides. If anyone knows how to get this procedure to work with > >multisubunit proteins (hemoglobin, for example!) I would love to hear the > >details. It would be wonderful to be able to show students the difference > >between oxyHb and deoxHb with "real" molecules rather than using the same > >old textbook pictures! > > There are several kinemages floating around that are good animations > between oxyHb and deoxyHb. One is available on the kinemage ftp site, one > in Exploring Molecular Structures and one with "Biochemistry" by Voet, Voet > and Pratt. I just got through using them in my biochemistry course. Eric > used to have one of these animations on a kinemage description page > somewhere on the Rasmol website. I seem to have lost the link, though, so I > cannot point you to it. > Bob Bateman > > > ___________________________________________ > Robert C. Bateman, Jr. > Associate Professor and Graduate Coordinator > Department of Chemistry and Biochemistry > University of Southern Mississippi > Hattiesburg, MS 39406-5043 > 601-266-4707 (office), 6075 (fax), 5305 (lab), 5394 (secretary) > Robert.Bateman@usm.edu > http://ocean.otr.usm.edu/~rbateman > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.0.0.25.1.20001024145347.009ec8d0@ocean.otr.usm.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Image superimposition Date: Tue, 24 Oct 2000 17:32:54 -0400 To: rasmol@lists.umass.edu Hello, The hemoglobin files I use in my biochemistry class are at http://www.usm.maine.edu/~rhodes/BiochemViews/ProteinFunction/index.html The full Hb are superimposed by Fit: Fit Selected Residues, using the four hemes only. The beta subunits are aligned by 3-point superposition with the heme rings. Superposition in Deep View is not limited to single polypeptides. For Magic Fit, it will try to align just about anything. For more sophisticated alignments, all that you need is to have the same number of residues selected in the two layers being aligned. See the Deep View tutorial, section 11 for a one or two more variations. http://www.usm.maine.edu/~rhodes/SPVTut/index.html Cheers! ***************************** Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.0.0.25.1.20001024145347.009ec8d0@ocean.otr.usm.edu> <001901c03df7$20c14f50$ee64fed8@NETVISTAPC> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Image superimposition Date: Tue, 24 Oct 2000 17:38:21 -0400 To: rasmol@lists.umass.edu Cc: "Frieda S. Reichsman" At 4:15 PM -0400 10/24/00, Timothy Driscoll wrote: >There is also a great Chime tutorial on Oxygen-Binding Proteins at >http://www.worthpublishers.com/lehninger3d/ (accompanies the Lehninger >Principles of Biochemistry textbook). It includes a number of different Hb >alignments, single and multiple subunits, and a lot more. It's authored by >Frieda Reichsman, who will know more about the gory details of aligning Hb >subunits... (I think that she used Swiss-PDB Viewer, but I'm not certain.) The oxy and deoxy hemoglobin pdb files for the Lehninger tutorial were indeed aligned in Deep View (Swiss PDB Viewer). If I recall correctly, I was able to align these multi-chain files in a routine manner. There is an option that enables you to choose the reference points for the alignment, and I used that option to select the heme groups so that each functioned as a reference for the alignment. Other choices would of course provide somewhat different alignments. The biggest headache at the time was re-naming all the chain designations so that I could select subunits easily. I have done other alignments since, and now I simply give each protein in the file a model number and treat it like an nmr file. I also did alignments of myoglobin and a hemoglobin beta subunit, and trimeric G protein alpha subunits for another tutorial. If any more details are wanted, or if this is not clear, please feel free to email me. Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures Phone: (413) 253-2405 http://www.MoleculesInMotion.com Fax: (612) 397-9975 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Angel Herraez Subject: displaying side-by-side Date: Wed, 25 Oct 2000 10:57:09 +0200 To: rasmol@lists.umass.edu --Boundary_(ID_S1LoK41rSMDFCqTlP4668w) Content-description: Mail message body Karen Ocorr wrote: > I would like to be able to display both cyclin bound and cyclin-unbound > forms superimposed in the same frame or displayed side by side in two > frames I have done 2-molecule and 3-molecule side-by-side comparisons in Chime, using several Chime windows within the same HTM frame. You can see them at http://www2.alcala.es/biomodel/model1/dna/abz-2.htm http://www2.alcala.es/biomodel/model1/dna/abz-3.htm (Home page is at http://www.uah.es/otrosweb/biomodel, in spanish). However, molecules do not show up synchronized, i.e. in the same position. Probably they will do if you start without rotation (I need them rotating). Attached are the relevant files, based on Eric Martz's left.htm > Is it possible to turn off the rotation BEFORE the scripts are loaded so > that they come up stationary rather than rotating? I am not totally sure, but it may work if you edit the HTM file containing the chime window (e.g. left.htm ) so that it says startspin=0 within the tag Hope this helps. Good luck! ------------------------------------------------------------- Angel Herraez (Mr., Dr.) angel.herraez@uah.es Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain fax: +34-91 885 45 85 --Boundary_(ID_S1LoK41rSMDFCqTlP4668w) Content-description: Text from file 'Abz-3.htm'
A B Z

