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