>>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 16 Nov 1995 14:56:56 -0500 (EST) From: Eric Martz Subject: Welcome; Address correction To: rasmol@noc1.oit.umass.edu Welcome! The RasMol email list is off the ground (18 subscribers at the moment). Those of you who subscribed early got a welcome message containing an error: the address rasmol-request@lists.umass.edu is an alias for me, the "owner" of the list. All commands (such as subscribe, unsubscribe, review rasmol subscribers) intended for the listproc software must be sent to: listproc@lists.umass.edu Meanwhile, I was temporarily unable to fix the error while more of you subscribed (permissions snafu), but it is now fixed and future subscribers will receive the correct address. Also the info at the RasMol home page has been corrected. I think that does it. Sorry for the confusion. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 16 Nov 1995 14:58:50 -0500 (EST) From: Eric Martz Subject: Introductions, please To: rasmol@noc1.oit.umass.edu I'd like to invite each subscriber to send a paragraph or two introducing themselves and describing their uses of RasMol (already accomplished, or planned for the future), and any other information they wish to share. Bear in mind that the subscribers are a diverse group, including at one extreme investigators who do molecular modeling and structural research, and at the other end, people such as myself who know very little about macromolecular structure (mostly learned because of RasMol), and who have seen little or no other molecular visualization or modeling software, but who are enthusiastic about the teaching potential of RasMol. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 16 Nov 1995 15:01:14 -0500 (EST) From: Eric Martz Subject: Our RasMol Web Pages To: rasmol@noc1.oit.umass.edu As I learn about resources from people such as Roger Sayle and Marco Molinaro, I'm linking them to our RasMol Home Page as fast as I can (I'm always a bit behind). Please continue to inform me about those not on the web page and they will be added. Also don't feel shy about suggesting additions or changes to my hastily concocted descriptions of the resources (often based on too little experience). Also if the web page heading structure can be improved, make a suggestion -- it is metamorphosing quickly, usually when I have 15 minutes before I get totally unacceptably late for dinner (luckily my wife doesn't subscribe to this list :-). http://www.umass.edu/microbio/rasmol /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 22 Nov 1995 08:05:04 +1000 (EST) From: Keith Hoek -BIOCHEM Subject: Introduction To: RasMol group Hello all, I am currently trying to isolate a mammalian protein responsible for mRNA transport in oligodendrocytes. I have used RasMol to visualise the structures of other known RNA-binding proteins (staufen, U1A, etc). Once I have the sequence of my protein I want to compare it to the few examples of structurally characterised RNA- binders. I more frequently use RasMol to view the structures of RNA, to gain a better understanding of how proteins may interact with them. I also use other visualisation software (MAGE and insightII) and I hope to obtain SCULPT some time soon. Our lab has long experience with nmr, hopefully I will be able to place the structure of an active motif of my protein in the database. _____________________________________________________________________ Keith Hoek hoek@biosci.uq.edu.au mRNA transport http://florey.biosci.uq.edu.au/~hoek/Pg1.html From: b_duke@lacebark.ntu.edu.au >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 22 Nov 1995 08:39:47 -0500 (EST) Subject: Re: Introductions, please To: rasmol@noc1.oit.umass.edu Hi Eric, You asked for us to introduce ourselves. You did not say whether to post it you or to the list. Please post this to the list if you want. [Others: post directly to the list. Its for all of us to use! rasmol@lists.umass.edu --Eric] My interest in Rasmol is primarily educational. I head a team with an Australian Government grant to develop teaching materials for computational chemistry. Most are web based. See our page http://www.chem.swin.edu.au/CAUT.html We plan to use rasmol quite a lot as a web viewer for *.pdb files. Apart from that, my research interests are in ab initio quantum chemistry of heavy main group element compounds, and I teach all physical chemistry here and some introductory and first year stuff. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 089-466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@uncl04.ntu.edu.au >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 22 Nov 1995 15:47:45 -0500 (EST) From: Eric Martz Subject: Introducing yours truly To: rasmol@noc1.oit.umass.edu Dear RasMol aficionados: I discovered RasMol in February, 1995, and for many weeks subsequently got too little sleep. I loved being able to 'hold molecules in my hands, turn them over, and feel their parts', molecules which I had 'known' all my career but had never been able to see so clearly. I found that only a handful of the faculty at our university (23,000 students) knew about RasMol. So, I gave several demos to general audiences of biologists and chemists to popularize RasMol's use, especially for education. For this purpose, I wrote a script which illustrates DNA structure. It runs unattended, and is now available on our home page (see below). I also suggested to 'The Scientist' that they write an article on the wonderful free software now becoming available. This produced a nice article by free-lance author Robert Finn, "Finding full-featured free software for biologists on the Internet", July 1995 (vol. 9, page 14), in which RasMol's virtues were extolled. In April, Roger Sayle kindly provided me with an interim version of RasWin which supported the 'pause' command, allowing scripts which pause until a key is pressed. I teach immunology, so I wrote two 'paused' scripts which I projected during lectures, one on antibody structure and binding to antigen, and one on structure of major histocompatibility molecules, and binding to peptide antigens. These are also available on our home page. My research is on the mechanisms by which cytotoxic T lymphocytes interact with their target cells, including the integrin LFA-1. This work is at the cell function level and has little to do with molecular structure (there are no 3D structures for integrins yet). It seemed to me that RasMol users needed a way to communicate, and to help solve each other's problems (perhaps freeing some of Roger's time), so I suggested to Roger that I start this email list. (He was not aware of any existing list on RasMol.) I look forward to linking the RasMol resources each of you has to offer to our web page. Still-GIF's from the 3 scripts mentioned above are featured in the RasMol Gallery on our web page (http://www.umass.edu/microbio/rasmol). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 22 Nov 1995 17:23:03 -0500 (EST) From: Eric Martz Subject: Scripts for Macs To: rasmol@noc1.oit.umass.edu I'm trying to make my RasMol scripts optimally accessible to Mac users but I never use Macs and hardly know anything about them. I tried the DNA script on RasMac 2.6 today and it worked fine. Would someone very familiar with Macs and RasMac please advise me on the best way to distribute scripts for RasMac? There are (at least) two different issues. 1. What file format is best? I assume a .sit (stuffit) file, in binhex format (.sit.hqx) is best. However, since this will require some time at my end I may never get around to it. Will someone volunteer to convert my DOS-ready EXE files to .sit.hqx files and make them accessible by web? (The annoying part will be when I fix bugs or otherwise improve them -- this would have to be done again each time. However, I don't "plan" any major work on the scripts in the near future.) Or can my EXE files (which are compressed with pkzip and readable by pkunzip) somehow be unzipped directly on a mac? 2. How can RasMac 2.6 best access the script and sub-script files? (Each of my 'scripts' consists of a multitude of files.) A command (typed in the RasMac command window) such as 'script dna/dna1.top' fails (where dna is a folder under the folder containing the rasmac program). Is there some way to make this work (equivalent to specifying a working directory under windows)? The script works if placed in the same directory as the rasmac program. However, if all 3 scripts were placed here, they would make a tangle of >50 files. In Windows, Properties->Working directory allows one to make a copied RasWin icon operate in a specified directory. Is there any way to do that on the Mac? One possibility is to make a separate folder for each script, each containing a (redundant) copy of rasmac plus the script. If this is the best solution, it means that in (1) above, the .sit.hqx file should unstuff to a FOLDER containing the script files (not the script files themselves). 