--Boundary_(ID_S1LoK41rSMDFCqTlP4668w) Content-description: Text from file 'Abz-2.htm' --Boundary_(ID_S1LoK41rSMDFCqTlP4668w)-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: displaying side-by-side Date: Wed, 25 Oct 2000 10:16:00 -0400 To: rasmol@lists.umass.edu Here is a small molecule side by side I have done, with rotation togle http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html todd carlson ______________________________ Reply Separator _________________________________ Author: "Angel Herraez" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: displaying side-by-side Date: 10/25/2000 4:57 AM Karen Ocorr wrote: > I would like to be able to display both cyclin bound and cyclin-unbound > forms superimposed in the same frame or displayed side by side in two > frames I have done 2-molecule and 3-molecule side-by-side comparisons in Chime, using several Chime windows within the same HTM frame. You can see them at http://www2.alcala.es/biomodel/model1/dna/abz-2.htm http://www2.alcala.es/biomodel/model1/dna/abz-3.htm (Home page is at http://www.uah.es/otrosweb/biomodel, in spanish). However, molecules do not show up synchronized, i.e. in the same position. Probably they will do if you start without rotation (I need them rotating). Attached are the relevant files, based on Eric Martz's left.htm > Is it possible to turn off the rotation BEFORE the scripts are loaded so > that they come up stationary rather than rotating? I am not totally sure, but it may work if you edit the HTM file containing the chime window (e.g. left.htm ) so that it says startspin=0 within the tag Hope this helps. Good luck! ------------------------------------------------------------- Angel Herraez (Mr., Dr.) angel.herraez@uah.es Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain fax: +34-91 885 45 85 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: bad page? Date: Wed, 25 Oct 2000 11:20:00 -0400 To: rasmol@lists.umass.edu I had a report that one of my pages crashes a computer. I have not had a problem with it. Has anyone else observed this or would know the problem? http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html thanks todd carlson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: has anyone else done this? Date: Wed, 25 Oct 2000 11:41:00 -0400 To: rasmol@lists.umass.edu I have put together a simple molecular geometry quiz/tutorial for general chemistry that uses interactive atom clicking in chime. I have not seen this feature on other on-line quizzes or tutorizals. I am planning on adding this feature to some of my biochemisty pages. Has anyone else done this? todd carlson grand valley state university non-graded version http://www.gvsu.edu/carlsont/chime/geoquiz/geoquiz.htm graded version http://www.gvsu.edu/carlsont/chime/geoquiz/geoquiz2.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: George Helmkamp Subject: Re: bad page? Date: Wed, 25 Oct 2000 11:02:31 -0500 To: rasmol@lists.umass.edu Yes, I could not get into your site using Netscape 4.7. % % % % % % % % % % % % % % % % % % % % % % % % % % % George M. Helmkamp, Jr., Ph.D. Professor Department of Biochemistry & Molecular Biology University of Kansas Medical Center 3901 Rainbow Boulevard Kansas City, Kansas 66160-7421 (U.S.A.) tel: 913.588.6958 fax: 913.588.7440 e-mail: ghelmkam@kumc.edu % % % % % % % % % % % % % % % % % % % % % % % % % % % >>> CarlsonT@gvsu.edu Wed, 25 Oct 2000 >>> I had a report that one of my pages crashes a computer. I have not had a problem with it. Has anyone else observed this or would know the problem? http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html thanks todd carlson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Robley Light Subject: RE: bad page? Date: Wed, 25 Oct 2000 13:04:37 -0400 To: rasmol@lists.umass.edu I am the one who reported the crash. I get the following message when Netscape is trying to load the page: I'm using Netscape 4.73 NETSCAPE caused an exception 10H in module NPCHIME.DLL at 015f:01f79c81. Registers: EAX=00000000 CS=015f EIP=01f79c81 EFLGS=00010246 EBX=00000000 SS=0167 ESP=00b5f434 EBP=04ca52e0 ECX=04c18b34 DS=0167 ESI=04c156cc FS=21df EDX=00000306 ES=0167 EDI=04bda38c GS=0000 Bytes at CS:EIP: dc 25 48 90 ff 01 dc 0d 50 90 ff 01 dd 5c 24 20 Stack dump: 04bdb088 04c096c8 00b5f4f0 00000000 00000001 00000000 00000000 04bdb088 00000000 00000000 00000000 000000ff 00000000 04ffffff 00000000 04ff0000 When I load it into IE (5.0) I get a message that an error occurred in a plug in, but then the page loads. Nothing is in the left window until I click on it, the ammonia appears. The right window contains what looks like a carbon-dioxide molecule with very short C-O bonds--it doesn't show up as trigonal. Maybe something to do with the javascript coding? Robley Light ************************************************************* Robley J. Light Professor of Chemistry Department of Chemistry Phone: (850) 644-3844 Florida State University Email: rlight@chem.fsu.edu Tallahassee, FL 32306-4390 Fax: (850) 644-8281 Home Page: http://www.sb.fsu.edu/~rlight > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Carlson, Todd > Sent: Wednesday, October 25, 2000 11:20 AM > To: rasmol@lists.umass.edu > Subject: bad page? > > > I had a report that one of my pages crashes a computer. I > have not had > a > problem with it. Has anyone else observed this or would know the > problem? > > http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html > > thanks > > todd carlson > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: bad page (follow up) Date: Wed, 25 Oct 2000 13:06:00 -0400 To: rasmol@lists.umass.edu With regards to my web page that was causing some problems: http://www.gvsu.edu/carlsont/chime/trigonal/trigonal.html Some have no problem, but others have. I fixed one mistake that made the lone pairs malfunction. I also found some extraneous meta commands that were presumable put in by the various web page composers I have used. I stripped these out. I don't know if this will help. Todd ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-MSMail-priority: Normal References: <0G2Z00E09WU0QC@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: bad page (follow up) Date: Wed, 25 Oct 2000 13:38:57 -0400 To: rasmol@lists.umass.edu Todd, In the SCRIPT attribute of your EMBED tag for methane.mol, there is a close tag delimiter (>), which you are using as the "greater than" symbol. That may be causing problems on this page, which seems fairly straightforward otherwise. Try escaping or encoding this character, or scripting around it (i.e., atomno=1,atomno=2,atomno=3,atomno=4). Tim -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA 508 864 6516 voice 781 899 4108 fax ----- Original Message ----- Sent: Wednesday, October 25, 2000 1:06 PM From: "Carlson, Todd" Subject: bad page (follow up) To: > With regards to my web page that was causing some problems: > > http://www.gvsu.edu/carlsont/chime/trigonal/trigonal.html > > Some have no problem, but others have. I fixed one mistake that made > the > lone pairs malfunction. I also found some extraneous meta commands > that > were presumable put in by the various web page composers I have used. > I > stripped these out. I don't know if this will help. > > Todd > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: my bad pages - the problem, solution and hints. Date: Thu, 26 Oct 2000 10:43:00 -0400 To: rasmol@lists.umass.edu Yesterday, I asked for some feedback on my web page at: http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html Some people were having problems, but others didn't. Tim Driscoll read my source code and seems to have found the problem. When writing web pages, I have found it convenient to use a chime web page to generate the image I desire and then use the copy chime script command to create a chime script which will reproduce that image. I paste this into a word processor and then transfer it to a script in my chime embed tag so the page now creates the desired image. It is a great system on my platform, but the copy chime script command generate chime scripts with select commands which use greater than signs [such as "(select atomno>=7) and (atomno<=10)"]. It seems that some browsers (but apparently not all) interpret the > in the script as an end tag symbol. I have rewritten this page without the > so hopefully it works now. I apologize if I crashed your computer, but this doesn't happen on our campus network. It is very useful to have other people try my stuff. Thank much. Nevertheless, the copy chime script command is still very useful, but you have to be careful with those > signs. I have also been successful in storing the script as an .spt file (with > signs) and executing the script from the embed tag. This makes your source page much less wordy, but you have the inconvenience of working with multiple files. I have also had problems when working with proteins. The copy chime script command generates script files that are very long and awkward. I had one that was so large it couldn't fit into Notepad, which I use for simple text editing. This was because every atom was selected and colored individually making a script hundreds (or thousands) of lines long. Ultimately the best use of this feature was to use the automatically generated scripts to help write scripts manually. It's particularly helpful in identifying x, y, z rotations and zoom factors todd carlson grand valley state university other chime pages at: www.gvsu.edu/carlsont/ although I haven't had time to fix all of the yet. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-MSMail-priority: Normal References: <0G310038XKZ4AN@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: my bad pages - the problem, solution and hints. Date: Thu, 26 Oct 2000 11:08:24 -0400 To: rasmol@lists.umass.edu The problem with using greater than and less than symbols is on the html side, b/c these are reserved html symbols. Using them in an external Chime script doesn't pose a problem b/c the Chime script isn't read by the browser as html (it's read by Chime). Different browsers appear to accept varying levels of html fuzziness w/o complaint, though I've never figured out the pattern. You should be able to get around this particular problem by replacing the greater than and less than symbols ("<" and ">") in the html document with their corresponding html entities: "<" (<) and ">" (>), respectively (don't include the quotation marks). If that doesn't work, you can also try "<" and ">" (again, no quotes - these are the entitites in decimal format). For example, ...SCRIPT="select atomno>=1... instead of ...SCRIPT="select atomno>=1... Of course, don't replace actual tag delimiters with these codes; for example, should not become <EMBED...> Also, don't use these codes in external Chime scripts - just use < and > as normal. If this doesn't work, you can either move all of the embedded script commands to an external spt file and call that file from the embed command, or rewrite your selection commands so they don't use these symbols (yuck). -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA 508 864 6516 voice 781 899 4108 fax ----- Original Message ----- Sent: Thursday, October 26, 2000 10:43 AM From: "Carlson, Todd" Subject: my bad pages - the problem, solution and hints. To: > Yesterday, I asked for some feedback on my web page at: > > http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html > > Some people were having problems, but others didn't. Tim Driscoll read > my > source code and seems to have found the problem. When writing web > pages, I > have found it convenient to use a chime web page to generate the image > I > desire and then use the copy chime script command to create a chime > script > which will reproduce that image. I paste this into a word processor > and > then transfer it to a script in my chime embed tag so the page now > creates > the desired image. It is a great system on my platform, but the copy > chime > script command generate chime scripts with select commands which use > greater than signs [such as "(select atomno>=7) and (atomno<=10)"]. It > > seems that some browsers (but apparently not all) interpret the > in > the > script as an end tag symbol. I have rewritten this page without the > > so > hopefully it works now. I apologize if I crashed your computer, but > this > doesn't happen on our campus network. It is very useful to have other > people try my stuff. Thank much. > > Nevertheless, the copy chime script command is still very useful, but > you > have to be careful with those > signs. I have also been successful in > storing the script as an .spt file (with > signs) and executing the > script > from the embed tag. This makes your source page much less wordy, but > you > have the inconvenience of working with multiple files. > > I have also had problems when working with proteins. The copy chime > script > command generates script files that are very long and awkward. I had > one > that was so large it couldn't fit into Notepad, which I use for simple > text > editing. This was because every atom was selected and colored > individually > making a script hundreds (or thousands) of lines long. Ultimately the > best > use of this feature was to use the automatically generated scripts to > help > write scripts manually. It's particularly helpful in identifying x, y, > z > rotations and zoom factors > > todd carlson > grand valley state university > other chime pages at: > www.gvsu.edu/carlsont/ > although I haven't had time to fix all of the yet. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: es-AR, es, en References: <0G2Z00I3ZRXEGA@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Re: bad page? Date: Thu, 26 Oct 2000 21:06:12 -0300 To: rasmol@lists.umass.edu Hello, I have enter in the page using a WIn Netscape 4.74 and works perfectly, and I see the Chime examples. And I have enter using a Linux Netscape, but I can't see the examples, of course. Regards "Carlson, Todd" wrote: > I had a report that one of my pages crashes a computer. I have not had > a > problem with it. Has anyone else observed this or would know the > problem? > > http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html > > thanks > > todd carlson > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: dank@hq.lindsayelec.com (Dan Kolis) Subject: Hi res OP using Povray Date: Fri, 27 Oct 2000 14:14:56 -0400 To: rasmol@lists.umass.edu >I've been trying to incorporate RASMOL pictures into various >presentations using standard PC graphics programs such as Designer or >Picture Publisher by exporting as BMP or GIF files. The quality of the >graphics is, however, not awfully good. The resolution appears to be >very low and the effect is highly " digitized". As I am a fan of RASMOL, >especially its simplicity, this rather frustrates me. Can anybody advise >me as to how I might obtain better quality molecular graphics outputs >using RASMOL? >Thanks >Lee Yup. There is some way to have it write a Pov-ray file. http://www.bernstein-plus-sons.com/software/rasmol/ Povray is unbelievably amazing. Not hard to program either. I did a search along these lines.... Explore this search request if you like: http://hotbot.lycos.com/?MT=povray+and+rasmol&SM=B&LG=any&AM0=MC&AT0=words&A W0=&AM1=MN&AT1=words&AW1=&NUMMOD=2&date=within&DV=0&DR=newer&DM=1&DD=1&DY=20 00&FS=&RD=RG&RG=all&Domain=&PS=A&PD=&DC=10&DE=2&submit.x=44&submit.y=5 There is a sort of warning on some pages that maybe outputs to Rasmol don't work right on PC's and Mac's are preferred. Well, the input to Povray is very easy to work with, intercept, etc. http://www.povray.org/ text files get rendered of the general form: circle 3 color blue 3.444 2.222 -9.3344565 light ( 10 11 15) 4 5 8 so if you get this text file out it has to make a rasterable image. Regards, Dan Kolis Dan Kolis - Lindsay Electronics Ltd dank@hq.lindsayelec.com 50 Mary Street West, Lindsay Ontario Canada K9V 2S7 (705) 324-2196 Phone (705) 324-5474 Fax (888) 326-5654 Pager Anywhere (888) DANKOLIS {Same #) An ISO 9001 Company; SCTE Member ISM-127194 /Document end ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Loren Williams Subject: Hi res images using rasmol and adobe illustrator Date: Fri, 27 Oct 2000 15:04:34 -0400 To: rasmol@lists.umass.edu Povray is very nice. Here is a different method that works well for us, too. 1) write out a vector postscript file (I don't think all versions of rasmol can do this, rasmac 2.7.1 does it) 2) open the vector postscript file in adobe illustrator (you can edit the file at this stage) 3) scale everything uniformly by 300% (for very high resolution and a very big file go higher) 4) write out whatever pixilated format you want (jpg, photoshop, etc) 5) reduce back down in photoshop, designer, etc. Here are some examples of some figures that I made in that way. http://www.chemistry.gatech.edu/faculty/williams/bPublications/fig_5.jpg http://www.chemistry.gatech.edu/faculty/williams/bPublications/fig_1_hex_tot.jpg Because Illustrator is so powerful, for certain purposes, this method is better than povray. But it depends on your level of expertise with illustrator and the amount of time that you want to invest. For the first figure above, I wrote out two different vector files from rasmol, without moving anything. The wire representation was originally a different file from the rest of it, which was space-filling + stick representation. I superimposed the two files and did a lot of other types of editing in illustrator before writing out the jpg file. Cheers, Loren Williams Georgia Tech >>I've been trying to incorporate RASMOL pictures into various >>presentations using standard PC graphics programs such as Designer or >>Picture Publisher by exporting as BMP or GIF files. The quality of the >>graphics is, however, not awfully good. The resolution appears to be >>very low and the effect is highly " digitized". As I am a fan of RASMOL, >>especially its simplicity, this rather frustrates me. Can anybody advise >>me as to how I might obtain better quality molecular graphics outputs >>using RASMOL? >>Thanks >>Lee > > >Yup. There is some way to have it write a Pov-ray file. > >http://www.bernstein-plus-sons.com/software/rasmol/ > >Povray is unbelievably amazing. Not hard to program either. > >I did a search along these lines.... Explore this search request if you like: > >http://hotbot.lycos.com/?MT=povray+and+rasmol&SM=B&LG=any&AM0=MC&AT0=words&A >W0=&AM1=MN&AT1=words&AW1=&NUMMOD=2&date=within&DV=0&DR=newer&DM=1&DD=1&DY=20 >00&FS=&RD=RG&RG=all&Domain=&PS=A&PD=&DC=10&DE=2&submit.x=44&submit.y=5 > >There is a sort of warning on some pages that maybe outputs to Rasmol don't >work right on PC's and Mac's are preferred. Well, the input to Povray is >very easy to work with, intercept, etc. > >http://www.povray.org/ > >text files get rendered of the general form: > >circle 3 color blue 3.444 2.222 -9.3344565 >light ( 10 11 15) 4 5 8 > >so if you get this text file out it has to make a rasterable image. > >Regards, >Dan Kolis > > >Dan Kolis - Lindsay Electronics Ltd dank@hq.lindsayelec.com >50 Mary Street West, Lindsay Ontario Canada K9V 2S7 >(705) 324-2196 Phone (705) 324-5474 Fax >(888) 326-5654 Pager Anywhere (888) DANKOLIS {Same #) >An ISO 9001 Company; SCTE Member ISM-127194 >/Document end > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- published data? References: <0G2Z00I3ZRXEGA@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ji Hoon Ahn Subject: Does anyone give me an advice how to build 3-D image of a protein from Date: Fri, 27 Oct 2000 13:47:52 -0700 To: rasmol@lists.umass.edu Hi everyone, I have a quick question about building 3-D image of a protein. The thing is that 3-D structure of a protein, which is highly homologous to my protein (50% identical), has been published and I want to know how to build 3-D image of my protein by using the published protein's data. Any suggestion would be appreciated. Thank you very much in advance. Best regard, JH ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Michael S. Bartlett" Date: Fri, 27 Oct 2000 13:53:53 -0700 To: rasmol@lists.umass.edu >I've been trying to incorporate RASMOL pictures into various >presentations using standard PC graphics programs such as Designer or >Picture Publisher by exporting as BMP or GIF files. The quality of the >graphics is, however, not awfully good. The resolution appears to be >very low and the effect is highly " digitized". As I am a fan of RASMOL, >especially its simplicity, this rather frustrates me. Can anybody advise >me as to how I might obtain better quality molecular graphics outputs >using RASMOL? >Thanks >Lee Be sure to increase the resolution of your monitor to its highest possible values. Try exporting a screen-filling version of your picture and see if it suffices. If not, zoom in on the structure and scan (translate) across, exporting "snapshots" covering the entire structure (being very careful not to rotate the structure at all). Assemble the snapshots in a graphics program (it's easier than you think, especially if you can do semitransparent overlays of the snapshots during assembly--Photoshop works very well) and voila, a very high resolution, publication quality picture from good old RasMol. [see "Engines of gene expression" E. Peter Geiduschek & Michael S. Bartlett, Nature Structural Biology 7, 437 - 439 (2000) for one example using this technique] -- ........................................................ Michael S. Bartlett, Ph.D. Center for Molecular Genetics University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0634 Phone: (858)534-2451 Fax: (858)534-7073 email: bartlett@biomail.ucsd.edu ....................................................... ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg Subject: Re: Hi res OP using Povray Date: Sat, 28 Oct 2000 00:12:27 +0200 (MET DST) To: rasmol@lists.umass.edu >>I've been trying to incorporate RASMOL pictures into various >>presentations using standard PC graphics programs such as Designer or >>Picture Publisher by exporting as BMP or GIF files. The quality of the >>graphics is, however, not awfully good. The resolution appears to be >>very low and the effect is highly " digitized". As I am a fan of RASMOL, >>especially its simplicity, this rather frustrates me. Can anybody advise >>me as to how I might obtain better quality molecular graphics outputs >>using RASMOL? >>Thanks >>Lee >Yup. There is some way to have it write a Pov-ray file. It can also write vectorised postscript: RasMol> set vectps on RasMol> write vectps file.ps To import them to M$-products, you should convert them to a high-res (approx. 2000x2000 Pixel) image in your favourite format, e.g.: gs -sDEVICE=ppmraw -r300 -q -dSAFER -dNOPAUSE -sOutputFile=- \ file.ps quit.ps | pnmcrop | \ pnmtopng -transparent '#FFF' > file.png This of course requires ghostscript and the netpbm utilities. There is one caveat: This works for wireframe and ball-and-stick models only (none of the scondary structure elements are rendere in PS). Regards, Michael -- Michael Sternberg | On assignment at: http://www.phys.upb.de/~stern/ | Argonne National Lab, Chemistry Division phone: (630) 252-7020 fax: -9555 | 9700 S Cass Ave, Argonne, IL 60439-4831 "Who disturrrbs me at this time?" << Zaphod Beeblebrox IV >> <*> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- from published data? ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: Re: Does anyone give me an advice how to build 3-D image of a protein Date: Sat, 28 Oct 2000 17:46:36 +1300 To: rasmol@lists.umass.edu Hi JH, just submit your sequence to either http://www.bmm.icnet.uk/3djigsaw/form.html or http://www.expasy.ch/swissmod/SWISS-MODEL.html and they will send you the model by e-mail ... Regards Markus -- Dr. Markus Winter Department of Molecular Medicine Room 3301 School of Medicine 85 Park Road Grafton Auckland New Zealand Tel: 373 7599 ext 3960 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 published data? ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: Re: Does anyone give me an advice how to build 3-D image of a protein Date: Sat, 28 Oct 2000 17:47:17 +1300 To: rasmol@lists.umass.edu > I have a quick question about building 3-D image of a protein. The > thing is that 3-D structure of a protein, which is highly homologous > to my protein (50% identical), has been published and I want to know > how to build 3-D image of my protein by using the published protein's > data. Hi JH, just submit your sequence to either http://www.bmm.icnet.uk/3djigsaw/form.html or http://www.expasy.ch/swissmod/SWISS-MODEL.html and they will send you the model by e-mail ... Regards Markus -- Dr. Markus Winter Department of Molecular Medicine Room 3301 School of Medicine 85 Park Road Grafton Auckland New Zealand Tel: 373 7599 ext 3960 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 published data? References: <200010280445.RAA18403@postbox.auckland.ac.nz> ++++------+------+------+------+------+------+------+------+------+------+ From: Ji Hoon Ahn Subject: Re: Does anyone give me an advice how to build 3-D image of a protein Date: Fri, 27 Oct 2000 22:31:50 -0700 To: rasmol@lists.umass.edu Dear Markus, Thank you very much for your immediate response. I sent my protein sequence to both of them but 3D-JIGSAW didn't work, it said there is no template which is similar to the protein. Now I am waiting for the SWISSPROT MODEL data. Hopefully it shows something. Anyhow thanks so much again. Best, JH >Hi JH, > >just submit your sequence to either > >http://www.bmm.icnet.uk/3djigsaw/form.html > >or > >http://www.expasy.ch/swissmod/SWISS-MODEL.html > >and they will send you the model by e-mail ... > >Regards > >Markus > > >-- > >Dr. Markus Winter >Department of Molecular Medicine >Room 3301 >School of Medicine >85 Park Road >Grafton >Auckland >New Zealand >Tel: 373 7599 ext 3960 > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 published data? References: <0G2Z00I3ZRXEGA@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael H. Patrick" Subject: Re: Does anyone give me an advice how to build 3-D image of a protein Date: Sat, 28 Oct 2000 08:25:58 -0500 To: rasmol@lists.umass.edu In addition to computer visualization, many workers in structural biology find a physical model is a valuable tool. At The Center for BioMolecular Modeling (CBM), co-directed by Tim Herman and myself, we use state-of-the-art rapid prototyping technology to build custom 3D physical models of proteins from existing pdb files. These models are made available to the research and science education communities through our recently developed company, 3D Molecular Designs. Please visit our web site: http://www.rpc.msoe.edu/3dmd this will link you to CBM as well. >Hi everyone, > >I have a quick question about building 3-D image of a protein. The >thing is that 3-D structure of a protein, which is highly homologous >to my protein (50% identical), has been published and I want to know >how to build 3-D image of my protein by using the published >protein's data. Any suggestion would be appreciated. Thank you very >much in advance. > >Best regard, > >JH > -- Michael H. Patrick, Ph.D. CEO; 3D Molecular Designs, LLC 912 North Milwaukee Milwaukee, WI. 53202 Phone: (414) 277-7152 Fax: (414) 277-7470 Email: models@execpc.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Walter Rothschild Subject: RasMol 2.6 Date: Sun, 29 Oct 2000 13:26:57 -0500 To: rasmol@lists.umass.edu Hello: Can I make four copies of the same structure (consisting of about 1000 atoms), as visualized by RasMol v. 2.6, and then rotate/translate each of the four in order to attach it to a common central core structure to form one image? I am hoping I made myself clear: The scheme would be A', A", A"',A"", each rotated differently and attached to common core B. Best regards, Walter G. Rothschild wrothschild@earthlink.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Stereo/VR Rasmol Date: Mon, 30 Oct 2000 12:36:43 +1100 To: rasmol@lists.umass.edu I'm presently using the program VMD to display stereo images of a molecule for use in a virtual reality room, as opposed to using VR specs on a PC or workstation. Is it possible, in a simple manner, to modify the source code in Rasmol to render to overlapping and angularly displaced images of a molecule such that it can be used in this environment. The present setup of two side by side windowsfor stero is not appropriate for the VR system I'm working with, but I'm very fond of Rasmol, and would love to be able to use it in this environment. I'm aware that a simple solution may be wishful thinking but if anyone has experience in the area I would gratefully appreciate any help. Brendan O'Malley ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 V5.00.2615.200 X-MSMail-priority: Normal References: <0G2Z00I3ZRXEGA@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: bad page? Date: Mon, 30 Oct 2000 10:24:10 +0100 To: rasmol@lists.umass.edu No problem - I tried Netscape 4.7, IE 5.0 and Opera 3.x Best regards Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Wednesday, October 25, 2000 4:20 PM From: Carlson, Todd Subject: bad page? To: > I had a report that one of my pages crashes a computer. I have not had > a > problem with it. Has anyone else observed this or would know the > problem? > > http://www.gvsu.edu/carlsont/CHIME/trigonal/trigonal.html > > thanks > > todd carlson > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 V5.00.2615.200 X-MSMail-priority: Normal References: <20001027181456665.AAA250%hq.lindsayelec.com@dank> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Hi res OP using Povray Date: Mon, 30 Oct 2000 11:00:44 +0100 To: rasmol@lists.umass.edu Dear Dan, To convert chemistry to POV-Ray input files you may try Mol2mol, which can generate a*.pov input files with several options. Have a look to http://www.klte.hu/~gundat/povraya.htm or Mol2mol homepage: http://www.compuchem.com/mol2mol.htm Take into consideration, however, that protein pov files can be quite big, especially if smoothed spline representation is used (Current version of Mol2mol accepts molecules with up to 8000 atoms) Best regards Tamas ------------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Friday, October 27, 2000 7:14 PM From: Dan Kolis Subject: Hi res OP using Povray To: > >I've been trying to incorporate RASMOL pictures into various > >presentations using standard PC graphics programs such as Designer or > >Picture Publisher by exporting as BMP or GIF files. The quality of the > >graphics is, however, not awfully good. The resolution appears to be > >very low and the effect is highly " digitized". As I am a fan of RASMOL, > >especially its simplicity, this rather frustrates me. Can anybody advise > >me as to how I might obtain better quality molecular graphics outputs > >using RASMOL? > >Thanks > >Lee > > > Yup. There is some way to have it write a Pov-ray file. > > http://www.bernstein-plus-sons.com/software/rasmol/ > > Povray is unbelievably amazing. Not hard to program either. > > I did a search along these lines.... Explore this search request if you like: > > http://hotbot.lycos.com/?MT=povray+and+rasmol&SM=B&LG=any&AM0=MC&AT0=words&A > W0=&AM1=MN&AT1=words&AW1=&NUMMOD=2&date=within&DV=0&DR=newer&DM=1&DD=1&DY=20 > 00&FS=&RD=RG&RG=all&Domain=&PS=A&PD=&DC=10&DE=2&submit.x=44&submit.y=5 > > There is a sort of warning on some pages that maybe outputs to Rasmol don't > work right on PC's and Mac's are preferred. Well, the input to Povray is > very easy to work with, intercept, etc. > > http://www.povray.org/ > > text files get rendered of the general form: > > circle 3 color blue 3.444 2.222 -9.3344565 > light ( 10 11 15) 4 5 8 > > so if you get this text file out it has to make a rasterable image. > > Regards, > Dan Kolis > > > Dan Kolis - Lindsay Electronics Ltd dank@hq.lindsayelec.com > 50 Mary Street West, Lindsay Ontario Canada K9V 2S7 > (705) 324-2196 Phone (705) 324-5474 Fax > (888) 326-5654 Pager Anywhere (888) DANKOLIS {Same #) > An ISO 9001 Company; SCTE Member ISM-127194 > /Document end > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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, zh, de, ja, ko ++++------+------+------+------+------+------+------+------+------+------+ From: Mark Walter Subject: BaCl2.2H2O Model Date: Mon, 30 Oct 2000 10:13:31 -0600 To: rasmol@lists.umass.edu Dear All! Does anyone know of a crystal structure file for barium chloride dihydrate that I could display with either rasmol or chime? My thanks Mark Mark Walter, Ph.D. Associate Professor of Chemistry Fellow, Carnegie Foundation for the Advancement of Teaching Oakton Community College 1600 E. Golf Road Des Plaines, IL 60016 847-376-7037 mwalter@oakton.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: dank@hq.lindsayelec.com (Dan Kolis) Subject: Povray protein molecules Date: Mon, 30 Oct 2000 14:39:51 -0500 To: rasmol@lists.umass.edu Tamas said: >Dear Dan, >To convert chemistry to POV-Ray input files you may try Mol2mol, which can generate a*.pov input files with several options. Have a look to >http://www.klte.hu/~gundat/povraya.htm >or Mol2mol homepage: >http://www.compuchem.com/mol2mol.htm > Take into consideration, however, that protein pov files can be quite big, especially if smoothed spline representation is used (Current version of Mol2mol accepts molecules with up to 8000 atoms) >Best regards >Tamas >Dr Tamas E. Gunda >Research Group for Antibiotics of the Hungarian Acad. Sci. >University of Debrecen, POBox 36 >H-4010 Debrecen, Hungary >tel.: (+36-52) 512 900/2472 >fax: (+36-52) 512 914 >e-mail: tamasgunda@tigris.klte.hu >home-page: www.klte.hu/~gundat/gunda.htm Dan K says: Yes thanks. I'd suggest leaning more on the Povray features and less on the translators. Pretty well I don't think looking a higher res pictures actually teaches anybody useful specifics. Its an expectation of the papers that there be a fancy (still) picture. SO fine. Get the XYZ and radiuses moved, the colors what you want in the translation, then tinker away in povray as opposed to hoping for a splined surface, which as you clearly correctly state, must make huge hard to alter representations. You can move lights, change textures. change camera location and lens, etc right in Povray, or vie its flat ascii scripts. Thanks and good luck to who asked the initial question. Maybe you could attach a gif of the result? Cool Dan K Dan Kolis - Lindsay Electronics Ltd dank@hq.lindsayelec.com 50 Mary Street West, Lindsay Ontario Canada K9V 2S7 (705) 324-2196 Phone (705) 324-5474 Fax (888) 326-5654 Pager Anywhere (888) DANKOLIS {Same #) An ISO 9001 Company; SCTE Member ISM-127194 /Document end ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-PMrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: Ericksson Rocha e Almendra Subject: calcium phosfates Date: Tue, 31 Oct 2000 11:58:09 -0200 To: rasmol@lists.umass.edu Dear All! Does anyone know of a crystal structure file for hidroxyapatite, apatite and other calcium phosfates that I could display with either rasmol or chime? My thanks Ericksson Prof. Ericksson Rocha e Almendra almendra@metalmat.ufrj.br ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Please don't attach files to the list Date: Wed, 01 Nov 2000 09:41:55 -0500 To: rasmol@lists.umass.edu Reminder: Please don't attach any files to messages you send to this list. It is a large waste of internet bandwith, and it means that over 500 people have to wait (many via modem, including myself) for the files to download, then most need to delete them. Instead, please put any files you wish to share on a web server, and give simply the url in your email. Thanks, -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Enter your Chime resources in the World Index Date: Wed, 01 Nov 2000 09:46:34 -0500 To: rasmol@lists.umass.edu This is a reminder that those of you who have authored Chime-based resources should enter the url's in the World Index of Molecular Visualization Resources at http://molvis.sdsc.edu/visres You simply fill out a form there and submit it. There are already 60-some resources by 30-some authors there. They are automatically alphabetically indexed by molecule, topic, keywords, title, and author. I am planning to add some new categories soon, such as for organic chemistry resources, SwissPDB Viewer resources, sources of molecules, etc. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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: Jesse Bernstein Subject: Re: solid state structures Date: Wed, 01 Nov 2000 11:30:13 -0500 To: rasmol@lists.umass.edu Hi, I am new to this list serve. I do subscribe to two others: chemed and ap. I would like to know if there are sources of 3d images for solid state structures and lewis structures. I know that there are plenty of organic and biochemistry examples. Thanks in advance. Perhaps, someone could tell me if a list of previous comments (a thread) exists and the web address. I teach H.S. Chemistry from Honors to A.P. and electives in quantitative and qualitative analysis. My school, Hawken School, is an independent H.S. located in an eastern suburb of Cleveland, Ohio. Jesse Bernstein ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: solid state structures Date: Wed, 01 Nov 2000 12:31:54 -0500 To: "'rasmol@lists.umass.edu'" Jesse, As far as using CHIME to teach VSEPR theory... there are a number of CHIMEd sites out there already including one that I wrote but do not maintain anymore. (I don't seem to have the time to teach general chemistry these days!) Any way... the URL is: http://webhost.bridgew.edu/fgorga/vsepr/default.htm I think that my site might be most useful for it's links to other (more complete) sites. However I think that my "example" page (http://webhost.bridgew.edu/fgorga/vsepr/examples.htm) is particularly well organized! As far as solid state structures (crystal lattices) go... I know that they are out there, I have seen some in the past... but I have not paid much attention. --- Frank ------------------------------------------ Frank R. Gorga, Ph.D., Chair Dept. of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 508-531-1785 (fax) fgorga@bridgew.edu http://webhost.bridgew.edu/fgorga ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0G3C00IMOOUJD4@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Enter your Chime resources in the World Index Date: Wed, 01 Nov 2000 13:33:00 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_VWMsfjelLaachfNOOJJAjg) Another possible category might be resources for K-12 teaching. Thanks Cindy Eric Martz wrote: > This is a reminder that those of you who have authored Chime-based > resources should enter the url's in the World Index of Molecular > Visualization Resources at http://molvis.sdsc.edu/visres You simply fill > out a form there and submit it. > > There are already 60-some resources by 30-some authors there. They are > automatically alphabetically indexed by molecule, topic, keywords, title, > and author. > > I am planning to add some new categories soon, such as for organic > chemistry resources, SwissPDB Viewer resources, sources of molecules, etc. > > -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://www.proteinexplorer.org > World Index of Chime Resources: http://molvis.sdsc.edu/visres > PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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 > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > --Boundary_(ID_VWMsfjelLaachfNOOJJAjg) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;work:540-568-2726 x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu fn:Cindy Klevickis end:vcard --Boundary_(ID_VWMsfjelLaachfNOOJJAjg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: RE: solid state structures Date: Wed, 01 Nov 2000 16:18:57 -0500 To: rasmol@lists.umass.edu >As far as solid state structures (crystal lattices) go... I know that they >are out there, I have seen some in the past... but I have not paid much >attention. Here are some: http://www.soils.wisc.edu/virtual_museum/index.html Cheers! ***************************** Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Re: solid state structures Date: Thu, 02 Nov 2000 15:40:16 +0100 To: rasmol@lists.umass.edu Gale Rhodes wrote: > > >As far as solid state structures (crystal lattices) go... I know that they > >are out there, I have seen some in the past... but I have not paid much > >attention. > > Here are some: > > http://www.soils.wisc.edu/virtual_museum/index.html > And here are some more: http://www.chem.arizona.edu/~salzmanr/molecule.html -- ***** J.H. (Hens) Borkent, CMBI, *CMBI * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CMBI* http://www.cmbi.kun.nl/staff/borkent.html ***** Centre for Molecular and Biomolecular Informatics ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3A017CD0.1DB4CA11@cmbi.kun.nl> X-Authentication-warning: crow.nrl.navy.mil: mehl set sender to mehl@crow.nrl.navy.mil using -f ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Mehl Subject: Re: solid state structures Date: Thu, 02 Nov 2000 10:23:01 -0500 To: rasmol@lists.umass.edu Hens Borkent wrote: > Gale Rhodes wrote: > > > > >As far as solid state structures (crystal lattices) go... I know that they > > >are out there, I have seen some in the past... but I have not paid much > > >attention. > > > > Here are some: > > > > http://www.soils.wisc.edu/virtual_museum/index.html > > > > And here are some more: > > http://www.chem.arizona.edu/~salzmanr/molecule.html And here are some more: http://cst-www.nrl.navy.mil/lattice/ Caveats: These are mostly intermetallic alloys, with a few ionic systems, carbon and silicon thrown in. Since bonding in a metal is a matter of interpretation, I stuck to the XYZ format, rather than PDB. We run various versions of Unix here, so there are no Chime scripts. (The extended rant "Why Win4Linux is Not4Me" is available upon request.) -- M. J. Mehl (mehl@dave.nrl.navy.mil), Center for Computational Materials Science Naval Research Laboratory For a Computational Physicist's View of Interesting Structures, see http://cst-www.nrl.navy.mil/lattice/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: pdb into movie? Date: Fri, 03 Nov 2000 12:01:55 +1300 To: rasmol@lists.umass.edu Hi all, can anyone tell me what the easiest way would be to make a movie out of a pdf file - preferrably with custom effects (show and then hide active site residues etc). Thanks Markus ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <200011022259.LAA25738@postbox.auckland.ac.nz> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: pdb into movie? Date: Thu, 02 Nov 2000 15:47:58 -0800 To: rasmol@lists.umass.edu I do this with AppleScript, Prefab Player (an AppleScript extension that controls mouse movement and menu commands), Flash-It (a screen capture utility) QuickTime Pro and After Effects. I started to put together instructions at: http://www.biology.washington.edu/molecular/ In a nutshell, Applescript scripts drive Rasmol or SwissPDBViewer to change views, colors, display type, etc., and then a frame is saved after each incremental change. Even a simple 360 degree rotation will generate hundreds of files, but these can be assembled automatically by QuickTime Pro into a movie. After Effects can then be used to do crossfades and other effects. I can post other examples if there is interest. Dave Hurley Senior Computer Specialist (a biologist in disguise) University of Washington Biology Program 318 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-685-1728 >Hi all, > >can anyone tell me what the easiest way would be to make a movie out of a >pdf file - preferrably with custom effects (show and then hide active site >residues etc). > >Thanks > >Markus > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: pdb into movie? Date: Thu, 02 Nov 2000 21:01:10 -0500 To: rasmol@lists.umass.edu >> Hi all, >> >> can anyone tell me what the easiest way would be to make a movie out of a >> pdf file - preferrably with custom effects (show and then hide active site >> residues etc). >> >> Thanks >> >> Markus >> You can also use Chime and the move command to create 3D movies; for literally hundreds of examples of movies written in Chime, visit http://www.worthpublishers.com/lehninger3d/. Each movie script file can be very small (less than 10k in almost all examples) and requires nothing more than Netscape, Chime, and the pdb file of interest. And, of course, some knowledge of Chime scripting :-) A lot is possible, including fades, smooth movements, pauses, color changes, etc. Tim -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: move script question Date: Fri, 03 Nov 2000 10:12:00 -0500 To: rasmol@lists.umass.edu I have used the move command in Chime tutorials to rotate, translate, and zoom images to give the operator the desired view. However, if the operator has rotated the molecule, the move command will move the image to a differnt final position. The only way around this that I know of is to reset the image prior to moving. However, I find this disorienting from the operator's point of view. Does anyone know of a way scripting a move to a prescribed orientation, independent of the starting point? This would be a nice feature if I could figure out how to do it. Thanks todd carlson Dept of Chemistry GVSU Allendale MI carlsont@gvsu.edu www.gvsu.edu/carlsont/index.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: move script question Date: Fri, 03 Nov 2000 14:44:58 -0600 To: rasmol@lists.umass.edu Todd- Try using Chime's "view save" command, as follows: # Saving current view view save 1; # End saving view Then you can recall the view you saved (by the number you gave it): # Begin restoring display script AllOff.scr view restore 1; # End restoring display Note when returning to the view, I am running a script that turns all atomic displays (spacefill, ribbon, etc.) off. The view save seems to only restore molecular position zooms, translations, rotations, so if you have color schemes and such you want also restored, I put these in manually following the "view restore" command. Jamie At 10:12 AM 11/3/00 -0500, you wrote: > I have used the move command in Chime tutorials to rotate, translate, >and > zoom images to give the operator the desired view. However, if the > operator has rotated the molecule, the move command will move the image >to > a differnt final position. The only way around this that I know of is >to > reset the image prior to moving. However, I find this disorienting >from > the operator's point of view. Does anyone know of a way scripting a >move > to a prescribed orientation, independent of the starting point? This >would > be a nice feature if I could figure out how to do it. Thanks > > todd carlson > Dept of Chemistry > GVSU > Allendale MI > carlsont@gvsu.edu > www.gvsu.edu/carlsont/index.htm > __________________________________ Dr. James W. Caras Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 (512) 471-0416 caras@mail.utexas.edu http://www.sciencetechnologies.com/HomePaige/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Chime/RasMol Continuous Play? Date: Fri, 10 Nov 2000 10:48:32 -0500 To: "Gregory D. Fisher" Cc: rasmol@lists.umass.edu At 11/09/2000, you wrote: >Dr. Martz: > >1. I teach high school chemistry. To help interest students, I recently >acquired a 486 computer, the monitor of which I point into the hallway to >catch the view of passing students. I'd love to play some scripts - e.g., >bilayer1. Is this possible with RasMol (in the case of bilayer)? Can you >suggest scripts for Chime or otherway to accomplish this? > >2. I love using Chime - although I'm just a beginner. > >3. Best regards, >Gregg Fisher >Ridgefield H.S. >Ridgefield, CT 06877 >tel (h): 203/263-6283 > >email: gfisherphd@earthlink.net > >website: www.docfish.com > Dear Gregg: I'm delighted you're interesting high school students in molecular structure. You may wish to contact Brian Fortney, a Wisconsin high-school teacher very active in this area. If so, contact me again as I have temporarily misplaced his email. His students have made Chime presentations, and he uses physical plastic models of macromolecules in collaboration with the 3D Molecular Designs project (http://www.rpc.msoe.edu/3dmd). The only resource I know about currently enabled for continuous play is hemoglobin in Netscape + Chime at http://www.umass.edu/microbio/chime/hemoglob/index.htm (See the link "Continuous-play mode, endless loop"). You can download this Hemoglobin resource for off-line continuous loop running. Unfortunately I've never managed to get anyone to port the bilayer script into Chime and RasMol has no true looping capability. RasMol "movie" scripts are an obsolete format (Chime presentations are much more effective pedagogically and much easier to use). However, if bilayer1 is more interesting to you than hemoglobin, you can easily make a top level RasMol script file named e.g. biloop.spt containing script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top script bilayer1.top Or as many copies as you want. If you put in enough copies of this line, it will run all day (RasMol has no true looping mechanism, unlike Chime). Regards, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Limitation on XYZ animation frames in Chime? Date: Fri, 10 Nov 2000 10:52:22 -0500 To: Li Cai Cc: chime-feedback@mdli.com, rasmol@lists.umass.edu Dear Dr. Cai: I am copying this to chime-feedback@mdli.com since they of course are the source of Chime. I am also copying it to the Molecular Visualization Freeware email list in case some subscribers can help. I have almost no experience with XYZ files. Because the XYZ format has no provision to identify types of atoms (e.g. alpha carbon) or residue names (amino acids) it is not useful for animations of proteins. I know that Chime can load a PDB file (single model) of size 12 megabytes and I think larger. But I don't know about the limitation you have encountered for XYZ animations. Please let me know what you find out. You can subscribe to the email list at http://www.umass.edu/microbio/rasmol/raslist.htm Also if you get this working and on the web, please submit the URL to the World Index (see url below). -Eric At 11/09/2000, you wrote: >Professor Martz, > >We are a polymer research group in University of Utah. >We were trying to make some animation movies using CHIME. >We just can not find any source on the Web about how big >the input file for CHIME could be. When we use an XYZ file >with a size of 5.73 MB and 500 snapshots/frames. CHIME seems >read only the first 20 - 30 snapshots, and it does the >animation , but repeat only the forst 20 - 30 snapshots. >But the Xmol program can show the whole 500 snapshots and >animate the whole changing procedure. I just do not know if >there is a way to make CHIME read all the snapshots. >(maybe I did not hit on the right link when i was searching >on the web). Thank you in advance. > > >Regards, > >Li Cai > >Materials Science Dept. >University of Utah > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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: Fergus Doherty Subject: Oubain or digoxin co-ordinate files? Date: Mon, 13 Nov 2000 11:44:35 +0000 To: rasmol@lists.umass.edu Hi all, Does anyone have, or know where to get, co-ordinate (pdb) files for oubain and/or digoxin? Thanks for any help Fergus Doherty _____________________________________________________________________ Fergus Doherty PhD, School of BioMedical Sciences, D Floor, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH mailto:Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 970 9969 URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: German/Germany, de-DE, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: Oubain or digoxin co-ordinate files? Date: Mon, 13 Nov 2000 13:01:47 +0100 To: rasmol@lists.umass.edu For hetero component DGX DIGOXIN you may have a look at http://www.imb-jena.de/ImgLibPDB/pages/hetDir/hetDir.php3?hetDirTab=ShellHetDir&Residue=dgx&field=Residue Regards, Jan Fergus Doherty wrote: > Hi all, > > Does anyone have, or know where to get, co-ordinate (pdb) files for oubain > and/or digoxin? > > Thanks for any help > > Fergus Doherty > > _____________________________________________________________________ > Fergus Doherty PhD, > School of BioMedical Sciences, > D Floor, > University Medical School, > Queen's Medical Centre, > Nottingham NG7 2UH > > mailto:Fergus.Doherty@nottingham.ac.uk > Tel: 0115 970 9366 > FAX: 0115 970 9969 > URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html > -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3A0FD82B.7592A7FA@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Can I target more than one chime with the same button? Date: Mon, 13 Nov 2000 13:45:52 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_O19N9YDAe9GIWzuPHV1cxw) Here is the web page I'm working on: http://www.isat.jmu.edu/users/klevicca/shoebox/glucose.html I have six water molecules that I want to highlight all at once. They are each separate chimes but I want them all to respond to the same button. Has anyone done this before? --Boundary_(ID_O19N9YDAe9GIWzuPHV1cxw) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;work:540-568-2726 x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu fn:Cindy Klevickis end:vcard --Boundary_(ID_O19N9YDAe9GIWzuPHV1cxw)-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Can I target more than one chime with the same button? Date: Mon, 13 Nov 2000 14:23:11 -0500 To: rasmol@lists.umass.edu on 11.13.00 1:45 PM, Cindy Klevickis at klevicca@jmu.edu wrote: > Here is the web page I'm working on: > http://www.isat.jmu.edu/users/klevicca/shoebox/glucose.html > > I have six water molecules that I want to highlight all at once. They are > each separate chimes but I want > them all to respond to the same button. Has anyone done this before? > > > I believe that if you name all of your plugins the same name (the ones that hold the water molecules), you can send one script to them all using TARGET="name_of_plugins" in the button's embed tag. I don't know if you want to do this, b/c you will lose the ability to access each plugin separately, but there it is anyway. The other way to do it is using javascript and multiple calls of the executeScript function, but you will lose Windows IE compatibility if you do this. Can't have your cake and eat it, too, I guess! BTW, I couldn't view the xyz animation on your site - it prompted me for the plugin. You may need to define the type in your embed tag for this animation (i.e., type="chemical/x-xyz"), which my Chime is configured to recognize (I don't know why it won't infer that from the file src like it does with pdb, but it won't). Good luck! -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Can I target more than one chime with the same button Date: Tue, 14 Nov 2000 08:53:00 -0500 To: rasmol@lists.umass.edu, Timothy Driscoll I wanted to execute chime scripts from a javascript program too. Could you suggest a reference on how to use this executeScript function. Does someone have a page that uses this feature so I can see how it is done? Thanks Todd Carlson ______________________________ Reply Separator _________________________________ Author: "Timothy Driscoll" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: Can I target more than one chime with the same button? Date: 11/13/2000 2:23 PM on 11.13.00 1:45 PM, Cindy Klevickis at klevicca@jmu.edu wrote: > Here is the web page I'm working on: > http://www.isat.jmu.edu/users/klevicca/shoebox/glucose.html > > I have six water molecules that I want to highlight all at once. They are > each separate chimes but I want > them all to respond to the same button. Has anyone done this before? > > > I believe that if you name all of your plugins the same name (the ones that hold the water molecules), you can send one script to them all using TARGET="name_of_plugins" in the button's embed tag. I don't know if you want to do this, b/c you will lose the ability to access each plugin separately, but there it is anyway. The other way to do it is using javascript and multiple calls of the executeScript function, but you will lose Windows IE compatibility if you do this. Can't have your cake and eat it, too, I guess! BTW, I couldn't view the xyz animation on your site - it prompted me for the plugin. You may need to define the type in your embed tag for this animation (i.e., type="chemical/x-xyz"), which my Chime is configured to recognize (I don't know why it won't infer that from the file src like it does with pdb, but it won't). Good luck! -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Can I target more than one chime with the same button Date: Tue, 14 Nov 2000 09:29:45 -0500 To: rasmol@lists.umass.edu on 11.14.00 8:53 AM, Carlson, Todd at CarlsonT@gvsu.edu wrote: > I wanted to execute chime scripts from a javascript program too. Could > you > suggest a reference on how to use this executeScript function. Does > someone have a page that uses this feature so I can see how it is done? > > Thanks > > Todd Carlson > Hi Todd, I know of no reference, and an admittedly brief look around the MDLI Wed site turned up nothing related to the executeScript() function. You may try Eric Martz's site (http://www.umass.edu/microbio/chime/). But essentially, if you are familiar with JavaScript, here is the code: document.chimestructure.executeScript("color structure;cartoon on"); where "chimestructure" in the name given to the plugin in its embed tag, and the argument is any string of Chime commands (distinct commands are separated by semicolons). Multiple plugins and framesets do make it more complicated, but only on the JavaScript side. Fair warning: I've found that the executeScript() function DOES NOT WORK in IE for Windows (Chime doesn't work at all in IE for Mac) so if you use this method, you'll lose those users who don't want to download a Netscape product. I'm sure many people on the list have examples of pages that use executeScript(); here are two published examples of my own: http://www.worthpublishers.com/lehninger3d/ (a fairly complex page built for Lehninger Principles of Biochemistry) http://www.umass.edu/microbio/molvis/drums/ Regards, Tim -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- X-Accept-Language: en References: <0G4000E71PA04W@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Re: Can I target more than one chime with the same button Date: Tue, 14 Nov 2000 16:19:06 +0100 To: rasmol@lists.umass.edu, CarlsonT@gvsu.edu "Carlson, Todd" wrote: > > I wanted to execute chime scripts from a javascript program too. Could > you > suggest a reference on how to use this executeScript function. Does > someone have a page that uses this feature so I can see how it is done? > > Thanks > > Todd Carlson > Dear Todd, Following up on Timothy's message I constructed a small example based on a javascript function: and a form button:
Clicking the button sends the three commands to chime structures named chime1, chime 2, and chime3. Instead of a button, an area map could work as well (href="javascript:spacefill()") I embedded it (temporarily) in one of my course pages, just as an example: http://www.cmbi.kun.nl/wetche/organic/stereo/mb126.html Bye, Hens -- ***** J.H. (Hens) Borkent, CMBI, *CMBI * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CMBI* http://www.cmbi.kun.nl/staff/borkent.html ***** Centre for Molecular and Biomolecular Informatics ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Can I target more than one chime with the same button Date: Tue, 14 Nov 2000 10:37:00 -0500 To: rasmol@lists.umass.edu, Hens Borkent Thanks I have been able to get the executeScript command to work. As for operating on multiple chime images in the same window, isn't there a command that will link one window to another, so rotations in one will act on another? I know I have seen this but can't find the command. Does this linking of images also affected other commands or just movement? ______________________________ Reply Separator _________________________________ Author: "Hens Borkent" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: Can I target more than one chime with the same button Date: 11/14/2000 10:19 AM "Carlson, Todd" wrote: > > I wanted to execute chime scripts from a javascript program too. Could > you > suggest a reference on how to use this executeScript function. Does > someone have a page that uses this feature so I can see how it is done? > > Thanks > > Todd Carlson > Dear Todd, Following up on Timothy's message I constructed a small example based on a javascript function: and a form button:
Clicking the button sends the three commands to chime structures named chime1, chime 2, and chime3. Instead of a button, an area map could work as well (href="javascript:spacefill()") I embedded it (temporarily) in one of my course pages, just as an example: http://www.cmbi.kun.nl/wetche/organic/stereo/mb126.html Bye, Hens -- ***** J.H. (Hens) Borkent, CMBI, *CMBI * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CMBI* http://www.cmbi.kun.nl/staff/borkent.html ***** Centre for Molecular and Biomolecular Informatics ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Can I target more than one chime with the same button Date: Tue, 14 Nov 2000 11:46:38 -0500 To: rasmol@lists.umass.edu At 11/14/2000, Todd Carlson wrote: > Thanks > > I have been able to get the executeScript command to work. > As for operating on multiple chime images in the same window, isn't >there a > command that will link one window to another, so rotations in one will >act > on another? I know I have seen this but can't find the command. Does >this > linking of images also affected other commands or just movement? Go to www.proteinexplorer.org (in Windows -- the functionality you want didn't make it into Mac Chime 2.0a -- if you think it is important, contact chime-feedback@mdli.com) At the FrontDoor page, in the left-most gray box, click Protein Comparator (under More Quick-Start Molecules) At FirstView, click Explore More. In QuickViews, click the Synch button (last button in the button cluster Spin, Zoom, etc.). Rotate with the mouse. This button is a toggle. You'll see the commands involved in the message box, lower left (send mouse on/off). You can View Source in the Chime frames to see the embed tag parameters involved, namely name="chime_graphics" sendmouse=false target="chime_2graphics" and vice versa in the other one. I describe the method in Protein Explorer/Comparator because this is a good general method to see commands in action, and to learn the scripting language. You can also copy command sequences out of the message box to make script files. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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: Marthenn Salazar Subject: Re: [RasMol 2.6] Date: Tue, 14 Nov 2000 10:35:24 -0800 (PST) To: rasmol@lists.umass.edu Hello, I've not seen a response to Walter's post some time back. I have a similar question but I am dealing with three copies of the same structure (subunits). If anyone has any ideas, it would be greatly appreciated. Thank you, Marthenn Salazar Walter Rothschild wrote: Hello: Can I make four copies of the same structure (consisting of about 1000 atoms), as visualized by RasMol v. 2.6, and then rotate/translate each of the four in order to attach it to a common central core structure to form one image? I am hoping I made myself clear: The scheme would be A', A", A"',A"", each rotated differently and attached to common core B. Best regards, Walter G. Rothschild wrothschild@earthlink.net ____________________________________________________________________ Get your own FREE, personal Netscape WebMail account today at http://home.netscape.com/webmail ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0G4000D7LX1SVP@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: RE: Can I target more than one chime with the same button Date: Tue, 14 Nov 2000 10:42:48 -0800 To: rasmol@lists.umass.edu One possible alternative solution to multiple windows is by using ISIS/Draw from MDLI to create one file containing multiple structures. I don't think this will enable you to rotate different compounds around their own centers, but it has worked for me for other uses. Dave Hurley Senior Computer Specialist (a biologist in disguise) University of Washington Biology Program 318 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-685-1728 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer upgraded to 1.72 Date: Tue, 14 Nov 2000 18:20:51 -0500 To: rasmol@lists.umass.edu I've upgraded Protein Explorer (including the downloadable package) to version 1.72. The changes are minor (major additions are in progress but not yet ready): 1. The annoying Science Netwatch black window no longer pops up every time the FrontDoor page is loaded. 2. There is a cascade of warnings to avoid leaving molecules spinning unnecessarily, especially in multiple concurrent sessions, because this severely degrades computer performance (nearly "freezing" the computer in some circumstances). (After 30 sec of spinning, it asks you whether to stop spinning. Should you want to leave a molecule spinning indefinitely, you need only cancel the first warning, and then cancel the second immediately following, which offers to remind you later. If requested, reminders occur in multiples of 2 of the default delay, e.g. 60, 120 sec etc., but if you cancel the reminder, you'll never be bothered again in that session -- unless you stop and restart spinning.) 3. PE now verifies during startup that the version of files in the shared folder is matched to that in the protexpl folder. 4. There are now icons linked to the DRuMS site of standard color schemes where appropriate. To upgrade a previously downloaded copy, follow the instructions at the downloading site. Be sure to get both protexpl.exe and shared.exe. If anyone needs to process multiple sequence alignments in MSA3D that are too long to fit in the form box (>32K bytes), please contact me. A temporary workaround is available (and a real fix is in progress). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Bruist Subject: RE: [RasMol 2.6] rotating molecules Date: Tue, 14 Nov 2000 18:35:20 -0500 To: rasmol@lists.umass.edu Marthenn, I use a spreadsheet to manipulate the coordinates to accomplish translations and rotations. A sample of an Excel workbook that does this can be found on my web page at http://tonga.usip.edu/bruist/mfb_chime/chime_index.html Simply down load the file MolMover.xls. This is a two page spreadsheet. The first page, when saved as space delimited text (*.prn), produces a file in PDF format. The second page is used to rotate and translate the coordinates. Z-axis rotation is entered in cell J2, X-axis rotation cell N2, Y-axis rotation in cell R2. These rotations are performed in this order. X, Y, Z translations are entered in cells U3, V3, and W3. There is also a feature whereby the best rotations and translation to fit your molecule to a target can be found. You have to add target atoms in register with their corresponding atoms in the structure. The use the "Solver..." under the TOOLS menu to perform a nonlinear least-squares fit of the rotations and translations to fit the two molecules. The sum of the squared residuals in cell AK3 is minimized. The resultant coordinates should be pasted into the first page using "paste values" and saved as a *.prn file. Warning: Do not change the column spacing as that will put the pdb file out of register. The example in the sheet moves a 20 base-pair segment of DNA to overlap with target sugars at the base pair of residues 1 and 20. Mike Dr. Michael F. Bruist Associate Professor of Biochemistry Department of Chemistry and Biochemistry Griffith Hall 142 University of the Sciences in Philadelphia 600 South 43rd Street Philadelphia, PA 19104-4495 Phone (Office & Voice Mail):(215) 596-8530 Dept. Phone: -8839 Dept. Fax: -8543 E-mail: m.bruist@usip.edu -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Marthenn Salazar Sent: Tuesday, November 14, 2000 1:35 PM From: owner-rasmol@lists.umass.edu Subject: Re: [RasMol 2.6] To: rasmol@lists.umass.edu Hello, I've not seen a response to Walter's post some time back. I have a similar question but I am dealing with three copies of the same structure (subunits). If anyone has any ideas, it would be greatly appreciated. Thank you, Marthenn Salazar Walter Rothschild wrote: Hello: Can I make four copies of the same structure (consisting of about 1000 atoms), as visualized by RasMol v. 2.6, and then rotate/translate each of the four in order to attach it to a common central core structure to form one image? I am hoping I made myself clear: The scheme would be A', A", A"',A"", each rotated differently and attached to common core B. Best regards, Walter G. Rothschild wrothschild@earthlink.net ____________________________________________________________________ Get your own FREE, personal Netscape WebMail account today at http://home.netscape.com/webmail ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: rotating molecules Date: Wed, 15 Nov 2000 11:53:00 -0500 To: rasmol@lists.umass.edu I have a different question about rotation. Does anyone know of a mathmatical algorithm that can convert the sequence of rotate, translate and zoom commands that you get from a copy chime script command (such as): rotate z -50 rotate y -40 rotate x 42 translate x -28 translate y -14 zoom 194 to a single move command (such as): move 42 -40 -50 194 -28 -14 0 0 1 These do not give the same result. Also, what does z translation do in the move command? Also, how are move commands calculated? Enquiring minds want to know. thanks in advance todd carlson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "Shaw, Stephen" Subject: Can script name be supplied as command line argument on rasmol startup? Date: Thu, 16 Nov 2000 06:07:38 -0500 To: rasmol@lists.umass.edu I have not found any documentation on rasmol startup command line arguments, and know only of the ability to supply a .pdb filename to load. 1. Is it possible to supply a script as a command line argument when starting rasmol (in windows/DOS) and have rasmol automatically execute that script. 2. What other options are allowed for the rasmol startup line? Regards Steve Shaw ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Bruist Subject: RE: rotating molecules Date: Thu, 16 Nov 2000 09:47:57 -0500 To: rasmol@lists.umass.edu Todd, The ORDER of rotations is critical. Rotation about one axis moves the other axes. Consider the series rotate about Z 90 deg, rotate about Y 90 deg, rotate about Z -90 deg. You do not get the initial orientation back because the Y rotation moved the Z axis. Mike -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Carlson, Todd Sent: Wednesday, November 15, 2000 11:53 AM From: owner-rasmol@lists.umass.edu Subject: RE: rotating molecules To: rasmol@lists.umass.edu I have a different question about rotation. Does anyone know of a mathmatical algorithm that can convert the sequence of rotate, translate and zoom commands that you get from a copy chime script command (such as): rotate z -50 rotate y -40 rotate x 42 translate x -28 translate y -14 zoom 194 to a single move command (such as): move 42 -40 -50 194 -28 -14 0 0 1 These do not give the same result. Also, what does z translation do in the move command? Also, how are move commands calculated? Enquiring minds want to know. thanks in advance todd carlson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Michael Sternberg Subject: Re: Can script name be supplied ... Date: Thu, 16 Nov 2000 15:45:27 +0100 (MET) To: rasmol@lists.umass.edu "Shaw, Stephen" writes: >1. Is it possible to supply a script as a command line argument when >starting rasmol (in windows/DOS) and have rasmol automatically execute that >script. > >2. What other options are allowed for the rasmol startup line? The man page which comes with the unix version (2.6.4) lists some of the switches: RASMOL(1) RASMOL(1) NAME rasmol - Molecular Graphics Visualisation Tool v2.6 SYNOPSIS rasmol [-nodiplay] [[-format ] filename] [-script scriptfile] FORMATS -pdb Brookhaven Protein Databank -mdl MDL's MOL File Format -mol2 Tripos' Sybyl MOL2 Format -xyz MSC's XYZ (XMol) Format -mopac MOPAC Input or Output File Format -alchemy Alchemy File Format -charmm CHARMm File Format ... Upon inspection of the source, I found some more: -noconnect does not calculate bond map for files that do not have bond information (e.g. xyz-files) -insecure allow writes upon startup even for non-interactive use -format The following formats are recognised: -alchemy -biosym -cif -charmm -fdat -gaussian -macromodel -mdl -mmdb -mol2 -mopac -nmrpdb -pdb -shelx -xyz Upon startup, Rasmol searches rc-files ("ini"-files in windows-parlance) in the following order, stopping on the first one found and sourcing it: Unix Dos/Win ----------------------------------------------------------- .rasmolrc (current directory) rasmol.ini $HOME/.rasmolrc $HOME/rasmol.ini (?) $RASMOLPATH/rasmolrc $RASMOLPATH/rasmol.ini If $RASMOLPATH is not set, a compiled-in default is used. Note that I cannot confirm the DOS/Win behaviour. Stopping upon the first of these file may be inconvenient, if you want to place some lobal settings. However, if you put "source ~/.rasmolrc" or equivalent first line in a local script, you reduce duplications. More at http://www.phys.uni-paderborn.de/~stern/rasmol/ . Regards, -- Michael Sternberg | On assignment at: http://www.phys.upb.de/~stern/ | Argonne National Lab, Chemistry Division phone: (630) 252-7020 fax: -9555 | 9700 S Cass Ave, Argonne, IL 60439-4831 "Who disturrrbs me at this time?" << Zaphod Beeblebrox IV >> <*> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- startup? References: <0G420068PSBF1Y@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Can script name be supplied as command line argument on rasmol Date: Thu, 16 Nov 2000 12:11:58 -0500 To: rasmol@lists.umass.edu Cc: sshaw@nih.gov At 11/16/2000, Steve Shaw wrote: >I have not found any documentation on rasmol startup command line arguments, >and know only of the ability to supply a .pdb filename to load. > >1. Is it possible to supply a script as a command line argument when >starting rasmol (in windows/DOS) and have rasmol automatically execute that >script. > >2. What other options are allowed for the rasmol startup line? > >Regards >Steve Shaw RASMOL For RasMol 2.6-beta-2a, look in the RasMol Reference Manual (http://www.umass.edu/microbio/rasmol/distrib/rasman.htm) under General Operation, for MS Windows: "It is possible to specify either a coordinate filename or both on the windows command line. The format for specifying a script file to add the option '-script ' to the command line. A molecule co-ordinate file may be specified by placing its name on the command line, optionally preceded by a file format option. If no format option is given, the specified co-ordinate file is assumed to be in PDB format. Valid format options include '- pdb', '-mdl', '-mol2', '-xyz', '-alchemy' and '-charmm', which correspond to Brookhaven, MDL Mol file, Sybyl Mol2, MSC's xyz, Alchemy and CHARMm formats respectively. If both a co-ordinate file and a script file are specified on the command line, the molecule is loaded first, then the script commands are applied to it. If either file is not found, the program displays the error message 'Error: File not found!' and the user is presented the RasMol prompt." For portability, I prefer to have all necessary pdb files and scripts in the same directory. If you start RasWin in that folder, it looks for files there by default. So, for example, the "load" command in a script can say "load 'xxxx.pdb'" and RasWin will look for the file xxxx.pdb in the same folder. This avoids using pathnames that typically are nonportable. One could also use the rasmol.ini strategy. Windows-relevant excerpts from the Ref Manual: "Each time RasMol is started, it searches for an initialisation file of commands to run before the command prompt is presented to the user. The file is called RASMOL.INI on Microsoft Windows Systems. The format and execution of this file is identical to that of the RasMol script command. RasMol first looks for the initialisation file in the current directory, and if it is not found will look for it in the user's home directory. On all systems the environment variable HOME may be used to name the user's home appropriate directory. If no personal initialisation file is found the program looks for the file rasmolrc (or RASMOLRC) in the RasMol system directory pointed to by the environment variable RASMOLPATH. This directory should also contain the on-line help file rasmol.hlp." CHIME Chime behaves the same way. So, for example, if you put a script and the pdb file referenced by its load command on an http server, or in a local folder, and start chime with a hyperlink to the script, Netscape will invoke Chime and execute the script. The directory containing the script and invoking Chime becomes Chime's default directory. This means that a pdb filename without prepended path, e.g. in a load command in the script, will be sought in the same directory as that containing the invoking script. For example: http://www.umass.edu/microbio/chime/beta/pdb/1fby-1.spt This script starts "load '1lbd1fby.pdb'", and that pdb file (containing an alignment of two protein chains) is in the same directory on the server. PROTEIN EXPLORER This principle has been used in implementing the 'Project Folder' capability of Protein Explorer. When a project folder is set, Chime is invoked from that folder (using the requisite file pe_proj.htm), which defines the location Chime looks for all scripts and pdb files not prepended with paths. This enables pathless script and pdb files to be executed/loaded from PE's command line, so long as they reside in the current project folder. (One can hope that in a future version of Chime, there will be a new 'set basepath {path}' command to enable better control of this!) Finally, I am working on a mechanism to specify a startup script for Protein Explorer. The script will be specified as a query parameter in the URL, and will be the initial view shown in PE. This should be available by the end of the calendar year if things go as planned -- possibly sooner. A related capability that should become available about the same time is support for tutorial presentations in PE, including a script recorder to aid in saving scripts to attach to buttons in the presentation. The latter two are currently partially implemented and working in a private alpha test version, being tested by students in my fall class here at UMass. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: view show/set Date: Thu, 16 Nov 2000 13:18:26 -0500 To: rasmol@lists.umass.edu Those interested in rotations may want to look up the 'view' commands in Chime documented at http://www.mdli.com/support/chime/rasmol.html view show reports a 'view set' command that will re-establish the current orientation. View set command rotate in order Z, Y, X as documented above. Unlike the 'move' command this does the rotation instantly. For example, view set 170.70 -29.13 -77.54 146.02 These are easy to try out using the command line input slot in Protein Explorer. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: pdblite.org Date: Sat, 18 Nov 2000 13:01:34 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org, edmolvis@lists.umass.edu The PDB Lite search engine is now accessible via http://www.pdblite.org. This easy-to-remember URL was implemented in the past few days, although PDB Lite has been available since 1998. The mirrors on the above page update their copies of the PDB database weekly using data released by RCSB, so you will find the most recently published structures in PDB Lite. PDB Lite is designed for students and educators, and for scientists who do searches for 3D structures on an occasional basis. Specialist jargon is avoided or explained. There is step-by-step help on how to save a PDB file to your disk. This assists with file-naming and folder location issues that sometimes have been known to make the saved file difficult to find or to load into Protein Explorer, RasMol, Chime, Swiss PDB Viewer/DeepView, or other applications. PDB Lite has several advantages over SearchLite at RCSB. PDB Lite warns you when it cannot properly process your query (for example, use of parentheses*). It automatically finds alternative spellings; for example, "hemoglobin" finds "haemoglobin". A checkbox limits hits to sequence-nonredundant structures (reducing the hits for "lysozyme" from 682 to 3). The tabular "Short Descriptions" listing lines up a given field, making it easier to scan through multiple hits (e.g. ligand). On the other hand, SearchLite can find "phospholipase c" while PDB Lite ignores the "c", finding all phospholipases. -Eric Martz ------------------- * "phospholipase and (choline or inositol)" returns zero hits at SearchLite with no explanation. PDB Lite refuses to accept a query containing parentheses, and explains that precedence is left to right, giving an example. Thus informed, you can rephrase to "choline or inositol and phospholipase", which in fact works both in PDB Lite and SearchLite. Note that "(lysozyme)" also returns zero hits in SearchLite with no explanation. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.pdblite.org 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: Joel Kowit Subject: protein explorer 1.72 beta Date: Mon, 20 Nov 2000 11:09:07 -0500 To: rasmol@lists.umass.edu I'm having some trouble with Protein Explorer 1.72beta 1) I just downloaded PE 1.72 into its folder, downloaded shared into its folder 2) I opened PE and set the folder to a project folder (I had previously used, successfullyl) 3) I clicked on "Bare PE", clicked on "Start Explorer Session" 4) PE opened with 3 windows. The right window had my protein. The lower left window had the message box. But the upper left window was blank [first problem]. I was able to bring up the "menu/scheme" with the .X command, but previouslly this was automatic on opening PE. 5) Also, there was no green(ready) or red (busy) button on the protein window. I would appreciate suggestions. Thanks. Joel Kowit Biology/Emmanuel College ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Netscape 6 incompatible with Chime Date: Wed, 22 Nov 2000 12:23:08 -0500 To: rasmol@lists.umass.edu Dear fellow chimeleons: It has just come to my attention that Netscape 6 has been released. Here are my observations thusfar (Win 98 4.10.1998). The bottom line is that Netscape 6 won't work with most of my Chime resources. 1. Chime 2.0.3 for Windows installer does not recognize the Netscape application when you try to install by specifying the directory. So I copied the chime files from the plugins directory of another version. 2. Chime is invoked with a pdb mime, and can display a pdb file, e.g. http://www.umass.edu/microbio/chime/atp.pdb 3. When I try a Chime embed button that attempts to load a script file, e.g. at http://www.umass.edu/microbio/chime/hemoglob The status line shows Requesting="Script 'glycine1.spt"' NOTICE THE INCORRECTLY PLACED CLOSE QUOTES! Netscape hangs, its icon disappears from the Alt-Tab list, and it has to be killed with Ctrl-Alt-Del. 3A. The 'heme only' button at http://www.umass.edu/microbio/chime/chimehow/chime_1.htm doesn't use a script file, lacks single quotes, but still fails. 4. The old immediate-mode button, dummy frame kludge works for sending a script to Chime, e.g. http://www.umass.edu/microbio/chime/quizzer 5. The 'move' sequences in the Quizzer have occasional momentary pauses followed by a 'catch-up' jerk not seen in Navigator 4.7x; i.e. Netscape is interrupting Chime. Not serious but a step backwards. 6. LiveConnect appears to be broken, e.g. http://www.mdli.com/support/chime/tutorial/tuts/chimedemos/java.html works in 4.7x (with lots of js errors that are the fault of the document, but it works), but doesn't work in 6. 7. Protein Explorer? Don't ask. --------------- Non-chime-related observations: Default font sizes are smaller. Under preferences, appearance, themes, you can select classic so at least the buttons are recognizable. It takes a long time to start, but the startup panel will now go behind other applications. I can't get it to start with any window except a tiny one. Every new window has to be manually full-screened. Also Ctrl-N is on the menu but fails to open a new window. The frame source viewer is different; I can't see any way to discern the name of the file in a frame from the frame source. Pages jerk around during loading before they settle down so you can read them. Sadly, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael H. Patrick" Subject: Re: Netscape 6 incompatible with Chime Date: Wed, 22 Nov 2000 14:01:39 -0600 To: rasmol@lists.umass.edu Eric: How and where can this be addressed...and resolved? Michael ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Neil Saunders Subject: Re: Netscape 6 incompatible with Chime Date: Thu, 23 Nov 2000 09:49:58 +1100 To: rasmol@lists.umass.edu > It has just come to my attention that Netscape 6 has been released. Here > are my observations thusfar (Win 98 4.10.1998). The bottom line is that > Netscape 6 won't work with most of my Chime resources. There seem to be a lot of serious problems with the new Netscape 6; for an enjoyable review of it go here. http://www.webdevelopersjournal.com/columns/ajs_n6_preview.html For those who don't follow these things closely, it goes like this. Once upon a time there was Netscape and it was the king of browsers. Then the time came for a serious revamp, to fend of the competition from MSIE. So Netscape opened up their source code for the Mozilla people, and they found that it was so awful, they just had to start again. It's well known, for instance, that NS4 support for cascading stylesheets, a wonderful concept, is dreadful because it's based on a proprietary interpretation of CSS, not the W3C standard. Hence the 3 year delay in a new Netscape, skipping over v5 to v6 in a sad attempt to one-up MSIE at v5. In the meantime Netscape sold out to AOL, resulting in a heap of features in the new browser that you don't want-shopping buttons, buttons directing you to AOL/Netscape and word has it, some rather dodgy AOL spying features. I used NS happily for years, but saw the light and moved to MSIE starting with version 4. Frankly, a lot of people like to jump on the anti-Microsoft bandwagon and are therefore ignorant of the simple fact that MSIE is the superior browser. It renders a whole lot faster, has more useful features and is more W3C standards compliant. I know from my website traffic that a lot of biologists are both Mac and Netscape users and have to be catered for. But I think developers of CHIME like-resources should bear in mind that more and more computer users in molecular biology are using PC platforms and MSIE because the combination generally performs a whole lot better. It looks like NS6 could crash and burn, and NS4 is in danger of becoming a legacy browser. Neil Saunders School of Microbiology & Immunology, University of New South Wales, Sydney 2052, Australia Ph: +61 2 9385 2093 Fx: +61 2 9385 1591 email: neil.saunders@unsw.edu.au http://www.crosswinds.net/~nfws/index.htm ArchaeaWeb http://www.crosswinds.net/~nfws/archaea/index.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Netscape 6 incompatible with Chime Date: Wed, 22 Nov 2000 19:15:32 -0500 To: Neil Saunders , rasmol@lists.umass.edu on 11.22.00 5:49 PM, Neil Saunders at neil.saunders@unsw.edu.au wrote: > I used NS happily for years, but saw the light and moved to MSIE starting > with version 4. Frankly, a lot of people like to jump on the anti-Microsoft > bandwagon and are therefore ignorant of the simple fact that MSIE is the > superior browser. It renders a whole lot faster, has more useful features > and is more W3C standards compliant. I know from my website traffic that a > lot of biologists are both Mac and Netscape users and have to be catered > for. But I think developers of CHIME like-resources should bear in mind > that more and more computer users in molecular biology are using PC > platforms and MSIE because the combination generally performs a whole lot > better. It looks like NS6 could crash and burn, and NS4 is in danger of > becoming a legacy browser. Hi Neil, Here's my two cents, which I'll try to tone down despite being an avid Mac user and Microsoft basher. (That means I'll refrain from arguing that IE really isn't the superior browser at all ;-) I for one would love to accommodate IE. Unfortunately, in order for Chime resources to be developed for IE, Chime has to work in IE. IE-Chime does not work at all on the Mac (I learned that the hard way, as with most Microsoft products that I try - sorry, but I had to bash a little). In addition, Chime resources for Windows IE lack functionality because there are only a few, severely-limited methods for accessing the events that pass between IE and Chime. Access to these events, or at least knowledge about them, is key to developing powerful browser-based tools that allow a user to interact with the 3D structure in simple, "clickable" ways. Netscape browsers allow the Chime developer a lot of freedom to create helpful interactive controls (one example is the executeScript() function discussed recently on this list). Many sites now make use of these types of controls, and I hope you agree they are much more accessible and useful than is the Chime MDL menu. I recognize that IE is a popular Web browser with a large share of the market; you'd have to live in a box not to acknowledge it. As soon as I can offer more than the default gray checkbox as a tool for user input, and as soon as IE and Chime work on a Mac, I'll happily develop Chime resources for IE. I hope that day comes soon. To staunch any talk of a Doomsday fast approaching, I have a three-year old PowerComputing machine (you remember those six months when Mac clones were actually sold, before Apple bought them all out? Well, I got one!). Despite being stuck with three-year old technology, it still runs my Web site just fine. Sometimes good tools don't turn over quite as fast as we may be used to these days. Well, that's my hope anyway. Happy Thanksgiving! -- Timothy Driscoll MolVisions - Molecular Visualization on the Internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- boundary="Boundary_(ID_zYxA7dJkducW7f4JwKfsKw)" X-Accept-Language: fr,en-US References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: Netscape 6 incompatible with Chime Date: Wed, 22 Nov 2000 19:50:15 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_zYxA7dJkducW7f4JwKfsKw) > Chime resources for Windows IE lack functionality because there > are only a few, severely-limited methods for accessing the events that pass > between IE and Chime. Access to these events, or at least knowledge about > them, is key to developing powerful browser-based tools that allow a user to > interact with the 3D structure in simple, "clickable" ways. Netscape > browsers allow the Chime developer a lot of freedom to create helpful > interactive controls (one example is the executeScript() function discussed > recently on this list). Many sites now make use of these types of controls, > and I hope you agree they are much more accessible and useful than is the > Chime MDL menu. > I'm not an expert in Chime ressources, but I found a simple way to use both Netscape and MSIE. With Netscape (4.7 at least) you can use the ExecuteScript command, and with MSIE, you can use the 'via dummy' mechanism. The thing is that you are not obliged to use a framed site in MSIE to use this trick because you can send imediate buttons to an hidden Inline Frame ( You can send rasmol scripts with the javascript function send_script(script,chime) Or you can add a link that will invoke your molecule. Link ---------------------- Jean-Philippe Demers --Boundary_(ID_zYxA7dJkducW7f4JwKfsKw) 
Chime resources for Windows IE lack functionality because there
are only a few, severely-limited methods for accessing the events that pass
between IE and Chime.  Access to these events, or at least knowledge about
them, is key to developing powerful browser-based tools that allow a user to
interact with the 3D structure in simple, "clickable" ways.  Netscape
browsers allow the Chime developer a lot of freedom to create helpful
interactive controls (one example is the executeScript() function discussed
recently on this list).  Many sites now make use of these types of controls,
and I hope you agree they are much more accessible and useful than is the
Chime MDL menu.