3. A related (but less important) issue is how to get a RasMac icon to start a script automatically. The manual mentions an RSML file, but we think that means the file must be created by RasMol (which currently excludes all manually edited scripts). Does anyone know how to do this? BTW, I tried the '-script filename' method (under Properties, Command line) in Windows. This revealed a bug in RasWin 2.6-beta (which I've reported to Roger). A script started this way dies on the first pause, but when run from the command window, works fine. Thanks for any help... /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 23 Nov 1995 09:44:14 +1000 To: rasmol@noc1.oit.umass.edu From: pierre@anatomy.su.oz.au (Pierre Moens) Subject: introduction Dear rasmol people, I am using fluorescence resonance energy transfer spectroscopy to study the modifications of conformation of contractile proteins (actin and myosin) in solution (i.e. the modification of actin filament conformation when myosin binds to it). I am using rasmol to visualize the monomeric actin and the myosin structure, the actin filament (kindly provided by Michael Lorenz) and the structure of the fluorescent probes I am using. I also use rasmol to "prepare" (highlighting specific residues or chains) the structure for the kinemage software. I then used kinemage to generate postscript files. Cheers Pierre Moens Muscle Research Unit ph: (61-2) 351 6543 Dept of Anatomy & Histology fax: (61-2) 351 2813 The University of Sydney, 2006 AUSTRALIA email: pierre@anatomy.su.oz.au >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 23 Nov 1995 09:24:19 +0000 From: Bruce_Livett.BioChem@muwaye.unimelb.edu.au (Bruce Livett) Subject: Re: Introductions, please To: rasmol@noc1.oit.umass.edu Hi Rasmollers, I have been interested in Rasmol for several years now, both as an educational tool and for its ability to display molecules of interest to me in my research on strucute-function of small peptide conotoxins. Like Eric Martz, I became entranced with Rasmol and set about to popularize it among my colleagues and encourage students to make use of it. To this end, I wrote an article on "Molecular Graphics" for the Melbourne PCUser Group magazine (circulation over 6,000; PCUpdate 11: (6) 72-74, 1994), that included high resolution colour illustrations. I found out that many of my colleagues are avid readers of computer magazines (surprise surpise !) and I had a far greater interest and immediate response to this article than I normally get to my biochemical research publications which tend to get lost in the plethora of scientific journals out there. Encouraged by this response I modified the article for the newsletter of the Australian Society for Biochemistry and Molecular Biology (ASBMB Newsletter 25 (3), 16-19, 1994) and demonstrated the program at the poster/trade display of the annual meeting of the ASBMB in September 1994, and at a Molecular Modelling Workshop hosted by the Ludwig Institute, in Melbourne, making copies available on disk to all who asked. Many of my colleagues are now acquainted with Rasmol, most using it on the PC, as do the graduate students who have had exposure to it either in the final year of undergraduate classes or in their research. Within the Department my colleagues have have been using RasWin as a teaching tool in both lectures and practical classes. In second year Biochemistry lectures RasWin has been used to reveal the surface location of charged residues and hydrophobicity of the heme pocket in myoglobin, and to demonstrate the ability of proline to teminate a helical stretch in a protein. In practical classes devised by Prof. Bill Sawyer, the students have been using RasWin to determine whether the structural predictions of sequence alogarithms are accurate (eg. those of Chou and Fasman, Kyte and Doolittle). We continue to be impressed by enhancements in each new version of RasWin and by the rapid response by Roger Sayle to questions put to him over the last two years. His talent, vision and generosity are most appreciated. Thanks Eric for setting up this mailing list. I am sure it will grow rapidly and expand our horizons on the applications of this wonderful graphics display program. --------------------------------------------------------------------------- Bruce Livett, b.livett@biochemistry.unimelb.edu.au Reader in Biochemistry Department of Biochemistry and Molecular Biology University of Melbourne Parkville, Victoria 3052 AUSTRALIA >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 23 Nov 1995 12:50:25 +0000 (GMT) From: Sayle Dr R A To: rasmol@noc1.oit.umass.edu Subject: Re: Introductions, please Dear All, I just thought that I'd introduce and let my presence be known on this mailing list. I have the dubious honour of being Roger Sayle, author of RasMol. I'm currently on a form of research fellowship at Glaxo Wellcome (the worlds largest pharmaceutical company), where they let me write whatever programs I like and even pay me for the pleasure. RasMol was originally developed at the Biocomputing Research Unit at the University of Edinburgh as a spare time hobby under the guidance of Dr Andrew Coulson (who I also believe is on this list). I must admit that I'm a computer scientist by training and have no formal knowledge of molecular biology, biochemistry or chemistry. However, I've picked up a great through contact with Dr Coulson and the various RasMol users that ask for additional enhancements to better support their field. The very first use of RasMol was to aid a computing practical in the undergraduate biology course "Protein Structure, Function and Mechanism" at Edinburgh. Since then its widepread use in teaching, even to have its own mailing list, has quite astonished me. I hope that by listening to the novel uses made of RasMol, I'll be able to make several changes to better support its use in education. For example, Eric's requests have prompted a number of improvements including the "refresh" and "pause" commands in version 2.6. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 23 Nov 1995 15:13:17 +0000 (GMT) From: Sayle Dr R A To: Eric Martz cc: rasmol@noc1.oit.umass.edu Subject: Re: Scripts for Macs Dear Eric, > 2. How can RasMac 2.6 best access the script and sub-script files? > The script works if placed in the same directory as the rasmac program. > However, if all 3 scripts were placed here, they would make a tangle > of >50 files. One possibility on the Macintosh is to make an "alias" of RasMac, i.e. a symbolic pointer to the real copy in a different directory/folder. This avoids having multiple copies of the application. > 3. A related (but less important) issue is how to get a RasMac icon to > start a script automatically. The manual mentions an RSML file, but we > think that means the file must be created by RasMol (which currently > excludes all manually edited scripts). Does anyone know how to do this? It should be possible to pick up the script file icon on a Mac and drop it on the RasMac application (or an alias of it). This instructs RasMol to open that file [similar to picking up a PDB file in the Windows File Manager and dropping it on the RasMol graphics Window]. By default, the Mac assumes that 'TEXT' files are PDB files. However, it is possible to modify the type of a file, using ResEdit or any of a number of public domain utilities, to 'RSML'. This means that when the file is dropped on RasMac it is treated as a script to be executed. Script files generated by RasMol on the Macintosh are by default type 'RSML'. Another feature is that ResEdit and other programs can change the owner or creator of a file. By setting this to 'RSML', when the script file's icon is double clicked, RasMac is started up (from anywhere on the machine) and the script is executed. I hope this unravels some of the mysteries of the Mac... Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 >>>>------>------>------>------>------>------>------>------>------>------> Date: Sun, 26 Nov 1995 22:13:19 +0000 To: rasmol@noc1.oit.umass.edu From: Bernhard Vogler Subject: introduction Dear rasmol people, I'am an organic chemist, mostly dealing with NMR. However since a short time I felt myself responsible for the Organic Praktikum. There I started to biuld up an information server based on WWW, so that the students wotking in our laboratory classes have a chance to refresh the necessary chemistry on a computer. For that reason I got interested in rasmol, because I think it's an easy and handsome tool to show 3-dimensional organic structures ( even simpler ones ). It seems to me that so far I'm the only one dealing with smaller molecules, nevertheless rasmol is a perfect program to use. I'm also planning to probably use rasmol for NMR-teaching. I found some hints that clicking NMR-maps can show changes in the representation in the rasmol-view. So far I haven't had the time to go in depth and use it. This however looks very promosing to me, highlighting specific protons after clicking on let's say a cross-peak in a HH-COSY-spectrum.... cheers B. Vogler ------------------------------------------------ Bernhard Vogler Institut fuer Chemie Universitaet Hohenheim Garbenstrasse 30 70593 Stuttgart Tel.: (49)711 - 459 - 2944 - 2963 - 3908 FAX:(49)711 - 459 - 2951 e-mail: chemvogl@uni-hohenheim.de ------------------------------------------------ >>>>------>------>------>------>------>------>------>------>------>------> Date: Sun, 26 Nov 1995 16:54:43 -0800 To: rasmol@noc1.oit.umass.edu From: molinaro@lcbvax.cchem.berkeley.edu (Marco Molinaro) Subject: Introduction Hello to all you Rasmollers out there, I started using Rasmol as a graduate student working on 3D structure-function relationships in RNA for Professor I. Tinoco, Jr. at UC Berkeley. I enjoyed teaching and using computers so much I decided that once done with my doctorate, I would devote my time to using computers as educational tools to teach undergraduates chemistry and molecular biology. In my last year of school I teamed up with a few professors and helped write a grant to the National Science Foundation to restructure the undergraduate curriculum. We got funded and I started the MultiCHEM facility to develop computer-based materials for instruction in support of the ModularCHEM Consortium of schools (for more info on our consortium refer to http://www.cchem.berkeley.edu:8080, for the MultiCHEM home page go to http://www.cchem.berkeley.edu/MultiCHEM/ ). So what does any of this have to do with Rasmol you ask, well, I thought Rasmol was an excellent program with a great many desirable features except two - the ability to show multiple molecules, and a simple to use interface for students. In the Spring of 1995, I created an assignment for a class of 80 students enrolled in a non-majors introductory chemistry course. Using RasMac 2.5 and Netscape, they were led through observing and comparing various molecules (http://www.cchem.berkeley.edu:8080/Chem10/assign2.html). I observed the students and listened to their praise and complaints about the program. Starting in July, an excellent programmer, Gary Grossman, and I started to modify RasMac. We added the capability of multiple molecules, a simple to use interface for students, and several other modifications, so was born RasMac 2.5 UCB 1.3 (our Rasmol page with information and pictures of our interface along w/ a link to download the Mac version is at http://hydrogen.cchem.berkeley.edu:8080/Rasmol/). In the Spring of 1996 we will have the opportunity to test our enhanced program on the non-majors as well as the majors course. Since early November, we have started working with Roger Sayle - THE Rasmol creator - and by Christmas we will have an enhanced version of RasMol 2.6 UCB 1.3 for the Mac and Windows (Eric Martz is currently beta testing our Windows version). Within a few months we will have a version of Rasmol with VCR controls which allows one to record frames in a movie (which is all saved in a compact text file) and play them forwards, backwards, or as a movie with interpolation between frames. We already have the code working on the Mac and are currently debugging and testing with people in the area to see how they use it and what we should add. By the way, we have a Smells database (a collection of small molecules with odoriferous properties at http://www.cchem.berkeley.edu:8080/Smells/index.html) as well as a very brief VSEPR tutorial (at http://www.cchem.berkeley.edu:8080/VSEPR/VSEPR.html) both of which rely on Rasmol. These materials are the beginning of our instructional web material, much more is under development. If you use any of our materials, whether personally or in the classroom, please send me comments so that we may improve our product and document your interest in our work for the National Science Foundation. Look forward to hearing from you all on the mailing list ! Thank you Eric for starting it ! Ciao, Marco _________________________________ Dr. Marco Molinaro molinaro@cchem.berkeley.edu MultiCHEM - Director of Multimedia Development Department of Chemistry University of California, Berkeley Berkeley, Ca. 94720-1460 510 643-1003 FAX : (510) 643-1471 >>>>------>------>------>------>------>------>------>------>------>------> Date: Fri, 01 Dec 1995 22:35:08 -0500 (EST) From: Eric Martz Subject: Custom PDB's To: rasmol@noc1.oit.umass.edu Craig Walsh of UCSD just informed me about the following. You serious protein guys have to realize how amazing all this is to armchair protein travelers such as myself. I've placed links to several of the Swiss resources on the RasMol branch I'm maintaining here. BEGIN QUOTE from Craig Walsh: ... those interested in protein structure may also find the following link useful: http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html This address is for the Swiss-Model home page which has a number of interesting programs for structural analysis of proteins. One useful feature is the ability to upload a protein sequence of interest and have the Swiss-Model server produce an protein structure databank file that can be analyzed with RasMol and other 3D viewers. This method doesn't always give the best results, because the algorithm used is based on searching the existing structure databases for homologies. But, for some genes, the results can be quite interesting. END QUOTE /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 05 Dec 1995 04:59:08 -0500 From: charlie@telemann.pse.umass.edu (leonard charles dickinson) To: rasmol@noc1.oit.umass.edu Besides the simple esthetic pleasure of having a manipulable color display of that fabulous imaginative object, the molecule, at my control through rasmol, I have interests in molecular displays for teaching and illustration of various effects such as Nuclear Overhauser Enhancements, couplings, etc which are integral to understanding Nuclear Magnetic Resonance. My special interest is in smaller molecules and I want to learn (easy?) ways of constructing, or finding libraries of, specific molecular coordinates I need, e.g. cholesterol, in proper rasmol-usable format. Charlie |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | | |Dr. L.Charles Dickinson voice mail and office (413)5771428 | |Director of NMR Instrumentation lab telephone (413)545-0630, -5413 | |Conte National Center for Polymer Research fax (413)5450082 | |Department of Polymer Science and Engineering office Conte Rm 428 | |University of Massachusetts | |Amherst MA 01003 USA charlie@telemann.pse.umass.edu | | | | A fact is only a fact; | | An idea is only an idea. | | -Jean Piaget | |>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<| >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 05 Dec 1995 17:36:00 -0500 (EST) From: Eric Martz Subject: cholesterol To: rasmol@noc1.oit.umass.edu Status: O Dear Charlie: Have you followed the links on the rasmol web page? I should think you would find cholesterol somewhere there. If not, there's a link to a place where you can specify the chemical forumula and it will return the PDB file to you, based on theory. I've added a number of links over the past couple of weeks. All under 'molecules galore'. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ From: jsb2@camsci.com >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 5 Dec 95 22:05:06 EST To: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu Subject: Re: cholesterol >Have you followed the links on the rasmol web page? I should think >you would find cholesterol somewhere there. If not, there's a link >to a place where you can specify the chemical forumula and it will >return the PDB file to you, based on theory. I've added a number of links >over the past couple of weeks. All under 'molecules galore'. That would be the CORINA project, at http://schiele.organik.uni-erlangen.de/services/3d.html It's one of the few places on the Web that will generate coordinates "from scratch", although you do need to give it *something* -- a formula won't do the trick, since a formula doesn't uniquely describe a molecule. There's a structure for cholesterol at http://chemfinder.camsoft.com, but not in a format that Rasmol can read. If you're into convoluted, you could download the structure from chemfinder.camsoft.com, convert it to SMILES using the free version of ChemDRaw, and use that SMILES string as your CORINA input. It should work, but for some reason I can't get through to the CORINA site just this second to check it out. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com >>>>------>------>------>------>------>------>------>------>------>------> Date: Mon, 11 Dec 1995 11:54:01 -0500 (EST) From: Eric Martz Subject: WPDB 2.0, CCMS, Swiss-PDBViewer To: rasmol@noc1.oit.umass.edu Status: O Thanks to help from Philip Crawford (U New South Wales, Sidney AU), I've found the origin of WPDB at the Computational Center for Macromolecular Structures (CCMS) at the San Diego Supercomputer Center (SDSC), and a bunch of other good things there including version 2.0 of WPDB. They are now linked to our RasMol web page under 'other free resources'. Nicolas Guex (Glaxo) provided a description of what his newly revised Swiss-PDBViewer can do, also now available under 'other free resources'. As time permits, I'll link some other suggestions I've received. If anyone wishes to suggest revisions, clarifications, or improvements in my brief and hastily authored descriptions of the above resources, or others on our web page, feel free to let me know. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 13 Dec 1995 00:44:01 -0500 (EST) From: Eric Martz Subject: New goodies @ RasMol To: rasmol@noc1.oit.umass.edu Thanks to Toni Kazic and Jonathan Brecher and some late night web browsing, I've added several new links to the RasMol home page. These include the Weblet version of RasMol (Eolas Technologies), Klotho as a source of micromolecules, ChemFinder as ditto with the free programs ChemDraw and Chem3D as viewers (from CambridgeSoft Corp.), the ProTeach kinemage series of the Protein Society, and the exciting chemistry pages at Leeds and Imperial College. The Principles of Protein Structure course will be linked tomorrow, I promise, Alan (Mills). Our server seems to be locking out telnet at 1:00 AM so I wasn't able to add it now. Keep the suggestions coming! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 13 Dec 1995 13:43:02 -0500 (EST) From: Eric Martz Subject: Scripts fixed; Drug Design Course To: rasmol@noc1.oit.umass.edu Cc: S.M.Green@chem.leeds.ac.uk Turns out I had botched up the packaging of two of the scripts I offered on the RasMol page, namely the antibody and MHC scripts. I've repackaged them, I believe correctly. If anyone has problems running them, let me know. Thanks to Benjamin Whitaker, I've linked Stuart Green's class page on Chemotherapy and Drug Design to my list of classroom uses of RasMol. This class page includes a RasMol-based exercise based on design of inhibitors of HIV-1 protease. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 14 Dec 1995 09:29:42 -0500 (EST) From: Eric Martz Subject: RasMol activity To: rasmol@noc1.oit.umass.edu Cc: kelley@flowcyt.cyto.purdue.edu (Steve Kelley) We now have 32 subscribers to the RasMol email list. If you're interested in who, send 'review rasmol subscribers' to listproc@lists.umass.edu. During the past week, the RasMol home page received visits from 207 unique Internet addresses (average 30/day). About half were from the USA (mostly .edu) and the other half from 22 countries. I would be interested in web page visiting rates others on this list have observed, for a frame of reference. I also manage a web catalog of free software for analysis of flow cytometry data, the only such catalog in the world. It has been getting visits from 500 unique IA's/month for the past several months (16/day). The email list for flow cytometry has about 1,000 subscribers. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 14 Dec 1995 15:13:31 -0500 (EST) From: Eric Martz Subject: RasMol and sendras To: rasmol@noc1.oit.umass.edu RasMol folks, Whilst creating a lecture course on computer-aided drug design with a web-based workshop, I've been experimenting with the interprocess communication (IPC) mechanism in RasMol2.6beta. The result is a short C program - sendras - that sends a rasmol script via a unix socket (sorry, but it won't work with PC's or Mac's) to a running rasmol process. This way I can control the rendering, labelling, highlighting, etc. of a molecule directly from HTML links without restarting rasmol. Unfortunately, I've had to make minor modifications at the RasMol IPC end. If anyone is interested, the several programs with instructions and examples can be found at http://www.chem.leeds.ac.uk/Project/Teaching/workshop.html Cheers, Stuart Stuart M. Green S.M.Green@chem.leeds.ac.uk School of Chemistry University of Leeds Tel +44 113 233 6596 Leeds, LS2 9JT, England Fax +44 113 233 6563 [Resent to the rasmol list by E. Martz] /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 14 Dec 1995 19:28:22 -0600 To: rasmol@noc1.oit.umass.edu From: nwinter@tigger.stcloud.msus.edu (nathan winter) Subject: Summer '96 Symposia: Molecular Graphics in Lecture and Lab. Hi, I am organizing a session for the CHEMED Division at the ACS national meeting in Orlando (Aug. 25-30). This session will focus on how chemistry instructors are using molecular graphics in their lectures, and any laboratory exercises they have designed where the students are using molecular graphics or similar programs interactively. If you have any interest in relating your experiences or exercises please contact me. Thank You, Nathan Winter St. Cloud State University nwinter@tigger.stcloud.msus.edu 612-255-2052 612-255-3031 Dr. Nathan S. Winter nwinter@tigger.stcloud.msus.edu 612-255-2052 Deptment of Chemistry 358 Math Sciences St. Cloud State University 720 Fourth Ave South St. Cloud, MN 56301-4498 >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 21 Dec 1995 14:42:28 -0500 (EST) From: Eric Martz Subject: RasMol page activity To: rasmol@noc1.oit.umass.edu I'm pleased to find that the number of visitors to the RasMol home page increased 1.8-fold between the past two weeks. The only way I know how to estimate the number of visitors to a web page is by counting the unique Internet addresses (UIA) in the log. Our log is discarded after one week because of its size so I can only do a week at a time. Here are the results for http://www.umass.edu/microbio/rasmol. Week Ending UIA Fetches F/U %USA Countries ---------------------------------------------------- 12/12/95 207 2416 11.7 50% 23 ca/uk/au 12/20/95 372 5740 15.4 50% 25 uk/jp/ca ---------------------------------------------------- Fetches: number of log entry lines. A single person looking at index.html only generates multiple fetches, one for index.html and one for each GIF linked to that page. F/U: Fetches/UIA, which should be proportional to how much each person looks at, but will also increase with increasing complexity of the branch. %USA: Percentage of UIA's with 3-letter ends (vs. 2-letter non-USA ends). The denominator is the UIA's with alphabetic ends (about 8% have numeric ends). The within-USA percentages are about 70% edu, 18% com, 9% net, 4% gov. Countries: number of countries including the USA. The three (excluding the USA) with the highest frequencies are indicated, highest first. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 28 Dec 1995 20:21:51 -0500 (EST) From: Eric Martz Subject: More goodies on our page To: rasmol@noc1.oit.umass.edu I've been sprucing up our RasMol web page with more goodies, including links to the following. This is an invitation to revisit it if you haven't taken a look in the past 2 weeks. http://www.umass.edu/microbio/rasmol Protein Motions Database (Stanford) under molecules galore. Dave Woodcock's Okanagan PDB's including aspartame, ibuprofen, LSD and 47 more of the same ilk (under micromolecules). Whole virus images from Univ Wisconsin. If you want to see RasMol huff and puff, try viewing their alpha-carbon PDB for the coat of rhinovirus (48,000 atoms). Kudos to Roger Sayle: RasMol didn't crash under the strain. >>On the other resources page: The DNA double helix on an earth-and-sky backdrop: Paul Thiessen's PovChem gallery (Univ Illinois). The fantastic Mathematics and Molecules pages of New York University. Molecular animations by MovieMol (MPEG). Gorgeous images from the Midas+ gallery at UCSF. And more ... Enjoy! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 28 Dec 1995 20:23:51 -0500 (EST) From: Eric Martz Subject: Introductions, please (reposting) To: rasmol@noc1.oit.umass.edu We now have 40-some subscribers on this list. This is a reposting of an earlier message for new subscribers who may not have seen it. I'd like to invite each subscriber to send a paragraph or two introducing themselves and describing their uses of RasMol (already accomplished, or planned for the future), and any other information they wish to share. Bear in mind that the subscribers are a diverse group, including at one extreme investigators who do molecular modeling and structural research, and at the other end, people such as myself who know very little about macromolecular structure (mostly learned because of RasMol), and who have seen little or no other molecular visualization or modeling software, but who are enthusiastic about the teaching potential of RasMol. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Sat, 30 Dec 1995 11:57:54 -0500 (EST) From: Thomas Andrew Manderfield To: rasmol@noc1.oit.umass.edu Subject: greetings... Hello Rasmolians, I wrote this introduction and soon realized I went on forever. Well, 2 or 3 paragraphs were requested, and it is difficult to justify 9 or 10. I have left it all here though, after all it'll give you a pretty good background of my work andhow I use Rasmol. I would like to invite any comments since my work so far has been without the benefit of your insight. What I do: I am creating educational media for the Biological Sciences Department at Carnegie Mellon. Biology is not my field of expertise, but integrating my computational skills on this project has taught me much about it. I found Rasmol a couple of months ago. I spend much of my time utilizing it to create animations that will be distributed with the media. What I have done: After some time, I considered trying something else. Mainly it was due to the disabled save function in scripts. I was trying to script it to produce many frames that I will compile into movies outside of Rasmol. While trying to find a "work around" to that situation, I looked around for other solutions. For some time I attempted to get the PDB file into another usable format for animations. Linus (aka MacMolecule) had some built in movie making but not the control I was looking for. I attempted finding a conversion to another 3D type. I desperately searched for a conversion to DXF. While that standard is not much liked it is *very* common in commercial 3D packages. With the conversion, I would easily been able to automate the animations and have control of the rendering. A minor detail is the 8-bit limit on the Macintosh side. I do not know if this is true on other platforms. Nonetheless, I found no conversion to the DXF problem. I found the PDB2POV but I am not sure of animating it and am more concerned with the speed of that solution. I found babel but as far as I know the conversion to MacroModel would've been the best bet. Unfortunately, I thought MacroModel meant MacroMedia's MacroModel, which is a commercial 3D modeling program (and most likely reads DXF) but I soon discovered that it was Columbia's and while I don't know if they support the conversion, I don't have access to it. So by this point commercial Chem Drawing companies were telling me that their next versions would include DXF export and others inquiring about it were being forwarded to me. I am a little confused by this link not existing between the two fields of 3D modeling and Molecular Modeling, but who am I to question it. My last hope was when I found MolView (aka Macinplot). I had a very difficult time learning how to use it and by the time I was able to "push all the buttons" I discovered that its export of DXF was not fully developed. So I returned to RasMac. It is by far the best I've seen out there and its command line interface and its script ability far outweigh the bit depth problem. I had also found that "work around" to scripting save. Although I just recently discovered it re-incorporation, I will most likely stick to "Print2Pict". It was an ironic solution, can't save?, all right I will print the picture to a file. (I have been able to Apple Script around the dialogue boxes) In addition, there is a Print2Quicktime extension to print2pict, which automates another step of assembling all those frames together. What I want to do: Actually, I have never had the opportunity to see someone else's script. I have planned all along to create movies from frames in RasMac, but then played through Quicktime. I was excited to see some scripts published on the Rasmol page at umass but until I have the time, I am unable to do the conversions. I attempted with Mac utilities but was unable to get into the guts of the scripts (I got some of the top level scripts but that is it). Do the scripts produce animations or are they closer to a slide show? I have been spending quite a bit of time trying to code the navigation to make clean pans with other scripting languages. Is there a way to get RasMac to do it? I can't tell if I am just dumb or if the math is that complex. Recently I came up with some code that converted two rotations of specific views, as they were outputted from Rasmol Scripts, into spherical coordinates and from there into Rectangular Coordinates, then computes a midpoint between them, converts that back to spherical coordinates. Unfortunately that approach and/or my math is flawed and I am still working with it. Does the right-hand rule work for all axis? My interpretation was to point your thumb towards the axis and the positive rotation about that axis was with the direction your fingers turned (counterclockwise). It seems like the +y goes down as you look at the screen, yet rotating y positively goes the other way. I am very inexperienced with dealing in 3d. Any help on this would be much appreciated. I would really like to know how to tell rasmol to pan cleanly between two locations, be it absolute or relative, does not matter. I would just like to get x number of views between two views as to create the frames for a movie. If any of you have scripts that you could share with me, it would be very valuable to get a perspective with my own work. I would also like to make those script files on the server more accessible. If I could get the files uncompressed from someone, I'd be willing to set up a RasMac version for the server. Not sure how they'd convert for other platforms or if there would be a more universal format to for PC/UNIX/Mac etc. Are the scripts huge? Can they be e-mailed? On the Mac side of things, they are just text and easy to move around. Are there differences in the scripts themselves for different platforms? Thanks for the time and a Happy New Year to all, Tom ___ ()-----------------------/ /\\----------------------------() / // \\\ // / | ()-------------------------------------------------------() | | | | /| Thomas Manderfield Footlocker Project | =/] [=| Graphic Commnctns Management Biological Sciences |=]/ | Carnegie Mellon Mellon College of