I'm not an expert in Chime ressources,
but I found a simple way to use both Netscape and MSIE.
With Netscape (4.7 at least) you can use the ExecuteScript command,
and with MSIE, you can use the 'via dummy' mechanism.
The thing is that you are not obliged to use a framed site in MSIE
to use this trick because you can send imediate buttons to an hidden
Inline Frame (<IFRAME>). So it is more flexible than the 'old' via duumy.
The happy news is that messages are not scrambled in the MessageCallback
command, since there is no LiveConnect mechanism in MSIE...
The bad news is that rasmol scripts take more time to arrive to Chime.
But it still works... in my Internet Explorer 5.5 with windows 95.
Imagine a Protein Explorer with all the MSIE technologies!

However, here's the script that you have to add within your <HEAD></HEAD>:

<script language='javascript'>
function send_script(script,chime) {
if (navigator.appName.toLowerCase().indexOf("netscape") != -1 &&
4.0 <= parseFloat(navigator.appVersion)) {
setTimeout('document.' + chime + '.executeScript("' + script + '")',10)}
else {with (document.fr_dummy.document) {
write('<embed type="application/x-spt" hidden=true');
write(' width=10 height=10 button=push target="' + chime + '"');
writeln(' script="' + script + '" immediate=1>');}}}
</script>

Add also this line before </BODY> :

<IFRAME NAME="fr_dummy" ALIGN=TOP WIDTH=0 HEIGHT=0 VSPACE=0 HSPACE=0 SCROLLING=no></IFRAME>

You can send rasmol scripts with the javascript function send_script(script,chime)

Or you can add a link that will invoke your molecule.

<A HREF="javascript:send_script('select all;spacefill 1.5','chime_graphics')">Link</A>

----------------------
Jean-Philippe Demers
  --Boundary_(ID_zYxA7dJkducW7f4JwKfsKw)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Netscape 6 incompability etc. Date: Thu, 23 Nov 2000 12:05:26 +0100 To: rasmol@lists.umass.edu Dear List Members, Yes, and there are other problems with Netscape 6 too. A few days ago I installed it, and after experiencing with it 1-2 hours, I removed it completely in a hurry and returned to Netscape 4.7. My main reasons were: 1) The Chime problem you wrote; 2) Its speed is about 1/2 - 1/3 of the earlier 4.7 version on the same OS and hardware, concerning especially java plug-ins; the number of bells-and-whistles added does not compensate for this at all. 3) The program wants to work as a server on the PC and it is a very repugnant, unpleasent feature in my eyes, as this is a potential security leak: it could itself send data or do whatever it wants in my PC. It is question of taste, of course, but I would be more interested in advanced basic functions of the browser and not in the so called "advanced services" of Netcenter or AOL (but this does not belong to this forum...) Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Defective Books Date: Thu, 23 Nov 2000 09:52:15 -0500 To: pdb-l@rcsb.org, discuspv@usm.maine.edu, rasmol@lists.umass.edu Hi, Structure Folks! This is not list business, but may apply to many of you. An abortive first printing of my book, Crystallography Made Crystal Clear (2nd edition), resulted in 3000 copies having a few figures with missing lines. Although the publisher assured me that none of these copies were shipped, a few got out, mostly to Europe, it appears. Knowing that some new books go to your shelves for later reference, I suspect that other bad copies are out there, and you should check now to be sure your copy is OK. If you have a copy of CMCC 2nd edition. Take a look at Figure 2.13, p. 21. If the graphs of cosine functions are missing, you have one of those defective copies that did not get out. You can get a free replacement without having to live without your present copy. Tear off the cover and title page, try to track down your proof of purchase (if not, proceed anyway), and send them to Carmen Osteloza AP Customer Service Department 6277 Sea Harbor Drive Orlando FL, 32887 (1-800-321-5068) What to expect: Customer Service will sent a free, correct replacement copy of the book in 5-7 business days. Sorry for the inconvenience. In the meantime, see http://www.usm.maine.edu/~rhodes/FixCMCC/ for the affected figures. Also readers have kindly notified me of some typos and goofs in the second edition. They are collected at and http://www.usm.maine.edu/~rhodes/CMCC/text/Oops.html If there is a second printing, all of these errors will get fixed, or so the publisher tells me. ;-) Thanks for your heartwarming response to both editions of my little book. Cheers! ***************************** Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Damir Zucic Subject: Free_mol_visualization Date: Mon, 27 Nov 2000 13:31:40 +0100 To: rasmol@lists.umass.edu Hi everybody, I have made a list of freely available molecular visualization programs for unix and unix compatible platforms. The list contains links to 17 such programs (including RasMol, of course). It may be found at: http://pref.etfos.hr/garlic/competition/index.html Damir Zucic zucic@pref.etfos.hr ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0G4400L4QQMF4X@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Questions Date: Tue, 28 Nov 2000 13:20:15 -0500 To: rasmol@lists.umass.edu I am helping students do Chime tutorials for the first time this year (WinPC, Navigator 4.7). We have obtained much useful help from Eric's RasMol page, but we still have some questions. An example of one of our tutorials is here: http://www2.kenyon.edu/depts/biology/courses/biol63/transposase/Frames/ 1. How can we set it so that when someone reading the tutorial to the end "reloads," it reloads the original PDB file? (Instead, it keeps the final PDB called later in the tutorial.) 2. How can we make the first PDB appear already modified by a script? (I believe James Caras may have addressed this, but we still don't quite get it.) 3. Is it possible to start a script by specifying absolute coordinates, instead of "rotate"? Otherwise, if the reader has already rotated the molecule, it won't give the proper position. 4. How does one select a single atom or groups such as Phosphate (see tutorial above). We tried "Select P107" (based on the phosphorus identity shown in the Chime window) but it didn't work. 5. What are the commands for making labels? 6. Why do some of our buttons appear offset above the line of text? It only seems to look that way inside the frame. Any help with any of these would be appreciated. Thanks, Joan Slonczewski http://www2.kenyon.edu/depts/biology/slonc/slonc.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Questions Date: Tue, 28 Nov 2000 13:52:21 -0500 To: rasmol@lists.umass.edu Hi Joan, on 11.28.00 1:20 PM, Joan Slonczewski at slonczewski@kenyon.edu wrote: > I am helping students do Chime tutorials for the first time this year (WinPC, > Navigator 4.7). We have obtained much useful help from Eric's RasMol page, > but > we still have some questions. An example of one of our tutorials is here: > http://www2.kenyon.edu/depts/biology/courses/biol63/transposase/Frames/ > > 1. How can we set it so that when someone reading the tutorial to the end > "reloads," it reloads the original PDB file? (Instead, it keeps the final PDB > called later in the tutorial.) Not sure what you mean by this; reloading the page via the browser toolbar? > > 2. How can we make the first PDB appear already modified by a script? (I > believe James Caras may have addressed this, but we still don't quite get it.) In the EMBED tag that loads the plugin (your left frame document), include a SCRIPT string like this, with commands separated by semicolons: > > 3. Is it possible to start a script by specifying absolute coordinates, > instead > of "rotate"? Otherwise, if the reader has already rotated the molecule, it > won't give the proper position. If I understand your question, try this: If you preface your RTZ (rotate/translate/zoom) set with reset, it is sort of an absolute positioning system. The reset command returns the molecule to the default position (all zeros and zoom 100). For example: reset rotate x 30 translate y -3 zoom 143 > > 4. How does one select a single atom or groups such as Phosphate (see > tutorial > above). We tried "Select P107" (based on the phosphorus identity shown in the > Chime window) but it didn't work. For single atoms: select atomno=107 For groups of atoms, you have to be creative. To select all phosphorus atoms, use select phosphorus To select the phosphorus and oxygen atoms in a particular phosphate (i.e., the one that includes phosphorus 107), try the within command select atomno=107 or (oxygen and within(1.8,atomno=107)) or select them all by atomno (the most precise). There are other ways as well. You can only select groups of atoms that are defined by Chime/RasMol (i.e., protein, acidic, etc.), defined in the pdb file (many hetero groups are done this way - for example, hem in hemoglobin structures), or that you define yourself in a script; for example, define phosphate (atomno=107 or (oxygen and within(1.8,atomno=107))) > > 5. What are the commands for making labels? select atomno=107 label Phosphorus > > 6. Why do some of our buttons appear offset above the line of text? It only > seems to look that way inside the frame. This is an html issue and is related to alignment and button size. All of your buttons are aligned with the text on my Mac (11152x870 resolution). The Rasmol and Chime manuals, despite being incomplete, explain such things as within, define, select, and label fairly well. Good luck! Tim -- Timothy Driscoll molvisions.com - molecular visualization on the internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Questions Date: Wed, 29 Nov 2000 10:25:00 -0500 To: rasmol@lists.umass.edu, Joan Slonczewski snip >4. How does one select a single atom or groups such as Phosphate (see >tutorial above). We tried "Select P107" (based on the phosphorus identity >shown in the Chime window) but it didn't work. snip >Any help with any of these would be appreciated. Thanks, >Joan Slonczewski >http://www2.kenyon.edu/depts/biology/slonc/slonc.htm --------------------------------------------------------------- I found this web site usefull for learning about selecting http://www.umass.edu/microbio/rasmol/seleccmd.htm Another trick is to select the atoms manually by clicking. Change their color to somethin unique. Then use copy chime script and paste the script into a text editor and look for the select commands generated by chime. A problem with this method is that the select commands generated by this method are often very inefficient and a greater than sign > in the script is interpreted as an end of tag symbol if embedded in an HTML tag. todd carlson GVSU ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0G4400L4QQMF4X@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Questions Date: Wed, 29 Nov 2000 13:07:22 -0500 To: rasmol@lists.umass.edu At 11/28/2000, you wrote: >I am helping students do Chime tutorials for the first time this year (WinPC, >Navigator 4.7). We have obtained much useful help from Eric's RasMol page, but >we still have some questions. An example of one of our tutorials is here: >http://www2.kenyon.edu/depts/biology/courses/biol63/transposase/Frames/ You appear to be using a template introduced by David Marcey ca. 1996. For future work, I urge you to use a newer template such as the one downloadable from http://www.umass.edu/microbio/chime/prsswc/template because: - it has dynamic font size control, allowing text and color keys to be read from the back of a large lecture hall or by those with poor eyesight. - it has a utility menu on every page, e.g. for changing the background to white for printing, measuring distances, etc. Also you may be interested in my Chime presentation design guidelines at the above url. I also strongly recommend that each script begin by loading the molecule ('load xxxx.pdb'). This makes each button independent, so it always gives the same image. This allows the buttons to be pushed in any order. There is no speed disadvantage to reloading the same molecule over and over (unless the PDB file is larger than several megabytes). Chime has a built-in intelligence: when asked to load a molecule already loaded, it behaves as though the molecule were loaded but doesn't actually reload it (default is 'set load check on'). Even when different molecules are requested, if they have been loaded once previously in the session, they'll be reloaded quickly from the local cache. What my 1997-8 template cited above lacks is a command-line interface. My solution to this (and a number of other issues) is that I am building a template to allow presentations within Protein Explorer. This allows one to explore at will any image in a presentation, yet return back into the presentation seamlessly. I hope to have it available late this year or early next year (an alpha is available now if anyone wants to play with it -- contact me). >1. How can we set it so that when someone reading the tutorial to the end >"reloads," it reloads the original PDB file? (Instead, it keeps the final PDB >called later in the tutorial.) Reloading is probematic with Chime/javascript sites. I don't recommend it. Protein Explorer has a 'Reset' link that will restore the initial image. >2. How can we make the first PDB appear already modified by a script? (I >believe James Caras may have addressed this, but we still don't quite get it.) For your present template, Tim Driscoll's suggestion should work. The (in progress, not yet released) support for Presentations in Protein Explorer has a 'frontispiece' option for each page. By default, it shows the image for the first button when the page is entered. The remainder of your questions have already been given good answers by other subscribers to this list. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <0G4400L4QQMF4X@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: Questions Date: Wed, 29 Nov 2000 14:45:39 -0500 To: rasmol@lists.umass.edu Eric, Thanks for these suggestions. The "load" feature is helpful; I did not realize that it would avoid re-downloading the molecule. I tried to take a look at your URL, but it said "forbidden." Joan Eric Martz wrote: > At 11/28/2000, you wrote: > >I am helping students do Chime tutorials for the first time this year (WinPC, > >Navigator 4.7). We have obtained much useful help from Eric's RasMol > page, but > >we still have some questions. An example of one of our tutorials is here: > >http://www2.kenyon.edu/depts/biology/courses/biol63/transposase/Frames/ > > You appear to be using a template introduced by David Marcey ca. 1996. > For future work, I urge you to use a newer template such as the one > downloadable from > > http://www.umass.edu/microbio/chime/prsswc/template > because: > - it has dynamic font size control, allowing text and color keys to be read > from the back of a large lecture hall or by those with poor eyesight. > - it has a utility menu on every page, e.g. for changing the background to > white for printing, measuring distances, etc. > Also you may be interested in my Chime presentation design guidelines at > the above url. > > I also strongly recommend that each script begin by loading the molecule > ('load xxxx.pdb'). This makes each button independent, so it always gives > the same image. This allows the buttons to be pushed in any order. There is > no speed disadvantage to reloading the same molecule over and over (unless > the PDB file is larger than several megabytes). Chime has a built-in > intelligence: when asked to load a molecule already loaded, it behaves as > though the molecule were loaded but doesn't actually reload it (default is > 'set load check on'). Even when different molecules are requested, if they > have been loaded once previously in the session, they'll be reloaded > quickly from the local cache. > > What my 1997-8 template cited above lacks is a command-line interface. My > solution to this (and a number of other issues) is that I am building a > template to allow presentations within Protein Explorer. This allows one to > explore at will any image in a presentation, yet return back into the > presentation seamlessly. I hope to have it available late this year or > early next year (an alpha is available now if anyone wants to play with it > -- contact me). > > >1. How can we set it so that when someone reading the tutorial to the end > >"reloads," it reloads the original PDB file? (Instead, it keeps the final > PDB > >called later in the tutorial.) > > Reloading is probematic with Chime/javascript sites. I don't recommend it. > Protein Explorer has a 'Reset' link that will restore the initial image. > > >2. How can we make the first PDB appear already modified by a script? (I > >believe James Caras may have addressed this, but we still don't quite get > it.) > > For your present template, Tim Driscoll's suggestion should work. > > The (in progress, not yet released) support for Presentations in Protein > Explorer has a 'frontispiece' option for each page. By default, it shows > the image for the first button when the page is entered. > > The remainder of your questions have already been given good answers by > other subscribers to this list. > > -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://www.proteinexplorer.org > World Index of Chime Resources: http://molvis.sdsc.edu/visres > PDB Lite molecule finder: http://www.pdblite.org > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Questions Date: Wed, 29 Nov 2000 15:16:56 -0500 To: rasmol@lists.umass.edu In my previous message in this subject thread, the url I gave for the presentation template was incorrect (I left the .htm off the end). The correct one is below. -Eric http://www.umass.edu/microbio/chime/prsswc/template.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein explorer minor bug fix Date: Wed, 29 Nov 2000 15:52:54 -0500 To: rasmol@lists.umass.edu Version 1.72-Beta of Protein Explorer, downloadable since November 14, had a minor but annoying bug. It asks whether you want to stop spinning the molecule in 2 seconds, instead of the intended 30 seconds. The downloadable file protexpl.exe now has this fixed (and also the missing graphic for the upper right of the frontdoor page). If you want to fix it without upgrading your entire file set, just use Word or any text editor (Notepad, Wordpad, BBEdit) on the file protexpl/top_vars.js, search for 2000 in this file, and change it to 30000. The corrected line will be var spinStopDelayDefault = 30000; Then be sure to save the file as plain ASCII or MS-DOS text. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://www.proteinexplorer.org World Index of Chime Resources: http://molvis.sdsc.edu/visres PDB Lite molecule finder: http://www.pdblite.org 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: CRAIG Subject: Chime and IE 5.5 Date: Wed, 29 Nov 2000 18:23:11 -0500 (EST) To: rasmol@lists.umass.edu I realize that IE is not the best place to use chime, but I would still like to get it working on my system. I recently installed IE 5.5 and I cannot get chime to work at all. The pages I'm trying to look at work on IE 5.5 on other computers, so I don't think it's the page. I should mention that I used to have the Camsoft Chem3D plugin installed and all the chime windows would open in that (and not work properly of course). I removed the chem3D plugin and reinstalled Chime, but it still doesn't work. Thanks for your help. Paul Craig ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Lothar Esser Subject: rasmol crash (linux) Date: Fri, 01 Dec 2000 11:08:36 -0600 (CST) To: rasmol@lists.umass.edu Hi, this is the first time for me to post a message on this mailing list and the reason why I signed up was to seek a solution to those crashes of rasmol on our linux platforms. In the meantime I found a solution and I am still curious to know whether someone else had this problem. Whenever I center ( with center I mean a command like center *A and 120) a molecule so that part of it falls outside of the view port, that part is visible on the other side: In other words the part of the molecule that extends past the right border becomes visible on the left side. This is annoying but one could live with it if it remained stable. But it is not. It crashes with as Seg. fault after a few manipulations. It was impossible for me to find the exact source of the error even with gdb. Then I compiled rasmol with pgcc and it worked as it should. So the result of this long story is, that there is a glitch in gcc and one should use pgcc to compile rasmol. Regards, Lothar. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: rasmol crash (linux) Date: Fri, 01 Dec 2000 11:45:34 -0700 (MST) To: Lothar Esser Cc: rasmol@lists.umass.edu Hi Lothar, > gcc -v : > Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66/specs > gcc version egcs-2.91.66 19990314/Linux (egcs-1.1.2 release) > > Don't know actually whether it is the default compiler. > I need to ask our sys admin. Ok, thanks I'll make a note of this compiler version should anyone else report a crash under Linux. Its difficult to call a compiler that's 19 months old, out-of-date, but a great deal has changed in GCC since then. For example, the EGCS project finished, and the changes were reintegrated to GCC, the most recent stable release being gcc-2.95.2. Indeed the version of pgcc you tried is probably based on a more recent copy. My recommendation is to download and install "gcc-2.95.2". The reason I asked about versions, is that the GCC folks were very unhappy when RedHat recently included an "unstable" development version of GCC with RedHat 7.0. This reports itself as "2.96 (experimental)" and I was wondering whether this was the compiler that was misbehaving. http://gcc.gnu.org/gcc-2.96.html Some of my own benchmarks show that the current experimental snapshots of GCC generate code thats 5-15% faster on Pentium* PCs. But unlike RedHat, I'd recommend waiting to upgrade until the next stable release, gcc-3.0 (which is due out before the end of the month). Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ Office 104, 441 Greg Avenue, Tel: (+1) 505-954-3281 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Lothar Esser Subject: Re: rasmol crash (linux) Date: Fri, 01 Dec 2000 19:35:55 -0600 (CST) To: rasmol@lists.umass.edu On Fri, 1 Dec 2000, Roger Sayle wrote: > > > Ok, thanks I'll make a note of this compiler version should anyone else > report a crash under Linux. Its difficult to call a compiler that's 19 > months old, out-of-date, but a great deal has changed in GCC since then. > For example, the EGCS project finished, and the changes were reintegrated > to GCC, the most recent stable release being gcc-2.95.2. Indeed the > version of pgcc you tried is probably based on a more recent copy. > > My recommendation is to download and install "gcc-2.95.2". I installed gcc 2.95.2 and recomiled rasmol SAME PROBLEM ! Maybe someone should ask the folks at gcc.gnu.org to compile rasmol as a critical test for the gcc compiler ... So for now I stick with pgcc. I wonder however if someone has had the same problem. Best regards, Lothar. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id eB2Mq7W06273 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: World Index of Molecular Visualization Resources Expanded Date: Sat, 02 Dec 2000 17:57:43 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Cc: tkramer@hampshire.edu The World Index of Molecular Visualization Resources (http://molvisindex.org) is a visitor-maintained website. Visitors may submit website URL's with descriptions and cross-indexing terms. You need only fill out a short form; no password nor account is required. Once approved by the moderator, additions are immediately alphabetized into the title, subject, and author indices. Visitors may also request revisions or deletions of existing entries. Additions and revisions involve simply filling in a form. The indices are grouped into categories, and eleven new categories have now been added to the original two. The categories now include: -Biochemistry Tutorials in Chime, Ready-to-Use -Biochemistry Structure Visualization Tutorials (not in Chime) -Organic Chemistry Structure Visualization Tutorials (with or without Chime) -Inorganic/Crystal Structure Visualization Tutorials (with or without Chime) -K-12 Molecular Visualization Tutorials (with or without Chime) -How to create new tutorials with Chime -Deep View / Swiss-PDBViewer Resources -Molecules: Sources of PDB Files -Galleries of Molecular Images (static - no plugins required) -EMail Lists and Newsgroups on Molecular Visualization -Deutsch? ¿Español? Francais? Japanese? -Freeware for Molecular Visualization (other than Chime and Deep View) -Commerical Software for Molecular Visualization and Modeling Please visit the site and add resources not already listed. Comments on indexed resources are invited (experiences with use, lesson plans, praise or criticism). Suggestions for new categories are welcome. Please forward this message to authors of relevant websites. The Visitor-Maintained Indices (VMI) system was programmed by Trevor D. Kramer, and is implemented to be independent of content. If you are interested in setting up a VMI site on a different main topic, please contact me. The VMI support software is free for non-profit use. -- Eric Martz, Professor, Dept Microbiolgy, U Mass Amherst. -Protein Explorer: http://proteinexplorer.org -World Index of Molecular Visualization Resources (visitor-maintained) http://molvisindex.org -PDB Lite Search Interface: http://pdblite.org ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.139.109.227 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id eB32SvW07608 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: World Index of Molecular Visualization Resources Expanded Date: Sat, 02 Dec 2000 21:27:33 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Cc: tkramer@hampshire.edu We note with great interest that this new site claims that "Rasmol 2.7 ... contains several enhancements of interest to advanced users, but also more bugs than the earlier version." While we are aware of a small number of bug reports against version 2.7.1, we have not, until now been informed of there being "more bugs" in RasMol 2.7.1 than there are in 2.6b2. Since we are working on the next release, it would be particularly helpful if those who are aware of bugs in version 2.7.1 would be kind enough to report them, so that they can be fixed. Bug reports on the 2.7.2 test version are also appreciated. Since the term "freeware" causes confusion about the conditions necessary to protect open source software, we will not be listing the current releases of RasMol at the molvis site. Those interested in the most recent open source versions of RasMol are inviting to visit http://www.OpenRasMol.org. -- H. J. Bernstein At 17:57 -0500 12/2/00, Eric Martz wrote: >The World Index of Molecular Visualization Resources >(http://molvisindex.org) is a visitor-maintained website. Visitors may >submit website URL's with descriptions and cross-indexing terms. You need >only fill out a short form; no password nor account is required. Once >approved by the moderator, additions are immediately alphabetized into the >title, subject, and author indices. Visitors may also request revisions or >deletions of existing entries. Additions and revisions involve simply >filling in a form. > >The indices are grouped into categories, and eleven new categories >have now been added to the original two. The categories now include: > > -Biochemistry Tutorials in Chime, Ready-to-Use > -Biochemistry Structure Visualization Tutorials (not in Chime) > -Organic Chemistry Structure Visualization Tutorials (with or without >Chime) > -Inorganic/Crystal Structure Visualization Tutorials (with or without >Chime) > -K-12 Molecular Visualization Tutorials (with or without Chime) > -How to create new tutorials with Chime > > -Deep View / Swiss-PDBViewer Resources > > -Molecules: Sources of PDB Files > -Galleries of Molecular Images (static - no plugins required) > -EMail Lists and Newsgroups on Molecular Visualization > -Deutsch? ¿Español? Francais? Japanese? > > -Freeware for Molecular Visualization (other than Chime and Deep View) > -Commerical Software for Molecular Visualization and Modeling > >Please visit the site and add resources not already listed. Comments on >indexed resources are invited (experiences with use, lesson plans, praise or >criticism). Suggestions for new categories are welcome. Please forward this >message to authors of relevant websites. > >The Visitor-Maintained Indices (VMI) system was programmed by Trevor D. >Kramer, and is implemented to be independent of content. If you are >interested in setting up a VMI site on a different main topic, please >contact me. The VMI support software is free for non-profit use. > >-- >Eric Martz, Professor, Dept Microbiolgy, U Mass Amherst. >-Protein Explorer: http://proteinexplorer.org >-World Index of Molecular Visualization Resources (visitor-maintained) > http://molvisindex.org >-PDB Lite Search Interface: http://pdblite.org > ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- or what? User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: So RasMol isn't a Molecular Visualization Resource, or it isn't free, Date: Sun, 03 Dec 2000 11:35:29 -0500 To: rasmol@lists.umass.edu on 12.02.00 9:27 PM, Herbert J. Bernstein at yaya@bernstein-plus-sons.com wrote: > We note with great interest that this new site claims that "Rasmol 2.7 ... > contains > several enhancements of interest to advanced users, but also more bugs than > the earlier version." While we are aware of a small number of bug reports > against version 2.7.1, we have not, until now been informed of there being > "more bugs" in RasMol 2.7.1 than there are in > 2.6b2. Since we are working on the next release, it would be particularly > helpful > if those who are aware of bugs in version 2.7.1 would be kind enough to > report them, > so that they can be fixed. > > Bug reports on the 2.7.2 test version are also appreciated. > > Since the term "freeware" causes confusion about the conditions necessary > to protect open source software, we will not be listing the current > releases of RasMol at the molvis site. Those interested in the most recent > open source versions of RasMol are inviting to visit > http://www.OpenRasMol.org. > > > -- H. J. Bernstein > I have not encountered any bugs using the precompiled 32-bit RasMac 2.7.1 under Mac OS 9.0.4. I have not attempted to build it myself, nor have I tested 2.7 on any other platforms. RasMac 2.6b2 also gave me few problems (though it was not bug free). I do not make extensive use of RasMac, so I am not in a position to comment on the differences between 2.6 and 2.7. In the grand scheme it means little to me, but I think it's a shame that the RasMol developers have decided not to include it in the list of freeware molvis programs at molvisindex.org. This list appears to be very popular, especially in the academic community, and represents a serious effort to compile and annotate the great number of excellent molvis resources available on the Web. It is a great loss if RasMol, the parent of many of these resources, could not be considered among them. Maybe someone more enlightened than myself can explain the "confusion" about the term freeware, and especially how it pertains to this situation. I have never assumed that freeware programs were open source; in fact, none of the freeware that I use (except RasMol ) is open source. They are just programs that you don't have to pay to use. In that sense, RasMol is (in my estimation) freeware with the added bonus of being able to modify (if conditionally) the source code. I note that, to the best of my knowledge, none of the software packages listed at molvisindex.org even offers their source code for public download. And most do require an EULA that in some way limits distribution of the software, especially for commercial purposes (i.e., you can give it away but you can't sell it). So, how is RasMol different, except that the source code is easily available and thus needs explicit language describing it's proper use? And how does that difference preclude it from being listed among other molvis resources? -- Timothy Driscoll molvisions.com - molecular visualization on the internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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-- or it isn't free, or what? X-pair-Authenticated: 209.139.110.111 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: So RasMol isn't a Molecular Visualization Resource, Date: Sun, 03 Dec 2000 14:18:21 -0500 To: rasmol@lists.umass.edu The RasMol 2.7 series is freely available subject to open source conditions (see http://www.OpenRasMol.org/Copyright.html#Copying ) Unfortunately, some people seem to think that "freeware" implies that there are no restrictions on what can be done with the software, including, unfortunately, mistakenly thinking that it is always OK to make closed source versions out of freeware programs distributed with source. Since we very much want to keep the source of RasMol freely available, both for the current versions and for new versions, I have done everything I can to avoid confusion about RasMol's open source conditions. I would be happy to post a listing of the current releases of RasMol at molvisindex.org if there were an "Open Source Software for Molecular Visualization and Modeling" category, but at present the only choices seem to be "Freeware for Molecular Visualization (other than Chime and Deep View)" and "Commerical Software for Molecular Visualization and Modeling", neither one of which seems to be appropriate. Please pardon my caution. -- H. J. Bernstein At 11:35 -0500 12/3/00, Timothy Driscoll wrote: > ... >In the grand scheme it means little to me, but I think it's a shame that the >RasMol developers have decided not to include it in the list of freeware >molvis programs at molvisindex.org. This list appears to be very popular, >especially in the academic community, and represents a serious effort to >compile and annotate the great number of excellent molvis resources >available on the Web. It is a great loss if RasMol, the parent of many of >these resources, could not be considered among them. > >Maybe someone more enlightened than myself can explain the "confusion" about >the term freeware, and especially how it pertains to this situation. I have >never assumed that freeware programs were open source; in fact, none of the >freeware that I use (except RasMol ) is open source. They are just programs >that you don't have to pay to use. In that sense, RasMol is (in my >estimation) freeware with the added bonus of being able to modify (if >conditionally) the source code. I note that, to the best of my knowledge, >none of the software packages listed at molvisindex.org even offers their >source code for public download. And most do require an EULA that in some >way limits distribution of the software, especially for commercial purposes >(i.e., you can give it away but you can't sell it). > >So, how is RasMol different, except that the source code is easily available >and thus needs explicit language describing it's proper use? And how does >that difference preclude it from being listed among other molvis resources? > ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- or it isn't free, or what? User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: So RasMol isn't a Molecular Visualization Resource, Date: Sun, 03 Dec 2000 14:53:30 -0500 To: rasmol@lists.umass.edu on 12.03.00 2:18 PM, Herbert J. Bernstein at yaya@bernstein-plus-sons.com wrote: > The RasMol 2.7 series is freely available subject to open source conditions > (see http://www.OpenRasMol.org/Copyright.html#Copying ) > > Unfortunately, some people seem to think that "freeware" implies that there > are no restrictions on what can be done with the software, including, > unfortunately, mistakenly thinking that it is always OK to make closed > source versions out of freeware programs distributed with source. > > Since we very much want to keep the source of RasMol freely available, both > for the current versions and for new versions, I have done everything I can > to avoid confusion about RasMol's open source conditions. I would be happy > to post a listing of the current releases of RasMol at molvisindex.org if > there were an "Open Source Software for Molecular Visualization and > Modeling" category, but at present the only choices seem to be "Freeware > for Molecular Visualization (other than Chime and Deep View)" and > "Commerical Software for Molecular Visualization and Modeling", neither one > of which seems to be appropriate. > > Please pardon my caution. > > -- H. J. Bernstein > > Caution is understandable; however, I am strongly in favor of allowing as many teachers, students, and informed laypeople to use RasMol as possible. As a result, I would like to see RasMol get the widest possible distribution and be included on all relevant indices of such software. It is very clear from your Web site about the restrictions placed on the use of the 2.7 source code, and that should be enough to discourage the evil programmers out to steal great code and make a buck. But of course, that is just my opinion and not really relevant here - it's not my software. So how about a compromise: Rather than create a whole new section on molvisindex.org just for RasMol, what if we convince Eric to change the category name to something more encompassing, say "Free Molecular Visualization and Modeling Software" (BTW Chime and SPDV are included in the category, despite the current category name)? That would remove the word Freeware and its implications, but still indicate that the software doesn't cost anything (at least, not money). Plus it would make the Index more complete and allow RasMol to reach a potentially larger audience. -- Timothy Driscoll molvisions.com - molecular visualization on the internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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: Wayne Decatur Subject: Chime-based tutorial on the Large Ribosomal Subunit Date: Sun, 03 Dec 2000 12:44:40 -0800 (PST) To: rasmol@lists.umass.edu Hello, I'd like to announce the Beta version of the Chime-based tour of the Large Ribosomal Subunit. Fitting the grand achievement by the Steitz lab this year, the full tour is rather extensive and explores many exciting facets of this massive structure. Although the crystal structure is from an Archaeal ribosome, the conserved nature of the ribosome assures that it will appeal to anyone interested in translation. One of the strengths of the Biochemistry and Molecular Biology Department at the University of Massachusetts at Amherst is that has several prominent labs working on aspects of the ribosome. As an outgrowth of several UMASS Amherst molecular biology journal club presentations discussing the Nature papers on the subunit structure, the tour took shape with input from several labs and technical guidance from Eric Martz and others. Unfortunately because the structure is so large it takes a bit more time than you are probably used to in order to download and generate the image so patience (and a non-modem internet connection) is needed. I'm calling it the Beta version because it hasn't had much user testing beyond a handful of people, but a lot of development time was spent before announcing it here and so there shouldn't be many errors. Another reason for calling it the beta version is that it currently is hosted on my much neglected UNIX account webpage; it will eventually be hosted at the webpage of Maurille 'Skip' Fournier's lab, of which I'm a member. But don't worry, I'll leave a redirection link when that finally happens. For non-Netscape Communicator(Navigator) users there is also a sample tour with a few of the key images from the full tour, but unfortuantely, as far as I know even the sample tour does not work for Internet Explorer on Mac. I hope you'll check it out and let me know what you think. Thanks, Wayne Decatur ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne Decatur Subject: Chime-based tutorial on the Large Ribosomal Subunit Date: Sun, 03 Dec 2000 12:45:56 -0800 (PST) To: rasmol@lists.umass.edu Hello, I'd like to announce the Beta version of the Chime-based tour of the Large Ribosomal Subunit. Fitting the grand achievement by the Steitz lab this year, the full tour is rather extensive and explores many exciting facets of this massive structure. Although the crystal structure is from an Archaeal ribosome, the conserved nature of the ribosome assures that it will appeal to anyone interested in translation. One of the strengths of the Biochemistry and Molecular Biology Department at the University of Massachusetts at Amherst is that has several prominent labs working on aspects of the ribosome. As an outgrowth of several UMASS Amherst molecular biology journal club presentations discussing the Nature papers on the subunit structure, the tour took shape with input from several labs and technical guidance from Eric Martz and others. Unfortunately because the structure is so large it takes a bit more time than you are probably used to in order to download and generate the image so patience (and a non-modem internet connection) is needed. I'm calling it the Beta version because it hasn't had much user testing beyond a handful of people, but a lot of development time was spent before announcing it here and so there shouldn't be many errors. Another reason for calling it the beta version is that it currently is hosted on my much neglected UNIX account webpage; it will eventually be hosted at the webpage of Maurille 'Skip' Fournier's lab, of which I'm a member. But don't worry, I'll leave a redirection link when that finally happens. For non-Netscape Communicator(Navigator) users there is also a sample tour with a few of the key images from the full tour, but unfortuantely, as far as I know even the sample tour does not work for Internet Explorer on Mac. I hope you'll check it out and let me know what you think. The address is: http://www-unix.oit.umass.edu/~wdecatur/ribosome/index.htm Thanks, Wayne Decatur ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- or it isn't free, or what? X-pair-Authenticated: 209.139.109.85 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: So RasMol isn't a Molecular Visualization Resource, Date: Sun, 03 Dec 2000 16:11:41 -0500 To: rasmol@lists.umass.edu At 14:53 -0500 12/3/00, Timothy Driscoll wrote: ... >So how about a compromise: Rather than create a whole new section on >molvisindex.org just for RasMol, what if we convince Eric to change the >category name to something more encompassing, say "Free Molecular >Visualization and Modeling Software" (BTW Chime and SPDV are included in the >category, despite the current category name)? That would remove the word >Freeware and its implications, but still indicate that the software doesn't >cost anything (at least, not money). Plus it would make the Index more >complete and allow RasMol to reach a potentially larger audience. > Naturally, the decision on such a change would have to be made by Eric Martz, but it sounds quite sensible to me, and I would be prepared to list the open source versions of RasMol under such a heading. -- HJB ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol 2.7 bug/crash survey Date: Mon, 04 Dec 2000 10:33:07 -0500 To: rasmol@lists.umass.edu As a followup to Herb Bernstein's request for bug reports for Open Source RasMol, I would like to hear from anyone who has used the Windows version of RasMol 2.7.1 or 2.7.2 (RasWin) extensively, whether or not you ran into bugs. If you found no serious bugs, that is important -- please send messages to me (emartz@microbio.umass.edu cc: to yaya@bernstein-plus-sons.com) and I'll summarize the results to the list. My statement in the World Index that RasMol 2.7 has more bugs than 2.6-beta-2a is based on very limited testing, and may be obsolete. On several occasions, I tried to use RasWin 2.7 and on each occasion, it crashed within a few minutes. I reported these bugs to Herb, but because of the instability, and because I did not need the new features, I stopped trying to use 2.7. Since then, on the rare occasions when I need RasWin I have used 2.6-beta-2a. (I use RasWin primarily for saving subsets of atoms with the nearby hetero atoms, for use in Chime and Protein Explorer.) These experiences with crashes were quite a while ago. So if more recent releases are stable and reliable, I'd like to know and I'll remove the "more bugs" statement in the World Index. Although I am primarily interested in the RasWin binaries (because those are the ones that I saw crash), we'd also like to hear from users of RasMac and linux compilations. Be sure to tell me what VERSION NUMBER you are reporting on. If bugs caused you to abandon 2.7, we don't require details of what the bugs were for this survey. However if you do have details of what operations led to a crash, please include them so the next release can be fixed! Remember to copy your message to to yaya@bernstein-plus-sons.com Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org 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-- or it isn't free, or what? References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: So RasMol isn't a Molecular Visualization Resource, Date: Mon, 04 Dec 2000 11:13:10 -0500 To: rasmol@lists.umass.edu Thanks to Tim Driscoll for suggesting a compromise wording for the former "Freeware" category in molvisindex.org I have implemented the changes, and also added a specific caution about the strict meaning of "Open Source". If you see the word "freeware" anywhere, Shift-Reload or clear the cache in your browser. Herb, please submit openrasmol.org to molvisindex.org -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- or it isn't free, or what? ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: So RasMol isn't a Molecular Visualization Resource, Date: Mon, 04 Dec 2000 16:37:45 -0500 (EST) To: rasmol@lists.umass.edu Done. -- HJB ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Mon, 4 Dec 2000, Eric Martz wrote: > Thanks to Tim Driscoll for suggesting a compromise wording for the former > "Freeware" category in molvisindex.org > > I have implemented the changes, and also added a specific caution about the > strict meaning of "Open Source". If you see the word "freeware" anywhere, > Shift-Reload or clear the cache in your browser. > > Herb, please submit openrasmol.org to molvisindex.org > > -Eric > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 boundary="Boundary_(ID_jsGxq6FLmGKHWtCz2D/rvA)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop bug Date: Tue, 28 Nov 2000 04:26:40 -0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_jsGxq6FLmGKHWtCz2D/rvA) Many of you tried RasTop and got the rather mystic message: "missing MFC42.DLL:6605". Thanks to the help of Michael Wilson from the University of Oxford, you can get RasTop working by installing an updated mfc42.dll file in the folder containing the rastop.exe file (only this folder). You can obtain a recent version of mfc42.dll either on another PC (the version number should start by a number 6, each PC has one copy of mfc42.dll in the C:\WINDOWS\SYSTEM folder) or by direct request to myself (valadon@ix.netcom.com). Microsoft allows the redistribution of mfc42.dll with software using mfcs, so you will not break the law! RasTop develops a user-friendly graphical interface around rasmol (version 2.6.4 and 2.7.1) and runs on Windows platforms 95, 98, and NT. RasTop is available for download on the rasmol opensource site at http://www.OpenRasMol.org. Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com --Boundary_(ID_jsGxq6FLmGKHWtCz2D/rvA)