Science | () | 412.688.8313 412.268.5647 | / | |/ ()_______________________________________________________() >>>>------>------>------>------>------>------>------>------>------>------> Date: Sat, 30 Dec 1995 16:12:05 -0500 (EST) From: Eric Martz Subject: Scripts for Mac's To: rasmol@noc1.oit.umass.edu In message Sat, 30 Dec 1995 11:57:54 -0500 (EST), Thomas Andrew Manderfield writes: > to make those script files on the server more accessible. If I could > get the files uncompressed from someone, I'd be willing to set up a > RasMac version for the server. I need a volunteer willing to convert my DOS-packaged RasMol scripts to a Mac-packaged (stuffit-compressed?) form, and ftp them back to me so I can put them on the RasMol home page. This should be someone conversant enough with Mac's to know how to package the scripts so people getting them from the web page will have the easiest possible installation. Thanks, Tom, for offering, but this will work best if we can locate a volunteer who has the DOS capability in conjunction with the Mac capability, since this will not be a one-time operation (see below). Altho developed under RasWin, the scripts themselves are all plain ASCII text, hence will run fine on a Mac (I've done it) and I presume on unix. Its just too inconvenient for me (and I lack any Mac expertise) to package them up in Mac format. The script files would be quite cumbersome to move around in raw form. The larger ones (antibody and MHC) have 35-45 separate files which include 30-some script files per se (*.top files which call *.scr files which call each other) and a few PDB files totaling about a megabyte per script, plus a few *.txt and readme documentation files. The scripts per se are not very bulky (40-80K bytes per script) but are broken into dozens of files to allow structured coding. So among the 4 scripts I'm currently offering on the web page as four compression-packaged files, there are 117 separate files including 2.6 megabytes of PDB files. When you download one of these packages, you run it under DOS (each is a self-extracting EXE file so you don't even have to know how to use PKUNZIP), and all you have to do is call the top level script in RasMol's command line window (e.g. 'script antibody.top'). If you want to keep separate scripts in separate directories (definitely a good idea!), there are some Windows tricks detailed in the accompanying TXT files. I don't know how to do these tricks on the Mac. The volunteer would need to be willing to re-package the scripts periodically when I improve or further debug them. That will probably be not more than a few times per year, if even that often. It would obviously be best if the volunteer test-runs each script on the Mac to be sure everything works as advertised. During the next year (but when? ...), I hope to incorporate Padlan's whole IgG into my antibody script, and hopefully use some of the Berkeley-enhancements to RasMac and RasWin to show relative movements of two molecules, as well as just make the scripts better. BTW, if anyone else wants to build on the starts I've made, go ahead, and we can link any enhanced scripts to the RasMol page for others to use. Is there a volunteer out there? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ Archive rasmol, file 96.01. Part 1/1, total size 70231 bytes: >>>>------>------>------>------>------>------>------>------>------>------> Date: Mon, 01 Jan 1996 17:46:25 -0500 (EST) From: Eric Martz Subject: Scripts available via ftp for Macs To: rasmol@noc1.oit.umass.edu Tom Manderfield at Carnegie Mellon Univ is working on how best to package my RasMol scripts for the Mac. We could use help from other Mac experts who may know how to make the script files cooperate most smoothly with RasMol on the Mac (sorry I don't know the right terminology), and how to keep different sets of script files separate (perhaps each with its own icon?). I'd like Mac people to be able to get the packaged scripts smoothly from the web (e.g. without knowing how to use anonymous ftp on large numbers of files, and with minimal fuss for installation). However, so that Tom wouldn't have to figure out how to unzip my DOS packages on his Mac, I put the ready-to-run, uncompressed ASCII files on our anonymous ftp server. Anyone else who wants to try the scripts on a Mac may prefer to get them this way. There are three major scripts on marlin.bio.umass.edu in /pub/shareware/rasmol/scripts/dna1 /pub/shareware/rasmol/scripts/antibody /pub/shareware/rasmol/scripts/mhc1 Unless you're an immunologist, you'll probably prefer to start with the DNA script. Note that it runs unattended, while the other two have frequent pauses (continuing when any key is pressed). The time delays I cobbled up for the DNA script are totally machine dependent, so may be too slow or too fast on different computers. Hopefully Roger (or Marco of the Berkeley group) will put a real time delay in a forthcoming version of RasMol to fix this (hint :-). Also, hopefully one of them will implement a key (such as Q to quit) which can break out of a script before the end. Its easy enough to set up a meta-script which calls the same script over and over 100 times so it will re-run continuously for unattended attention-getting, e.g. at a meeting. However, when someone passing by expresses an interest in trying RasMol, it's a bit crude to have to Ctrl-Alt-Del in Windows to stop it, then having to re-arrange the windows from scratch. Also rather painful when debugging the script in the first place (hint, hint :-}. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 2 Jan 1996 10:06:28 +0000 (GMT) From: Stuart Green To: rasmol@noc1.oit.umass.edu Subject: Introduction Hi, My research interests involve developing new computational techniques for the drug design/molecular modelling field. To this end, I use rasmol for molecular visualisation. Here at Leeds University, I run a course on computer-aided drug design. To enhance the material, I am currently developing a set of web pages containing the lecture notes with links to appropriate molecule files (rasmol is run as a helper application). As RasMol2.6beta (plus a minor modification) supports unix sockets, I have written a short C program that will send a set of rasmol commands to an already running rasmol process. In this way, rasmol rendering etc. can be controlled from HTML links to rasmol scripts. Check out http://www.chem.leeds.ac.uk/Project/Teaching/cadd.html Your thoughts, comments appreciated, Stuart Stuart M. Green S.M.Green@chem.leeds.ac.uk School of Chemistry University of Leeds Tel +44 113 233 6596 Leeds, LS2 9JT, England Fax +44 113 233 6563 >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 2 Jan 1996 19:40:14 -0600 To: rasmol@noc1.oit.umass.edu From: nwinter@tigger.stcloud.msus.edu (Nathan Winter) Subject: Introduction Hi, I'm the odd-ball on the list because I don't use Rasmol. I have been using David Richardson's Kinemage for my undergraduate biochemistry course. I use it during my lectures, and I also have a three hour computer lab where the students examine four different protein structures. The students' reactions have been overwhelming favorable to its use, particularly for the hands on lab. I'm organizing a symposium on using molecular graphics for teaching at the August ACS meeting in Orlando. There are going to be two talks on Kinemages, but so far I can't locate anyone who will say what they are doing with Rasmol. It would be wonderful if we could compare and contrast these graphics programs, so if there are any interested Rasmolers please drop me a line! Bye, Nate Dr. Nathan S. Winter nwinter@tigger.stcloud.msus.edu 612-255-2052 Deptment of Chemistry 358 Math Sciences St. Cloud State University 720 Fourth Ave South St. Cloud, MN 56301-4498 From: nohmi@smsnet.saga-med.ac.jp >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 04 Jan 1996 10:55:36 To: rasmol@noc1.oit.umass.edu Subject: introduction Hi. I am a physiologist, and have researched the intracellular calcium changes in response to the stimulus. I have not yet used Rasmol, but have a plan to use it in future. One of my interests is the interaction between the drug and membrane receptor. To visualize two molecules, I'd like to use Rasomol. My present position is the vice-president of Central Laboratories for