 
Many of you tried RasTop and got the rather mystic message: "missing MFC42.DLL:6605".  Thanks to the help of Michael Wilson from the University of Oxford, you can get RasTop working by installing an updated mfc42.dll file in the folder containing the rastop.exe file (only this folder). You can obtain a recent version of mfc42.dll either on another PC (the version number should start by a number 6, each PC has one copy of mfc42.dll in the C:\WINDOWS\SYSTEM folder) or by direct request to myself (valadon@ix.netcom.com).  Microsoft allows the redistribution of mfc42.dll with software using mfcs, so you will not break the law!
 
RasTop develops a user-friendly graphical interface around rasmol (version 2.6.4 and 2.7.1) and runs on Windows platforms 95, 98, and NT. RasTop is available for download on the rasmol opensource site at http://www.OpenRasMol.org.
 
Philippe
 
---------------------------
   *** RasTop ***  
---------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA.
valadon@ix.netcom.com
 
--Boundary_(ID_jsGxq6FLmGKHWtCz2D/rvA)-- X-PMrqc: 1 References: <0G5100KOLWRJT9@supai.oit.umass.edu> X-MIME-Autoconverted: from Quoted-printable to 8bit by marlin.bio.umass.edu id eB5B96W27227 ++++------+------+------+------+------+------+------+------+------+------+ From: Enrique Castro Subject: Problem with font in RasTop Command Panel Date: Tue, 05 Dec 2000 11:04:47 +0000 To: rasmol@lists.umass.edu Hello: I am experiencing a small but annoying problem with RasTop 1.3 in Win95 (I got the precompiled binary). The Command Panel appears in screen writen in english bur with GREEK characters. I suppose this is not intended, but I do not figure how to change this font. Any help? Thanks in advance Enrique #################################################### Enrique Castro Dept. Bioquímica, Biología Molecular y Fisioloía Universidad de Las Palmas de Gran Canaria (ULPGC) Facultad de Ciencias de la Salud c/ Doctor Pasteur s/n 35016 Las Palmas, Spain Tel: (34) 928 45 87 90 Fax: (34) 928 45 14 41 e-mail: ecastro@cicei.ulpgc.es ##################################################### ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-WebMail-UserID: tsygan X-EXP32-SerialNo: 00003214 ++++------+------+------+------+------+------+------+------+------+------+ From: tsygan Subject: RCPT: Problem with font in RasTop Command Panel Date: Tue, 05 Dec 2000 15:04:25 +0300 To: rasmol@lists.umass.edu *** Confirmation of Registered Mail *** Your message sent to tsygan has been read. Return Receipt Notification --------------------------- Hello: I am experiencing a small but annoying problem with RasTop 1.3 in Win95 (I got the precompiled binary). The Command Panel appears in screen writen in english bur with GREEK characters. I suppose this is not intended, but I do not figure how to change this font. Any help? Thanks in advance ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: es-AR, es, en ++++------+------+------+------+------+------+------+------+------+------+ From: Davinci Subject: RasMol in Spanish and exporting images Date: Tue, 05 Dec 2000 05:32:08 -0300 To: "rasmol@lists.umass.edu" Dear Rasmolers, I have traslated to Spanish the graphical menus and "terminal" messages in Rasmol Unix Version using Slackware Linux and Sawfish/Gnome Windows Manager (The original RasMol compilated version don't work using KDE 2 in my PC). I can send the "translated source files" (or complete src directory) to somebody (like Eric or Herbert) to post in somewhere. Unfortunately, I can't translate the script commands due to: first, I dont know too many C/C++; second, the possible scripts written using Spanish RasMol will not be compatible with an English RasMol, and the end user should need a "translator script". Besides, I have some troubles to export gif and bmp images using 8 or 16 bit (Linux) Rasmol. When I want to export a image, I receive the following message: Output Error: Only 8-bit GIF (or BMP) files supported. And when I want to export the image in Postcript format, the resolution is too poor. Do I need to recompilate the Rasmol using another options? Regards, ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0G3C00IMOOUJD4@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: hiding a chain Date: Tue, 05 Dec 2000 10:28:27 -0500 To: rasmol@lists.umass.edu My students using Chime are trying to hide one of three chains in a PDB file: http://www2.kenyon.edu/depts/biology/courses/biol63/CopG/FRAMES/index.htm We find that chain C can be hidden using "transparent," but if we try to hide chain B as well, it only turns black, and the black part obscures part of chain A as it turns. Any suggestions? Thanks a lot for the other help we've gotten--the whole class has benefited from this, and the students are really excited about it. Joan Slonczewski http://www2.kenyon.edu/depts/biology/slonc/slonc.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0G3C00IMOOUJD4@supai.oit.umass.edu> <3A2D099B.D15C5790@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: hiding a chain Date: Tue, 05 Dec 2000 12:00:18 -0500 To: rasmol@lists.umass.edu > >We find that chain C can be hidden using "transparent," but if we try to hide >chain B as well, it only turns black, and the black part obscures part of >chain A as it turns. Any suggestions? Since you have the chain initially displayed as a ribbon, the commands select :b ribbon off should do the trick, unless I am missing your point. Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures Phone: (413) 253-2405 http://www.MoleculesInMotion.com Fax: (612) 397-9975 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: hiding a chain Date: Tue, 05 Dec 2000 12:14:01 -0500 To: rasmol@lists.umass.edu on 12.05.00 10:28 AM, Joan Slonczewski at slonczewski@kenyon.edu wrote: > My students using Chime are trying to hide one of three chains in a PDB file: > http://www2.kenyon.edu/depts/biology/courses/biol63/CopG/FRAMES/index.htm > > We find that chain C can be hidden using "transparent," but if we try to hide > chain B as well, it only turns black, and the black part obscures part of > chain A as it turns. Any suggestions? > > Thanks a lot for the other help we've gotten--the whole class has benefited > from this, and the students are really excited about it. > Joan Slonczewski > http://www2.kenyon.edu/depts/biology/slonc/slonc.htm > > > Hi Joan, Try this from the MDL Chime menu: Select/Chain/C Select/Hide/Hide Selected Select/Chain/B Select/Hide/Hide Selected OR, from a command line interface, you can use the restrict command: restrict not :c # hides chain C restrict not (:c or :b) # hides both chains B and C Hope that helps! -- Timothy Driscoll molvisions.com - molecular visualization on the internet http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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: Filling out crystal unit cells, etc. Date: Tue, 05 Dec 2000 14:45:16 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org, discuspv@USM.MAINE.EDU Is there a website where one can submit a PDB file or code, and get back a PDB file with the unit cell, or multiple unit cells, filled out using crystallographic symmetry operations? What I'm interested in is being able to examine all the crystallographic contacts to a given chain. I am aware that this can be done with Deep View (Swiss-PDBViewer), but I'm hoping for an even faster and more convenient on-line solution for those who don't wish to spend the time to learn how to use Deep View. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.139.110.69 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol in Spanish and exporting images Date: Tue, 05 Dec 2000 19:30:32 -0500 To: rasmol@lists.umass.edu I would be delighted to have the sources of the Spanish version to add to the OpenRasMol web page. If I am given a list of English vs Spanish for the various script commands, I will be happy to add those options to the next release, so that both Spanish and English scripts would work. I think multilingual versions of RasMol would be a great service to the community, and Roger's structure for parsing commands makes it fairly inexpensive to implement. I will try to improve the bit-dependence of the GIF interface and look into the Postscript issue. Roger and I discussed possible solutions this past summer. -- H. J. Bernstein At 5:32 -0300 12/5/00, Davinci wrote: >Dear Rasmolers, > >I have traslated to Spanish the graphical menus and "terminal" messages >in Rasmol Unix Version using Slackware Linux and Sawfish/Gnome Windows >Manager (The original RasMol compilated version don't work using KDE 2 >in my PC). I can send the "translated source files" (or complete src >directory) to somebody (like Eric or Herbert) to post in somewhere. >Unfortunately, I can't translate the script commands due to: first, I >dont know too many C/C++; second, the possible scripts written using >Spanish RasMol will not be compatible with an English RasMol, and the >end user should need a "translator script". > >Besides, I have some troubles to export gif and bmp images using 8 or 16 >bit (Linux) Rasmol. When I want to export a image, I receive the >following message: > >Output Error: Only 8-bit GIF (or BMP) files supported. > >And when I want to export the image in Postcript format, the resolution >is too poor. Do I need to recompilate the Rasmol using another options? >Regards, > ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: es-AR, es, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Davinci Subject: Re: RasMol in Spanish and exporting images Date: Tue, 05 Dec 2000 16:22:03 -0300 To: rasmol@lists.umass.edu Dear Herbert, No problem, I can send a translated command list to avoid incompatibilities inter-languages in "external scripts", and the error and messages for the terminal. Regards, "Herbert J. Bernstein" wrote: > I would be delighted to have the sources of the Spanish version to add to > the OpenRasMol web page. If I am given a list of English vs Spanish for the > various script commands, I will be happy to add those options to the next > release, so that both Spanish and English scripts would work. > > I think multilingual versions of RasMol would be a great service to the > community, and Roger's structure for parsing commands makes it fairly > inexpensive to implement. > > I will try to improve the bit-dependence of the GIF interface and look into > the Postscript issue. Roger and I discussed possible solutions this past > summer. > -- H. J. Bernstein ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Rasmol versions in French Date: Wed, 06 Dec 2000 10:58:29 -0500 To: rasmol@lists.umass.edu >A French version of the short user interface and the GUI detailed menu >(Rasmenu) attached to the version 2.6 of Rasmol for Windows is available. >Sources may be transmitted immediately to H. J. Bernstein if suitable. > >We have also submitted to Philippe Valadon the idea of a French user >interface for the Windows version of RasTop 1.3 based on Rasmol 2.7.1= > version. > > >Naoum Salame >Institut National de Recherche Pedagogique >91, rue Gabriel P=E9ri, 92120 MONTROUGE, FRANCE >Tel.: (033) 1 46128712 ; Fax : (033) 1 46128701 ; email : salame@inrp.fr >Site Biogeo : http://www.inrp.fr/Acces/Biogeo/accueil.htm >Site Biotic : http://www.inrp.fr/Acces/biotic/accueil.htm > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.139.110.235 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Rasmol versions in French Date: Wed, 06 Dec 2000 11:25:45 -0500 To: rasmol@lists.umass.edu I will be delighted if we can get a French translation list for as many commands and menu items in RasMol as possible, and will be happy to incorporate them into RasMol along with the Spanish translations we hope to be able to include. We, as a community, owe a great debt to those who are taking the time and trouble to create these translation lists. Those who are familiar with RasMol and with other languages who wish to make a similar effort would find their contributions equally welcome. To avoid confusion on markup for special characters, if any characters not in, ASCII, the US national variant if the 7-bit ISO character set are used please specify which national variant of the ISO character set is being used, and please also provide the appropriate HTML "character references" or HTML "entity references" for any special characters used. There is no time limit for such contributions. They will be welcome whenever they are ready. -- H. J. Bernstein At 10:58 -0500 12/6/00, Eric Martz wrote: >>A French version of the short user interface and the GUI detailed menu >>(Rasmenu) attached to the version 2.6 of Rasmol for Windows is available. >>Sources may be transmitted immediately to H. J. Bernstein if suitable. >> >>We have also submitted to Philippe Valadon the idea of a French user >>interface for the Windows version of RasTop 1.3 based on Rasmol 2.7.1= >> version. >> >> >>Naoum Salame >>Institut National de Recherche Pedagogique >>91, rue Gabriel P=E9ri, 92120 MONTROUGE, FRANCE >>Tel.: (033) 1 46128712 ; Fax : (033) 1 46128701 ; email : salame@inrp.fr >>Site Biogeo : http://www.inrp.fr/Acces/Biogeo/accueil.htm >>Site Biotic : http://www.inrp.fr/Acces/biotic/accueil.htm >> > ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Frank Margolis Subject: NMR data into Protein Explorer Date: Fri, 08 Dec 2000 11:18:33 -0400 To: rasmol@lists.umass.edu I am a new user of Protein Explorer and have been downloading NMR data as a .pdb file from EXPLORE into Protein Explorer. I am running Protein Explorer downloaded from Netscape onto a Mac G4. The problem is that identification of helices and strands that is unambigous when my collaborators use other programs to look at this file do not appear in Protein Explorer. This raises two questions-1) what am I doing wrong and 2) can I assign structure residue by residue and if so how? Thanks Frank Frank L. Margolis Ph.D. Professor Department of Anatomy and Neurobiology HSF280 University of Maryland School of Medicine 685 West Baltimore Street Baltimore MD 21201 phone 410-706-8913/4 fax 410-706-2512 fmargoli@umaryland.edu http://neurobiology.umaryland.edu/ http://neuroscience.umaryland.edu/ "Any sufficiently advanced technology is indistinguishable from magic" Arthur C. Clarke ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: NMR data into Protein Explorer Date: Fri, 08 Dec 2000 12:37:20 -0500 To: rasmol@lists.umass.edu At 12/08/2000, Frank Margolis wrote: >I am a new user of Protein Explorer and have been downloading NMR >data as a .pdb file from EXPLORE into Protein Explorer. I am running >Protein Explorer downloaded from Netscape onto a Mac G4. The problem >is that identification of helices and strands that is unambigous when >my collaborators use other programs to look at this file do not >appear in Protein Explorer. This raises two questions-1) what am I >doing wrong and 2) can I assign structure residue by residue and if >so how? Currently, PE depends on Chime's built-in secondary structure capabilities, which were inherited from RasMol. These capabilities are explained in the QuickViews help, when you click Structure on the COLOR menu: BEGIN QUOTE Color by Structure: Often the authors of the PDB file designate ranges of residues with HELIX, SHEET and TURN records, in which case the molecule will be colored accordingly. In this case entering the command si reports 'Secondary Structure .. PDB Data Records'. If the PDB file does not specify secondary structure, Chime uses an optimized Kabsch & Sander algorithm to assign secondary structure. In this case, the 'show info' report says 'Secondary Structure . Calculated'. Even when the PDB file authors have specified secondary structure, you can force Chime to ignore the PDB-specified secondary structure with the command 'structure', after which you need to re-apply 'COLOR, Structure' and 'DISPLAY, Cartoon'. END QUOTE By now I presume you've figured out that QuickViews works only on model 1 in an NMR ensemble. Also, FirstView shows only model 1. But if you check "expert" in the preferences, then the first view shows all models. NMR ensembles are best handled with the NMR Model Selection page in Advanced Explorer, and with manually entered commands. The HELIX, SHEET, TURN records apply to all models. The 'structure' command assigns a different secondary structure to each model. This can be nicely demonstrated with 1TOR (only 75K, 5 models). It also works in a larger file such as 1CFC. I've noticed that it doesn't work in 1JSA and I haven't figured out why. Some PDB files contain only alpha carbon atoms, and for these, of course, the 'structure' command doesn't work. But this doesn't explain the 1JSA case. Frank, if there's something about your NMR file that doesn't square with the above, send me the NMR file in question, I'll take a look at it. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org 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: Lothar Esser Subject: more depth-cue ? Date: Sun, 10 Dec 2000 20:57:44 -0600 (CST) To: rasmol@lists.umass.edu Hi, I was just wondering if there is a parameter in rasmol that allows me to increase the effect of depth-cueing. It seems to me that there is some but at best very little depth-cue in the 32bit Linux version that I use and I would really like to enhance the effect. I have not used rasmol on sgi machines lately but I think I remember that it showed more depth-cueing. I could not find anything in the documentation (rasmol.hlp) and all I did was to play around with set ambient which had ( quite understandably ) no effect on depth-cueing but seemed somehow related. Also turning on backfade or off had no effect on my machine. Has anyone got an idea ? Am I missing something obvious ? Thanks, Lothar ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: more depth-cue ? Date: Sun, 10 Dec 2000 22:02:14 -0700 (MST) To: Lothar Esser Cc: rasmol@lists.umass.edu Hi Lothar, > I was just wondering if there is a parameter in rasmol that allows me > to increase the effect of depth-cueing. It seems to me that there is some > but at best very little depth-cue in the 32bit Linux version that I use > and I would really like to enhance the effect. I have not used rasmol on > sgi machines lately but I think I remember that it showed more > depth-cueing. I could not find anything in the documentation (rasmol.hlp) > and all I did was to play around with set ambient which had ( quite > understandably ) no effect on depth-cueing but seemed somehow related. > Also turning on backfade or off had no effect on my machine. Mysteriously, the "set ambient" command is the correct way to adjust depth cueing in RasMol and Chime. The command "set ambient 100" disables depth-cueing, and "set ambient 0" enables maximum contrast depth-cueing of wireframe images. There are however a few caveats, hints and tricks. The first is that unlike many OpenGL programs, RasMol does not perform depth-cueing on solid surfaces, such as spheres, cylinders or cartoons. Therefore its only wireframe and ribbons representations that are affected, and solids get darker self-shadowing. The second is that the bounds for depth-cueing are taken from the bounding box of the initial molecule. When a molecule is first loaded, an approximate radius is determined such that atoms right at the back appear darkest and those at he very front lightest. This means that restricting the view to a single amino acid in a large protein will result in poor depth-cueing. The answer is to write out the single amino acid to a file and load just that. Now the hither-and-yon distances are reset, resulting in much better depth-cueing. Finally, the backfade parameter is only effective when the background color is not black. Consider preparing an image for publication, with a blue wireframe on a white background. The desired effect is for wireframe to fade to white, not black, further from the viewer. This is achieved with the "set backfade true" command and gives the impression similar to the molecule emerging from a fog. Unfortunately, this has psycedelic Warholesque side effects when also displaying solids such as spheres, cylinders or cartoons. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ Office 104, 441 Greg Avenue, Tel: (+1) 505-954-3281 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Lothar Esser Subject: Re: more depth-cue ? Date: Mon, 11 Dec 2000 12:17:49 -0600 (CST) To: Roger Sayle Cc: rasmol@lists.umass.edu On Sun, 10 Dec 2000, Roger Sayle wrote: Hello, > > Mysteriously, the "set ambient" command is the correct way to adjust > depth cueing in RasMol and Chime. The command "set ambient 100" disables > depth-cueing, and "set ambient 0" enables maximum contrast depth-cueing > of wireframe images. Okay, I never tried set ambient 0 but stopped at about 10. In addition most of the time I used cpk models to better see depth-cue effects but this was all wrong as you pointed out. > There are however a few caveats, hints and tricks. The first is that > unlike many OpenGL programs, RasMol does not perform depth-cueing on solid > surfaces, such as spheres, cylinders or cartoons. Therefore its only > wireframe and ribbons representations that are affected, and solids get > darker self-shadowing. > > The second is that the bounds for depth-cueing are taken from the bounding > box of the initial molecule. When a molecule is first loaded, an > approximate radius is determined such that atoms right at the back appear > darkest and those at he very front lightest. This means that restricting > the view to a single amino acid in a large protein will result in poor > depth-cueing. The answer is to write out the single amino acid to a file > and load just that. Now the hither-and-yon distances are reset, resulting > in much better depth-cueing. > It really seems that depthcue works only on plain wireframe objects. Even objects created with wireframe 0.08 show no more deptcuing. They do get somewhat darker but there is not gradient as far as I can tell. Is this a correct observation ? Would it be a very large task to implement depthcuing for all objects ? In OpenGL it is a function you can turn on ( FOG ) and of course you have a performance hit but it is hardly noticeable on modern computers. The point is I guess that people have become used to it and it makes it easier to get a 3D impression of an object. So on my wish list would be depthcuing with the possibility to change near and far boundaries so that the user can adjust the level of depthcuing. One other question. I loaded a big pdb file that contained a few superimposed molecules and rasmol stopped with the message ( hope I remember it correctly ) : Database Error too many new residues. So I recompiled rasmol with MAXRES 300 and it worked. I am just not sure whether this was the right thing to do. What puzzles me is that my molecule contains far more than 300 residues in about 260 models ! Thanks for the advice ... Lothar. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-PMrqc: 1 X-MIME-Autoconverted: from Quoted-printable to 8bit by marlin.bio.umass.edu id eBDAlBW17096 ++++------+------+------+------+------+------+------+------+------+------+ From: Enrique Castro Subject: Re: RasTop problem Date: Wed, 13 Dec 2000 10:42:39 +0000 To: rasmol@lists.umass.edu Dear Philippe: Many thanks for sending a replacement for RasTop.exe. I am sorry for the delay in answering. I have been very busy with teaching. Now I have tested the RasTop.exe file you sent (585 728 bytes, 28/11/2000), but I have the same problem: the command panel (only this) is displayed with greek characters. This is not a fix. I am using Win95, (4.00.950b), with MS-office. I have also Rasmol 271. rastop is installed in a subdir of Rasmol 271. Thanks for you time #################################################### Enrique Castro Dept. Bioquímica, Biología Molecular y Fisioloía Universidad de Las Palmas de Gran Canaria (ULPGC) Facultad de Ciencias de la Salud c/ Doctor Pasteur s/n 35016 Las Palmas, Spain Tel: (34) 928 45 87 90 Fax: (34) 928 45 14 41 e-mail: ecastro@cicei.ulpgc.es ##################################################### ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-PMrqc: 1 X-MIME-Autoconverted: from Quoted-printable to 8bit by marlin.bio.umass.edu id eBDAlOW17107 ++++------+------+------+------+------+------+------+------+------+------+ From: Enrique Castro Subject: Re: RasTop bug Date: Wed, 13 Dec 2000 10:42:59 +0000 To: rasmol@lists.umass.edu Date sent: Tue, 28 Nov 2000 04:26:40 -0800 Send reply to: rasmol@lists.umass.edu From: Philippe Subject: RasTop bug To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_yo5FlbC+xgNp+EncaEEm8g) Many of you tried RasTop and got the rather mystic message: "missing MFC42.DLL:6605". Thanks to the help of Michael Wilson from the University of Oxford, you can get RasTop working by installing an updated mfc42.dll file in the folder containing the rastop.exe file (only this folder). You can obtain a recent version of mfc42.dll either on another PC (the version number should start by a number 6, each PC has one copy of mfc42.dll in the C:\WINDOWS\SYSTEM folder) or by direct request to myself (valadon@ix.netcom.com). Microsoft allows the redistribution of mfc42.dll with software using mfcs, so you will not break the law! RasTop develops a user-friendly graphical interface around rasmol (version 2.6.4 and 2.7.1) and run s on Windows platforms 95, 98, and NT. RasTop is available for download on the rasmol opensource site at http://www.OpenRasMol.org. Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com --Boundary_(ID_yo5FlbC+xgNp+EncaEEm8g)
 
Many of you tried RasTop and got the rather mystic message: "missing MFC42.DLL:6605".  Thanks to the help of Michael Wilson from the University of Oxford, you can get RasTop working by installing an updated mfc42.dll file in the folder containing the rastop.exe file (only this folder). You can obtain a recent version of mfc42.dll either on another PC (the version number should start by a number 6, each PC has one copy of mfc42.dll in the C:\WINDOWS\SYSTEM folder) or by direct request to myself (valadon@ix.netcom.com).  Microsoft allows the redistribution of mfc42.dll with software using mfcs, so you will not break the law!
 
RasTop develops a user-friendly graphical interface around rasmol (version 2.6.4 and 2.7.1) and runs on Windows platforms 95, 98, and NT. RasTop is available for download on the rasmol opensource site at http://www.OpenRasMol.org.
 
Philippe
 
---------------------------
   *** RasTop ***  
---------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA.
valadon@ix.netcom.com
 
--Boundary_(ID_yo5FlbC+xgNp+EncaEEm8g)-- #################################################### Enrique Castro Dept. Bioquímica, Biología Molecular y Fisioloía Universidad de Las Palmas de Gran Canaria (ULPGC) Facultad de Ciencias de la Salud c/ Doctor Pasteur s/n 35016 Las Palmas, Spain Tel: (34) 928 45 87 90 Fax: (34) 928 45 14 41 e-mail: ecastro@cicei.ulpgc.es ##################################################### ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 boundary="Boundary_(ID_bxOP+4XKA6fW/xS4UPEWjQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Chime install in IE 5.5 Date: Thu, 14 Dec 2000 09:24:33 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_bxOP+4XKA6fW/xS4UPEWjQ) Hello, I just installed Chime 2.6 in IE 5.5 on my Win2000 system. Now I can not view any Chime sites; it shows me the Win equivalent of a broken image icon. More info reports that I do not have an appropriate viewer for "chemical/x-pdb." I checked the IE/Plugins dir and it contains the files it should contain. I checked the Windows file mapping and both pdb and spt are mapped to IE. I have deleted and re-installed Chime twice. Help? I am at heart a Mac user... -- Timothy Driscoll molvisions.com - 3D molecular visualization http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA 508 864 6516 voice 781 899 4108 fax --Boundary_(ID_bxOP+4XKA6fW/xS4UPEWjQ)
Hello,
 
I just installed Chime 2.6 in IE 5.5 on my Win2000
system. Now I can not view any Chime sites; it
shows me the Win equivalent of a broken image
icon. More info reports that I do not have an
appropriate viewer for "chemical/x-pdb." I
checked the IE/Plugins dir and it contains the
files it should contain. I checked the Windows
file mapping and both pdb and spt are mapped to
IE. I have deleted and re-installed Chime twice.
Help? I am at heart a Mac user...
 
--
Timothy Driscoll
molvisions.com - 3D molecular visualization
http://www.molvisions.com/
driscoll@molvisions.com
Waltham, MA
508 864 6516 voice
781 899 4108 fax
--Boundary_(ID_bxOP+4XKA6fW/xS4UPEWjQ)-- CCL X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.3110.3 boundary="Boundary_(ID_smFv1w+zXtQmQGupV8buoQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Juan Alexander Padron Garcia Subject: Help with Homology SWISS-MODEL Date: Thu, 14 Dec 2000 08:15:45 -0600 To: PDBlist , rasmol , This is a multi-part message in MIME format. --Boundary_(ID_smFv1w+zXtQmQGupV8buoQ) Dear CCLs: I have obtain a homology model of a protein of unknown structure using SWISS-MODEL, but I would like to validate the method in order to see if it works OK on this type of protein family. I think that the best way will be modeling a known structure of the family and finding the rmsd of the model with the real one, but I will need to tell to the program to ignore that PDB file from the RCSB. Is there a way to do that? Is there any program that could do it? Any suggestions will be appreciated and sumarized. Best Regards, Juan Alexander Padron Garcia Molecular Modeling Laboratories Pharmaceutical Chemistry Center La Havana, Cuba --Boundary_(ID_smFv1w+zXtQmQGupV8buoQ)
Dear CCLs:
 
I have obtain a homology model of a protein of unknown structure using SWISS-MODEL, but I would like to validate the method in order to see if it works OK on this type of protein family. I think that the best way will be modeling a known structure of the family and finding the rmsd of the model with the real one, but I will need to tell to the program to ignore that PDB file from the RCSB. Is there a way to do that? Is there any program that could do it? Any suggestions will be appreciated and sumarized.
 
Best Regards,
Juan Alexander Padron Garcia
Molecular Modeling Laboratories
Pharmaceutical Chemistry Center
La Havana, Cuba
--Boundary_(ID_smFv1w+zXtQmQGupV8buoQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Help with Homology SWISS-MODEL Date: Thu, 14 Dec 2000 11:05:48 -0500 To: rasmol@lists.umass.edu Hi, Juan! Use Deep View (SwissPdbViewer) for your homology modeling, and you will be able to choose your templates rather than letting SwissModel choose them for you. For help with this, see http://www.usm.maine.edu/spdbv/text/modeling.htm If you are new to Deep View, see http://www.usm.maine.edu/~rhodes/SPVTut/index.html Hope this helps. Felice Navidad! ***************************** Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Please DON'T request confirmation of receipt Date: Thu, 14 Dec 2000 14:29:48 -0500 To: rasmol@lists.umass.edu Recently several messages were sent to this list with a request for confirmation of receipt. With over 570 subscribers, this caused quite a bit of extra work for me and temporary paralysis of the list. Please don't do this!! I have enquired whether we can automatically block such requests in the future, but such a blockade is not yet in place. Because of the amount of extra (volunteer, not-funded) work this entails, if it happens again, the subscriber responsible will be unsubscribed at least until I am assured that subscriber will not do it again. Thanks, -Eric - - - 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 at ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Berkeley RasMac 2.6 working on OS 9 Date: Sat, 16 Dec 2000 11:31:08 -0500 To: rasmol@lists.umass.edu >Date: Fri, 15 Dec 2000 13:19:18 -0500 (EST) >From: molinaro@scienceview.LHS.Berkeley.EDU >Subject: RasMAc working on OS 9 > >Hello RasMac users, >Thanks to a discovery made by Prof. Joel L. Sussman and one of his >students, RasMac 2.6 UCB works on Macintoshes with system 9.0 and >above. You can find the software at: >http://mc2.cchem.berkeley.edu/Rasmol/v2.6/. > >Happy Holidays, >Marco Molinaro >______________________________________________________ >Dr. Marco Molinaro >molinaro@scienceview.berkeley.edu >ScienceVIEW - Director of Multimedia Development >Lawrence Hall of Science, 120E (office), D-11 (development laboratory) >University of California, Berkeley, Berkeley, Ca. 94720-5200 >VOX: (510) 642-3153 FAX : (510) 642-7387 >http://scienceview.berkeley.edu > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V4.72.3110.3 boundary="Boundary_(ID_PKP1cfFHy46qc/2gXuxrcw)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Juan Alexander Padron Garcia Subject: Summary of Help with Homology SWISS-MODEL Date: Mon, 18 Dec 2000 08:12:20 -0600 To: rasmol@lists.umass.edu, CCL This is a multi-part message in MIME format. --Boundary_(ID_PKP1cfFHy46qc/2gXuxrcw) Dear All: First I would like to thanks to all the people who reply to my question. All the comments has been extremely usefull. Thanks again, Merry Chrismas and Happy New Millenium. Best Regards, Juan Alexander Padron Molecular Modeling Laboratories Pharmaceutical Chemistry Center La Havana, Cuba SUMARY Question: I have obtain a homology model of a protein of unknown structure using SWISS-MODEL, but I would like to validate the method in order to see if it works OK on this type of protein family. I think that the best way will be modeling a known structure of the family and finding the rmsd of the model with the real one, but I will need to tell to the program to ignore that PDB file from the RCSB. Is there a way to do that? Is there any program that could do it? Answers >From Gennady Poda: check this out: http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html >From Gales Rhodes Use Deep View (SwissPdbViewer) for your homology modeling, and you will be able to choose your templates rather than letting SwissModel choose them for you. For help with this, see http://www.usm.maine.edu/spdbv/text/modeling.htm If you are new to Deep View, see http://www.usm.maine.edu/~rhodes/SPVTut/index.html >From Don Gregory Structural homology modeling has been around for quite some time, and is regarded by many in the field, as a reliable method for generating starting models. Generally, the 'lower-limit' people have found, by experience, is that of having 30% identity in the area of interest, whether it is the whole protein, a domain, or an active site. Of course, evolutionary pressures tend to make the identity quite a bit higher in active sites. Several excellent papers on the techniques can be found on the web-site of Professor Andrej Sali, Rockefeller University. He has created an automated homology program, called Modeler. http://guitar.rockefeller.edu/publications/ref/ref.html Another thing I could suggest, would be to find a *family* of similar structures. Use one as the template, and build by homology, another family memeber who's structure is known, and then see how 'acceptable' that is to you. I might suggest using something like Profiles-3D to test the validity of the build model as well. This is a program developed by Professor David Eisenburg at UCLA, and is quite well respected in 'testing' a build model with respect to its likelihood of being a reasonable structure. You can find more info on this at: http://www.doe-mbi.ucla.edu/people/fischer/BENCH/benchmark1.html --Boundary_(ID_PKP1cfFHy46qc/2gXuxrcw)
Dear All:
 
First I would like to thanks to all the people who reply to my question. All the comments has been extremely usefull. Thanks again, Merry Chrismas and Happy New Millenium.
 
Best Regards,
Juan Alexander Padron
Molecular Modeling Laboratories
Pharmaceutical Chemistry Center
La Havana, Cuba
 
SUMARY
 
Question:
I have obtain a homology model of a protein of unknown structure using SWISS-MODEL, but I would like to validate the method in order to see if it works OK on this type of protein family. I think that the best way will be modeling a known structure of the family and finding the rmsd of the model with the real one, but I will need to tell to the program to ignore that PDB file from the RCSB. Is there a way to do that? Is there any program that could do it?
 
Answers
From Gennady Poda:
From Gales Rhodes
Use Deep View (SwissPdbViewer) for your homology modeling, and you will be
able to choose your templates rather than letting SwissModel choose them
for you.

For help with this, see

http://www.usm.maine.edu/spdbv/text/modeling.htm

If you are new to Deep View, see

http://www.usm.maine.edu/~rhodes/SPVTut/index.html
 
From Don Gregory
Structural homology modeling has been around for quite some time,
and is regarded by many in the field, as a reliable method for
generating starting models.
Generally, the 'lower-limit' people have found, by experience, is
that of having 30% identity in the area of interest, whether it is
the whole protein, a domain, or an active site.  Of course,
evolutionary pressures tend to make the identity quite a bit higher
in active sites.
Several excellent papers on the techniques can be found on the
web-site of Professor Andrej Sali, Rockefeller University.  He
has created an automated homology program, called Modeler.
http://guitar.rockefeller.edu/publications/ref/ref.html

Another thing I could suggest, would be to find a *family* of
similar structures.  Use one as the template, and build by
homology, another family memeber who's structure is known,
and then see how 'acceptable' that is to you.
I might suggest using something like Profiles-3D to test the
validity of the build model as well.  This is a program developed
by Professor David Eisenburg at UCLA, and is quite well
respected in 'testing' a build model with respect to its likelihood
of being a reasonable structure.  You can find more info on this
at:
http://www.doe-mbi.ucla.edu/people/fischer/BENCH/benchmark1.html
 
 
--Boundary_(ID_PKP1cfFHy46qc/2gXuxrcw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Phillip Barak Subject: Q: Display more than a single molecule in a Chime window? Date: Mon, 18 Dec 2000 09:42:23 -0600 To: rasmol@lists.umass.edu The instructions for Chime and Rasmol (2.6) are fairly clear in stating that only a single molecule file can be loaded into a window at a time. Is there any work-around that allows loading multiple molecules and locating them precisely in space? (A pointer to a worked example would be preferred). As a simple case, I have a monomer file of a substance that exists as a tetramer. Thanks for any and all help, Phillip Barak Assoc. Prof., Soil Science Dept of Soil Science University of Wisconsin-Madison 1525 Observatory Dr. Madison, WI 53706-1299 tel: 608-263-5450 fax: 608-265-2595 e-mail: pwbarak@facstaff.wisc.edu web: http://www.soils.wisc.edu/~barak/ ========================================= ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3.0.2.32.20001218094223.01059d40@facstaff.wisc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Q: Display more than a single molecule in a Chime window? Date: Mon, 18 Dec 2000 09:25:36 -0800 To: rasmol@lists.umass.edu I've used Isis/Draw from MDLI to create a pdb file with multiple structures. I haven't needed to be precise, but if you do I would try aligning molecules with SwissPDBViewer and exporting as a pdb file. The tricky part would be the numbering of the molecules so as to allow scripted viewing options in RasMol. You might have to edit the pdb file in a text editor to achieve this. Dave Hurley Senior Computer Specialist (a biologist in disguise) University of Washington Biology Program 318 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-685-1728 >The instructions for Chime and Rasmol (2.6) are fairly clear in >stating that only a single molecule file can be loaded into a window >at a time. Is there any work-around that allows loading multiple >molecules and locating them precisely in space? (A pointer to a >worked example would be preferred). As a simple case, I have a >monomer file of a substance that exists as a tetramer. > >Thanks for any and all help, > >Phillip Barak >Assoc. Prof., Soil Science > >Dept of Soil Science >University of Wisconsin-Madison >1525 Observatory Dr. >Madison, WI 53706-1299 > > tel: 608-263-5450 > fax: 608-265-2595 > e-mail: pwbarak@facstaff.wisc.edu > web: http://www.soils.wisc.edu/~barak/ > >========================================= > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Q: Display more than a single molecule in a Chime window? Date: Mon, 18 Dec 2000 12:42:34 -0500 To: rasmol@lists.umass.edu on 12.18.00 12:25 PM, Dave Hurley at dhurl@u.washington.edu wrote: > I've used Isis/Draw from MDLI to create a pdb file with multiple > structures. I haven't needed to be precise, but if you do I would try > aligning molecules with SwissPDBViewer and exporting as a pdb file. > The tricky part would be the numbering of the molecules so as to > allow scripted viewing options in RasMol. You might have to edit the > pdb file in a text editor to achieve this. > > > Dave Hurley > Senior Computer Specialist (a biologist in disguise) > University of Washington > Biology Program > 318 Hitchcock Hall > Box 355320 > Seattle, WA 98195-5320 > phone: 206-685-8038 > fax: 206-685-1728 > > > > >> The instructions for Chime and Rasmol (2.6) are fairly clear in >> stating that only a single molecule file can be loaded into a window >> at a time. Is there any work-around that allows loading multiple >> molecules and locating them precisely in space? (A pointer to a >> worked example would be preferred). As a simple case, I have a >> monomer file of a substance that exists as a tetramer. >> >> Thanks for any and all help, >> >> Phillip Barak >> Assoc. Prof., Soil Science >> >> Dept of Soil Science >> University of Wisconsin-Madison >> 1525 Observatory Dr. >> Madison, WI 53706-1299 >> Hi Phillip, I recommend Deep View/Swiss PDB Viewer (http://expasy.cbr.nrc.ca/spdbv/) for aligning multiple molecules or creating unit crystals - it's free, fast, and relatively straightforward. Plus the support is excellent - also check out Gale Rhodes site for lots of great help (http://www.usm.maine.edu/~rhodes/SPVTut/index.html). Before you do a lot of work, pay a visit to the EBI Macromolecular Structure Database (http://msd.ebi.ac.uk/Services/Quaternary/quaternary.html) - you may find your tetramer already built here. -- Timothy Driscoll molvisions.com - 3D molecular visualization http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 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: Lothar Esser Subject: Re: Q: Display more than a single molecule in a Chime window? Date: Mon, 18 Dec 2000 12:41:19 -0600 (CST) To: rasmol@lists.umass.edu On Mon, 18 Dec 2000, Phillip Barak wrote: > The instructions for Chime and Rasmol (2.6) are fairly clear in stating that only a single molecule file can be loaded into a window at a time. Is there any work-around that allows loading multiple molecules and locating them precisely in space? (A pointer to a worked example would be preferred). As a simple case, > I have a monomer file of a substance that exists as a tetramer. > If you have multiple pdb files with the proper coordinates so that the monomers would form a tetramer, all you need to do is to concatenate the pdb files and possibly edit the END cards out. You can then load the combined file into rasmol. To distinguish diffenent monomers you can use different chain ids or treat each molecule as a MODEL. The latter is exactly what I have been doing lately. I loaded so far up to 260 pdb files into rasmol and distinguish them by their model number ( because their chain ids are the same ). So add a line MODEL 1 in front of each pdb file ( update the number of course ). Selection in rasmol is done with select */1 ( all atoms in model 1 ) Hope this helps. Lothar. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Q: Display more than a single molecule in a Chime window? Date: Mon, 18 Dec 2000 15:00:14 -0500 To: rasmol@lists.umass.edu At 12/18/2000, you wrote: >The instructions for Chime and Rasmol (2.6) are fairly clear in stating that only a single molecule file can be loaded into a window at a time. Is there any work-around that allows loading multiple molecules and locating them precisely in space? (A pointer to a worked example would be preferred). As a simple case, I have a monomer file of a substance that exists as a tetramer. > >Thanks for any and all help, > >Phillip Barak For any published PDB file, the probable quaternary structure can be obtained from European Bioinformatics Institute, based on the authors' symmetry operations stated in the PDB file header. Just put the PDB ID code in the "Simple ID code interface" at: http://msd.ebi.ac.uk/Services/Quaternary/quaternary.html For example, 1hho contains only half of the hemoglobin tetramer. From EBI you can get 1hho.mmol with the full tetramer. Or for 2plv (polio virus) you can get the entire 31 megabyte capsid! These files work well in RasMol, Chime, Protein Explorer, etc. In cases where the PQS routines judge homo-oligomers in the asymmetric unit to be crystallographic artifact, you can also get a PDB file containing only a single chain. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <0G5S00HOS4IX2R@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: Q: Display more than a single molecule in a Chime window? Date: Mon, 18 Dec 2000 15:32:22 -0500 To: rasmol@lists.umass.edu Pat, I thought this might be helpful from the Chime web list, as a possible way to see the full B-galactosidase structure from a subunit. If you send me the PDB code of the file, I might try it out. Joan Eric Martz wrote: > At 12/18/2000, you wrote: > >The instructions for Chime and Rasmol (2.6) are fairly clear in stating > that only a single molecule file can be loaded into a window at a time. Is > there any work-around that allows loading multiple molecules and locating > them precisely in space? (A pointer to a worked example would be > preferred). As a simple case, I have a monomer file of a substance that > exists as a tetramer. > > > >Thanks for any and all help, > > > >Phillip Barak > > For any published PDB file, the probable quaternary structure can be > obtained from European Bioinformatics Institute, based on the authors' > symmetry operations stated in the PDB file header. > Just put the PDB ID code in the "Simple ID code interface" at: > > http://msd.ebi.ac.uk/Services/Quaternary/quaternary.html > > For example, 1hho contains only half of the hemoglobin tetramer. From EBI > you can get 1hho.mmol with the full tetramer. Or for 2plv (polio virus) you > can get the entire 31 megabyte capsid! These files work well in RasMol, > Chime, Protein Explorer, etc. > > In cases where the PQS routines judge homo-oligomers in the asymmetric unit > to be crystallographic artifact, you can also get a PDB file containing > only a single chain. > > -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: RasMol depths Date: Tue, 19 Dec 2000 12:50:33 -0500 To: rasmol@lists.umass.edu >From: Jean-Pierre Demailly >Subject: RasMol >To: emartz@microbio.umass.edu >Date: Tue, 19 Dec 2000 12:15:44 +0100 (MET) >Cc: demailly@rossini.ujf-grenoble.fr (Jean-Pierre Demailly) >X-Mailer: ELM [version 2.4ME+ PL47 (25)] > >Hi: > >This message to let you know that I have hacked a little bit the sources >of RasMol-2.7.1 (Unix version) to let it work simultaneously in all depths >8, 16, 24/32. You'll find the modified package on > > >ftp://ftp.ac-grenoble.fr/ge/chemistry/RasMol_2.7.1a.tgz > >I have too solutions for this: > >* Compile 3 binaries and add a wrapper which calls the correct version. >The wrapper is included in the above package. > >* Build a single binary which runs all 3 modes simultaneously. This >works not so bad, but at the moment it is still a bit slower, because my >solution is to make a copy of the XImage (by the way, this also spoils some >RAM!). I hope you are in a good position to fix this -- maybe this is >only a question of a few lines of code, but I couldn't get to the exact >point that could make it. > >Maybe you'll find my modifications useful for the next releases. We are >currently working on a software distribution for French educational >institutions, and are trying to release things that work "out of the >box". Hence our concern about rasmol having to be recompiled... > >Best regards, >Jean-Pierre Demailly > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 script problems in Mac Netscape Date: Tue, 19 Dec 2000 13:00:27 -0500 To: whreusch@pilot.msu.edu Cc: rasmol@lists.umass.edu >Date: Tue, 19 Dec 2000 11:47:37 -0500 >From: whreusch >Organization: Michigan State University >To: Eric Martz > >Professor Martz: >A few months ago you provided me with helpful information regarding >Chime and Internet Explorer. I would like to impose on your expertise >once more regarding the behavior of RasMol commands running as Chime >scripts. >My practice is to show molecules on a white background, and to orient >them using the rotate command. This works well with Netscape running >under Windows 98, but Netscape under the Macintosh OS is quirky. >Sometimes the displays load as intended, but often they load on a black >background without proper orientation. Subsequent changes initiated by >display buttons achieve the desired effects. This is annoying because I >am striving to achieve the broadest possible compatibility for users. >If you have any ideas for resolving this problem, I would be most >appreciative. >Bill Reusch > Dear Bill: I have not observed the problems you mention in Chime scripts on the Mac in Netscape. Others may have so I am copying this to the email list. There is a bug in Mac Netscape that causes random jumps in zoom and translation when rotating with the mouse, but I am not aware of this affecting the initial image resulting from a script. I think the best way for me to help is if you provide me with one script that has the problems you describe, and tell me what percentage of the time the initial image is incorrect. Are you running the scripts in your own html, my presentation template, or in Protein Explorer (project folder mode)? If either of the first two, best if you send me an sit file containing the entire html site. DO NOT ATTACH FILES TO THE LIST, ONLY TO ME PERSONALLY. A script can be included in an email to the list as plain text in the body of the message, not an attachment please. Please tell me what Mac OS and hardware you are using. Please let me know the version of Netscape and of Chime (2.0a or 2.6?) you are using. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org 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: Gale Rhodes Subject: Deep View Tutorial Date: Fri, 22 Dec 2000 11:08:11 -0500 To: rasmol@lists.umass.edu Holiday Greetings Rasmolluscs and Chimeleons! If you are also a user of Deep View (Swiss-PdbViewer), this may be of interest: I have revised the beginner's Deep View Tutorial for version 3.7b2. There is little change in content, but there should now be better agreement with the program regarding command locations and new or deleted functions. The tutorial is located at http://www.usm.maine.edu/~rhodes/SPVTut/index.html The tutorial's table of Deep View key modifiers ( http://www.usm.maine.edu/~rhodes/SPVTut/text/KeyMods.html ) is Mac-specific with all the PC corrections of which I am aware. If any PC user has documented differences in key modifier functions and is willing to construct a PC-specific table like the one in the tutorial, I will be happy to post it along with the current one. Same offer applies to users of SGI or Linux versions, where key and mouse mappings may be even more divergent. Thanks to many of you for corrections, suggestions, and encouragement. I welcome additional comments. Cheers! ***************************** Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_NHp++byY4vbEmwNiZE8jyQ)" X-Accept-Language: fr,en-US References: <000e01c065d9$97dc26f0$ee64fed8@NETVISTAPC> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: Chime install in IE 5.5 Date: Fri, 22 Dec 2000 21:01:40 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_NHp++byY4vbEmwNiZE8jyQ) Hi, I installed Chime 2.6 on my computer (IE 5.5 Win 95), and I have seen no difference... beside the fact that the installer made a mess with my registry. You could check by typing 'regedit' in the start -> run command line. Then, go to HKEY_CLASSES_ROOT > .pdb You should a text key named "Content Type" with the value "chemical/x-pdb". If it is not there, just create it. Although the installer have a checkbox that says "Automatically register file types" (or something like that), it will make changes to the registery even if this checkbox is not checked. The broken image is generally when MSIE can't find the appropriate plugin that correspond to the file extension. I hope this will be helpful for you, if you didn't already solved the problem. If so, you could tell me what was not working well. Jean-Philippe Demers > Hello,I just installed Chime 2.6 in IE 5.5 on my Win2000 > system. Now I can not view any Chime sites; it > shows me the Win equivalent of a broken image > icon. More info reports that I do not have an > appropriate viewer for "chemical/x-pdb." I > checked the IE/Plugins dir and it contains the > files it should contain. I checked the Windows > file mapping and both pdb and spt are mapped to > IE. I have deleted and re-installed Chime twice. > Help? I am at heart a Mac user...-- > Timothy Driscoll > molvisions.com - 3D molecular visualizationhttp://www.molvisions.com/ > driscoll@molvisions.com > Waltham, MA > 508 864 6516 voice > 781 899 4108 fax --Boundary_(ID_NHp++byY4vbEmwNiZE8jyQ) Hi, I installed Chime 2.6 on my computer (IE 5.5 Win 95),
and I have seen no difference... beside the fact that the installer
made a mess with my registry.
You could check by typing 'regedit' in the start -> run command line.
Then, go to HKEY_CLASSES_ROOT > .pdb
You should a text key named "Content Type" with the value "chemical/x-pdb".
If it is not there, just create it.
Although the installer have a checkbox that says "Automatically register file types"
(or something like that), it will make changes to the registery even if this checkbox
is not checked.
The broken image is generally when MSIE can't find the appropriate plugin that
correspond to the file extension.

I hope this will be helpful for you, if you didn't already solved the problem. If so,
you could tell me what was not working well.

Jean-Philippe Demers
 

Hello,I just installed Chime 2.6 in IE 5.5 on my Win2000
system. Now I can not view any Chime sites; it
shows me the Win equivalent of a broken image
icon. More info reports that I do not have an
appropriate viewer for "chemical/x-pdb." I
checked the IE/Plugins dir and it contains the
files it should contain. I checked the Windows
file mapping and both pdb and spt are mapped to
IE. I have deleted and re-installed Chime twice.
Help? I am at heart a Mac user...--
Timothy Driscoll
molvisions.com - 3D molecular visualizationhttp://www.molvisions.com/
driscoll@molvisions.com
Waltham, MA
508 864 6516 voice
781 899 4108 fax
--Boundary_(ID_NHp++byY4vbEmwNiZE8jyQ)-- boundary="Boundary_(ID_p9TyDceF3ral9Or5niA6+g)" User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime install in IE 5.5 Date: Sun, 24 Dec 2000 09:30:11 -0500 To: rasmol@lists.umass.edu, chime-feedback@mdli.com > This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_p9TyDceF3ral9Or5niA6+g) Jean-Philippe, Thanks for the suggestion! In fact, fixing my Win IE 5.5-Chime problem was a bit more complicated. I DID have the appropriate text keys for both pdb and spt file types in the registry, but IE still wasn't recognizing the types; however, the default keys for these types were some nondescript defns (pdbFile and sptFile, to be exact). Once I set the default keys for these file types to chemical/x-pdb and application/x-spt, IE loaded Chime pages okay. One other caveat about IE and Chime - calling an external script from the EMBED tag is problematic; that is, EMBED SRC="myfile.pdb" TYPE="chemical/x-pdb" SCRIPT="script setup.spt" does not work consistently. More often than not, the above syntax returned the message "An error occurred inside a plugin on the page." Strangely enough, it appears to be a "Temporary Internet Files" issue. (You can view these settings in IE 5 by choosing Tools/Internet Options, then clicking the Setting button under Temporary Internet Files.) The only option that works flawlessly with the above syntax is "Check for newer versions of the page: Every visit to the page" - all the others give various (and often fun) errors, from warnings to system crashes. Merry Christmas! -- Timothy Driscoll molvisions.com - 3D molecular visualization http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 fax on 12.22.00 9:01 PM, Jean-Philippe Demers at diane.demers@sympatico.ca wrote: Hi, I installed Chime 2.6 on my computer (IE 5.5 Win 95), and I have seen no difference... beside the fact that the installer made a mess with my registry. You could check by typing 'regedit' in the start -> run command line. Then, go to HKEY_CLASSES_ROOT > .pdb You should a text key named "Content Type" with the value "chemical/x-pdb". If it is not there, just create it. Although the installer have a checkbox that says "Automatically register file types" (or something like that), it will make changes to the registery even if this checkbox is not checked. The broken image is generally when MSIE can't find the appropriate plugin that correspond to the file extension. I hope this will be helpful for you, if you didn't already solved the problem. If so, you could tell me what was not working well. Jean-Philippe Demers Hello,I just installed Chime 2.6 in IE 5.5 on my Win2000 system. Now I can not view any Chime sites; it shows me the Win equivalent of a broken image icon. More info reports that I do not have an appropriate viewer for "chemical/x-pdb." I checked the IE/Plugins dir and it contains the files it should contain. I checked the Windows file mapping and both pdb and spt are mapped to IE. I have deleted and re-installed Chime twice. Help? I am at heart a Mac user...-- Timothy Driscoll molvisions.com - 3D molecular visualizationhttp://www.molvisions.com/ driscoll@molvisions.com Waltham, MA 508 864 6516 voice 781 899 4108 fax --Boundary_(ID_p9TyDceF3ral9Or5niA6+g) Re: Chime install in IE 5.5 Jean-Philippe,

Thanks for the suggestion!  In fact, fixing my Win IE 5.5-Chime problem was a bit more complicated.  I DID have the appropriate text keys for both pdb and spt file types in the registry, but IE still wasn't recognizing the types; however, the default keys for these types were some nondescript defns (pdbFile and sptFile, to be exact).  Once I set the default keys for these file types to chemical/x-pdb and application/x-spt, IE loaded Chime pages okay.


One other caveat about IE and Chime - calling an external script from  the EMBED tag is problematic; that is,

   EMBED SRC="myfile.pdb" TYPE="chemical/x-pdb" SCRIPT="script setup.spt"

does not work consistently.  More often than not, the above syntax returned the message "An error occurred inside a plugin on the page."  Strangely enough, it appears to be a "Temporary Internet Files" issue.  (You can view these settings in IE 5 by choosing Tools/Internet Options, then clicking the Setting button under Temporary Internet Files.)  The only option that works flawlessly with the above syntax is "Check for newer versions of the page: Every visit to the page" - all the others give various (and often fun) errors, from warnings to system crashes.


Merry Christmas!

--
Timothy Driscoll
molvisions.com - 3D molecular visualization
http://www.molvisions.com/
driscoll@molvisions.com
Waltham, MA  USA
508-864-6516 voice
781-891-4108 fax




on 12.22.00 9:01 PM, Jean-Philippe Demers at diane.demers@sympatico.ca wrote:

Hi, I installed Chime 2.6 on my computer (IE 5.5 Win 95),
and I have seen no difference... beside the fact that the installer
made a mess with my registry.
You could check by typing 'regedit' in the start -> run command line.
Then, go to HKEY_CLASSES_ROOT > .pdb
You should a text key named "Content Type" with the value "chemical/x-pdb".
If it is not there, just create it.
Although the installer have a checkbox that says "Automatically register file types"
(or something like that), it will make changes to the registery even if this checkbox
is not checked.
The broken image is generally when MSIE can't find the appropriate plugin that
correspond to the file extension.

I hope this will be helpful for you, if you didn't already solved the problem. If so,
you could tell me what was not working well.

Jean-Philippe Demers

Hello,I just installed Chime 2.6 in IE 5.5 on my Win2000
system. Now I can not view any Chime sites; it
shows me the Win equivalent of a broken image
icon. More info reports that I do not have an
appropriate viewer for "chemical/x-pdb." I
checked the IE/Plugins dir and it contains the
files it should contain. I checked the Windows
file mapping and both pdb and spt are mapped to
IE. I have deleted and re-installed Chime twice.
Help? I am at heart a Mac user...--
Timothy Driscoll
molvisions.com - 3D molecular visualizationhttp://www.molvisions.com/
driscoll@molvisions.com
Waltham, MA
508 864 6516 voice
781 899 4108 fax

--Boundary_(ID_p9TyDceF3ral9Or5niA6+g)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.80 beta released Date: Fri, 29 Dec 2000 16:30:15 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Protein Explorer (PE) has been upgraded to version 1.80 beta at http://proteinexplorer.org (which goes to the UMass site). (The version on the PDB servers remains at 1.0 with planned upgrading to 2.0 in 2001.) Contact Surfaces: The ease of producing an overview of noncovalent bonding interactions between two moieties (just two clicks are required in the QuickViews menu system) has been one of PE's most popular features. This version enhances QuickViews' Contacts display by providing numerous options to modify the resulting image. These include making the surface transparent, hiding non-contacted portions of the surface, and displaying the putatively noncovalently bonded atoms inside the surface as well as outside. Various subsets of atoms are selectable by clicking on the new links, making them easily available for subsequent display and coloring operations. Selection by clicking: QuickViews' SELECT menu has a new option "Clicked". This enables selection of atoms, residues, or chains by clicking on the 3d image with the mouse. Such selection can be followed with a Contact Surface display to powerful effect. The QuickViews Plus options to change display diameters for backbones, sticks, and spacefilling now update the image automatically when changed. In this version I believe I have fixed the bug "Fatal error: this is not your fault" that caused frustrating PE startup failures on certain Windows 2000/NT systems. This bug has been present for many months but was difficult to trap because it happened on none of the computers available to me (including a Windows 2000 system purchased solely to trap this one bug!). Thanks to Tim Driscoll who trapped the critical debugging information on his computer. If wider use confirms that the above bug has indeed been fixed, this will open the way for release of version 2.0 at the Protein Data Bank early in 2001. Since PE version 1.0 (the version at the PDB), ease of use and power have been greatly enhanced with the FirstView explanation page, the QuickViews menu system, Seq3D sequence to structure clickable interface, detection and display of cation-pi interactions and salt bridges, and MSA3D for coloring a 3d protein image by conservation/mutation in a multiple protein sequence alignment. PE is open-source freeware that works in Netscape 4.08-4.76 with free MDL Chime on Windows 95/98/2000/NT or Macintosh PPC systems. It also operates well on SGI's, linux, and other unix workstations in a Windows subsession. (Linux: Win4Lin www.trelos.com or VMWare www.vmware.com; SGI or unix: via Citrix Metaframe www.citrix.com.) -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org 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: "Herbert J. Bernstein" Subject: Re: Protein Explorer 1.80 beta released Date: Fri, 29 Dec 2000 18:44:32 -0500 (EST) To: rasmol@lists.umass.edu Cc: pdb-l@rcsb.org Could we have a clarification of the statement that "PE is open-source freeware"? The proteinexplorer.org web page does _not_ say that PE is open-source. Instead it says, "This version is free for all users, but downloaded copies or derivatives thereof may not be redistributed on CD's, served from publically-accessible websites, or redistributed by other means without permission," which would seem contrary to most current definitions of open source which encourage creation of derived works under conditions which ensure that those derived works are themselves also open source, and that proper credit is given. If PE is now open source, this would be very good news for the community and allow much wider use and application of the useful ideas in PE. In that case, a clear identification of the open source license terms would be helpful. For a more complete discussion of the issues in the term "open source", see http://www.gnu.org/philosophy/free-sw.html, http://www.opensource.org, http://www.openrasmol.org, and similar sites. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 29 Dec 2000, Eric Martz wrote: > Protein Explorer (PE) has been upgraded to version 1.80 beta at > http://proteinexplorer.org (which goes to the UMass site). (The version on > the PDB servers remains at 1.0 with planned upgrading to 2.0 in 2001.) > ... > > PE is open-source freeware that works in Netscape 4.08-4.76 with free MDL > Chime on Windows 95/98/2000/NT or Macintosh PPC systems. It also operates > well on SGI's, linux, and other unix workstations in a Windows subsession. > (Linux: Win4Lin www.trelos.com or VMWare www.vmware.com; SGI or unix: via > Citrix Metaframe www.citrix.com.) > > -Eric Martz > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > > 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--