Medical Study and Research Equipment. There are many users who use our machines. Some of them want to have the modeling system of the molecule. I need various informations about molecular imaging system. nohmi@smsnet.saga-med.ac.jp Mitsuo Nohmi Central Laboratories for Medical Study and Research Equipment Saga Medical School Nabeshima, Saga 849 ,Japan >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 4 Jan 1996 11:51:15 +0000 (GMT) From: Sayle Dr R A To: nwinter@tigger.stcloud.msus.edu cc: rasmol@noc1.oit.umass.edu Subject: Re: Introduction On Tue, 2 Jan 1996, Nathan Winter wrote: > I'm organizing a symposium on using molecular graphics for teaching > at the August ACS meeting in Orlando. There are going to be two talks on > Kinemages, but so far I can't locate anyone who will say what they are > doing with Rasmol. It would be wonderful if we could compare and contrast > these graphics programs, so if there are any interested Rasmolers please > drop me a line! An interesting comparison of the uses of RasMol, Kinemage, pdVwin and Hyperchem for teaching has recently been published in: Alvaro Sanchez-Ferrer, Estrella Nunez-Delicado and Roque Bru (Murcia Univeristy Spain), "Software for Viewing Biomolecules in Three Dimensions on the Internet", Trends in Biochemical Sciences (TIBS), July 1995, Volume 20, pages 286-288. It should make interesting reading to many of the people on this mailing list. It details which "course topics" are best covered by each of the programs. Personally, I regard Mage and RasMol as complementary [that's why I added the "write kinemage" command :>]. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 >>>>------>------>------>------>------>------>------>------>------>------> Date: Fri, 5 Jan 1996 00:04:26 +0000 To: rasmol@noc1.oit.umass.edu From: th@mrc-cpe.cam.ac.uk (Tim Hubbard) Subject: announcement of rmscript for mac/rmscop for unix Cc: S.E.Brenner@bioc.cam.ac.uk Hi everyone, I have just joined this list having been told about it by rasmol's author: rasmol users my be interested in the scop (structural classification of proteins database) on WWW which is mirrored worldwide and uses an embedding mechanism to specify rasmol commands related to PDB files in WWW pages. The database can be found at: http://scop.mrc-lmb.cam.ac.uk/scop/ The rasmol interface to scop does not send PDB files over the net, but sends commands using MIME types requesting that a local copy of rasmol loads a PDB file and display it in a certain way. On unix systems the simplest way to configure rasmol is to point it to a disk containing PDB, but a tcl/tk script 'rmscop' can also be installed which gives extra functionality. On mac systems, it is assumed that PDB is probably not local, so a facespan/applescript application 'rmscript' can be installed that handles PDB file fetching and caching from remote disks or internet servers. These helper scripts/applications and documentation is available from: http://scop.mrc-lmb.cam.ac.uk/std/rs/ The scripts were designed to support scop, but can be used generally to support PDB access from mac/unix. Best wishes, Tim Hubbard (for the scop authors) ------------------------------------------------------------------------------ Dr Tim Hubbard email: th@mrc-lmb.cam.ac.uk Centre for Protein Engineering (CPE) Tel: +44 1223 402131 MRC Centre, Hills Rd, Cambridge, Fax: +44 1223 402140 CB2 2QH. UK. URL: http://www.mrc-cpe.cam.ac.uk/th/ ------------------------------------------------------------------------------ >>>>------>------>------>------>------>------>------>------>------>------> Date: Fri, 5 Jan 1996 10:46:03 GMT To: rasmol@noc1.oit.umass.edu From: gbca05@udcf.gla.ac.uk (James Milner-White) Subject: Re: Introduction Dear Dr Winter I look after a Power Macintosh cluster at Glasgow on which mainly RASMOL is used for teaching aspects of biochemistry, microbiology, pharmacology and immunology to assorted undergraduate students. I have set up a 3 day teaching course on protein 3-D structure and protein-nucleic acid complexes, plus shorter courses on lactate dehydrogenase, ATP/GTP binding proteins, lambda repressor, antibodies, file retrieval via INTERNET, manipulation of coordinate files and 3Dstructure and sequence comparison. The September 1995 TIBS Computer Corner article Roger Sayle and I wrote benefitted from the courses I ran. I have given talks in the UK about previous versions of the courses and would welcome the chance to contribute to your meeting by putting a case for RASMOL, James Milner-White >Hi, > I'm the odd-ball on the list because I don't use Rasmol. I have >been using David Richardson's Kinemage for my undergraduate biochemistry >course. I use it during my lectures, and I also have a three hour computer >lab where the students examine four different protein structures. The >students' reactions have been overwhelming favorable to its use, >particularly for the hands on lab. > I'm organizing a symposium on using molecular graphics for teaching >at the August ACS meeting in Orlando. There are going to be two talks on >Kinemages, but so far I can't locate anyone who will say what they are >doing with Rasmol. It would be wonderful if we could compare and contrast >these graphics programs, so if there are any interested Rasmolers please >drop me a line! > >Bye, >Nate > >Dr. Nathan S. Winter nwinter@tigger.stcloud.msus.edu >612-255-2052 > >Deptment of Chemistry >358 Math Sciences >St. Cloud State University >720 Fourth Ave South >St. Cloud, MN 56301-4498 Dr E. James Milner-White Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G128QQ, UK. E-mail: gbca05@udcf.gla.ac.uk FAX: +44(0)141-330-4620 Tel.: +44(0)141-330-5283 >>>>------>------>------>------>------>------>------>------>------>------> Date: Fri, 5 Jan 1996 07:54:50 -0500 (EST) From: William McClure To: rasmol@noc1.oit.umass.edu Subject: Re: Introduction References: <8104.199601051046@lenzie.cent.gla.ac.uk> Dr. Milner-White, I read your response to Dr. Winter about the three-day course on protein structure, etc. Has any of it been placed on WWW pages? Will it be in the future? Sincerely, Will McClure >>>>------>------>------>------>------>------>------>------>------>------> Date: Sat, 06 Jan 1996 16:12:35 -0500 To: rasmol@noc1.oit.umass.edu From: Kent Smith Subject: Rasmol and Programs Is anybody using rasmol as a graphics file generator for making molecular movies? (flic files of changes of camaera position for a known molecule geometry). I am trying to do this and want to collaborate. thanks Kent Smith Kent Smith e:mail mmc@tyrell.net voice (913) 888-5719 fax (913) 888-3627 "The scenery only changes for the lead dog" >>>>------>------>------>------>------>------>------>------>------>------> Date: Mon, 8 Jan 1996 17:15:39 -0600 To: rasmol@noc1.oit.umass.edu From: nwinter@tigger.stcloud.msus.edu (Nathan Winter) Subject: Re: Introduction Dear Dr. Milner-White, Your material would fit in ideally into the program, and I'd be very interested in hearing what you're doing. I'm waiting for abstract forms from the ACS, and when they arrive I'll send some to you. I don't know if you have been to an ACS meeting before, but the talks are fast and furious. In a typical morning or afternoon session there are about six or eight talks of about one half hour each. If you have much to speak about, and it seems as if you do, occasionally people give more than one lecture. There is another professor who uses Rasmol who has expressed an interest in speaking, Duane Sears from the University of California at Santa Barbara. He has a website that you may be interested in examining: http://www.mcl.ucsb.edu/classes/biol108/108ahome.htm Bye, Nate >Dear Dr Winter >I look after a Power Macintosh cluster at Glasgow on which mainly RASMOL is >used for teaching aspects of biochemistry, microbiology, pharmacology and >immunology to assorted undergraduate students. I have set up a 3 day >teaching course on protein 3-D structure and protein-nucleic acid >complexes, plus shorter courses on lactate dehydrogenase, ATP/GTP binding >proteins, lambda repressor, antibodies, file retrieval via INTERNET, >manipulation of coordinate files and 3Dstructure and sequence comparison. >The September 1995 TIBS Computer Corner article Roger Sayle and I wrote >benefitted from the courses I ran. I have given talks in the UK about >previous versions of the courses and would welcome the chance to contribute >to your meeting by putting a case for RASMOL, >James Milner-White > > >>Hi, >> I'm the odd-ball on the list because I don't use Rasmol. I have >>been using David Richardson's Kinemage for my undergraduate biochemistry >>course. I use it during my lectures, and I also have a three hour computer >>lab where the students examine four different protein structures. The >>students' reactions have been overwhelming favorable to its use, >>particularly for the hands on lab. >> I'm organizing a symposium on using molecular graphics for teaching >>at the August ACS meeting in Orlando. There are going to be two talks on >>Kinemages, but so far I can't locate anyone who will say what they are >>doing with Rasmol. It would be wonderful if we could compare and contrast >>these graphics programs, so if there are any interested Rasmolers please >>drop me a line! >> >>Bye, >>Nate >> >>Dr. Nathan S. Winter nwinter@tigger.stcloud.msus.edu >>612-255-2052 >> >>Deptment of Chemistry >>358 Math Sciences >>St. Cloud State University >>720 Fourth Ave South >>St. Cloud, MN 56301-4498 > >Dr E. James Milner-White >Division of Biochemistry and Molecular Biology, Institute of Biomedical and >Life Sciences, University of Glasgow, Glasgow, G128QQ, UK. >E-mail: gbca05@udcf.gla.ac.uk >FAX: +44(0)141-330-4620 >Tel.: +44(0)141-330-5283 Dr. Nathan S. Winter nwinter@tigger.stcloud.msus.edu 612-255-2052 Department of Chemistry 358 Math Sciences St. Cloud State University 720 Fourth Ave. South St. Cloud, MN 56301-4498 >>>>------>------>------>------>------>------>------>------>------>------> Date: Mon, 8 Jan 1996 17:23:05 -0600 To: rasmol@noc1.oit.umass.edu From: nwinter@tigger.stcloud.msus.edu (Nathan Winter) Subject: Re: Introduction I'm sorry! I didn't mean to send my reply to everyone! Sincerest Apologies, Nate Dr. Nathan S. Winter nwinter@tigger.stcloud.msus.edu 612-255-2052 Department of Chemistry 358 Math Sciences St. Cloud State University 720 Fourth Ave. South St. Cloud, MN 56301-4498 From: moreaut@univ-tours.fr >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 9 Jan 1996 18:18:36 +0200 To: rasmol@noc1.oit.umass.edu Subject: Introduction X-VMS-To: SMTP%"rasmol@lists.umass.edu" dear rasmol users My name is Thierry MOREAU and I am a lecturer in biochemistry at the University of Tours, France. I have joined this list because I am interested in Rasmol for teaching purposes. My research interests are the structure-function relationships of serine and cysteine proteinases as well as their natural protein inhibitors. I have a good background with protein purification and enzyme kinetics but during the last 4 years, my major interest has shifted to structural aspects especially using molecular model(l)ing to study the structure-function aspects. I use InsightII on a Silicon Graphics station which is of course different from Rasmol but I think Rasmol can be very useful to visualize structural aspects. Some features of the last Rasmol version are very nice: interface to molscript, script, cartoon representation .....In the lab, I run Rasmol on a PowerMac 6100/66, pretty nice.... But my major interest in Rasmol lies in its use for teaching. This is exactly the soft I was waiting for this purpose. I dreamt for it, Roger Sayle has done it!!! I would like to introduce master's degree students to the manipulation of 3D structures. I will run Rasmol on PCs under Windows NT (from 486 to Pentium) so I think it will be fast enough on these machines. I plan to prepare a mini-project including visualisation (from wireframe to cartoons), coloring the different secondary elements, measuring distances, angles.... My first idea is to use MHC molecules complexed to a peptide and a proteinase-protein inhibitor complex (trypsin-aprotinin or papain-cystatin) in order to detail the interaction between a ligand (i.e the peptide) and a protein or the interaction between two proteins. In this respect, I was very interested by the MHC script available on the Rasmol page. This gives me now a clear idea of the powerful features of Rasmol though the time which is allocated for my students (5h) will be too short to go on with advanced aspects such as script writing. I also plan to prepare with InsightII a superimposition of two similar structures (e.g 2 MHC molecules), saving the coordinates in PDB format so they will be able to visualise two superimposed molecules using Rasmol. With all the features of Rasmol, I am sure my students will be very enthusiastic using Rasmol. I should be happy to hear from rasmol users which have similar objectives. Thanks in advance Best regards *------------------------------------------------------------------* | Dr. Thierry MOREAU | | | | Laboratoire d'Enzymologie et Chimie des Proteines | | | | URA CNRS 1334 Phone: (33) 47 36 62 06 | | 2bis, Bd Tonnelle Fax: (33) 47 36 60 46 | | 37032 TOURS cedex Email: moreaut@univ-tours.fr | | FRANCE | | | *------------------------------------------------------------------* >>>>------>------>------>------>------>------>------>------>------>------> Date: Sun, 14 Jan 1996 22:33:48 -0500 (EST) From: Eric Martz Subject: Interacting ligands To: rasmol@noc1.oit.umass.edu Dear Thierry MOREAU: Perhaps by now you have found out that the Berkeley-enhanced RasMac can move two molecules relative to each other. The publically released RasMac is built on RasMol 2.5 so won't run scripts. However, I believe the group at Berkeley will soon release enhanced RasMac as well as RasWin versions built on RasMol 2.6. Perhaps Marco Molinaro at Berkeley will provide more information (he subscribes to this list) -- Marco? When you have scripts ready, I look forward to seeing them! The link to Berkeley enhanced-RasMac is on the RasMol home page http://www.umass.edu/microbio/rasmol /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Mon, 15 Jan 1996 22:17:35 -0500 (EST) From: Eric Martz Subject: More subscribers & visitors To: rasmol@noc1.oit.umass.edu We now have 52 subscribers on this list. The command to see who they are is 'review rasmol subscribers' sent to listproc@lists.umass.edu. The breakdown by country is: 25 us/11 au/8 uk/2 jp de/1 ca se fr nz. The RasMol home page was visited by 607 people last week, up from the previous high of 372 in late December. As usual, half of the visits were from the USA. Among the 32 other countries, those with most visitors were de/uk/jp/ca. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ From: moreaut@univ-tours.fr >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 16 Jan 1996 18:25:36 +0200 To: rasmol@noc1.oit.umass.edu Subject: Help: printing via Postscript export X-VMS-To: SMTP%"rasmol@lists.umass.edu" dear Rasmol users: May be some of you have tried the Postscript option in the Export menu?? I have tried to create such Postscript files to print different views of the screen. The files created by the 3 sub-options seem to be EPSF files (i.e Encapsulated Poscscript). They are recognized by MacGhostcript (a Postscipt viewer on the Mac) but I can not send them to a Postscript laser writer to print them from utilities such as "Laser Writer utility" on a Mac. So my questions are: 1/ is it possible to create true Postscript files (i.e PS but not EPSF) if yes, how can we specify for that?? 2/ or how can we print EPSF files?? without Illustrator?? Thanks in advance for your comments, help or further details. *------------------------------------------------------------------* | Dr. Thierry MOREAU | | | | Laboratoire d'Enzymologie et Chimie des Proteines | | | | URA CNRS 1334 Phone: (33) 47 36 62 06 | | 2bis, Bd Tonnelle Fax: (33) 47 36 60 46 | | 37032 TOURS cedex Email: moreaut@univ-tours.fr | | FRANCE | | | *------------------------------------------------------------------* >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 17 Jan 1996 10:38:56 -0500 (EST) From: Eric Martz Subject: Fw: RE: rotation and writing pdb files To: rasmol@noc1.oit.umass.edu Walter Stafford in Boston asked Marco Molinaro some questions about the Berkeley-enhanced version of RasMol (available for the Mac thru our web page http://www.umass.edu/microbio/rasmol). I thought the replies, below, may be of interest to others on this list. ------------------------------ From: molinaro@lcbvax.cchem.berkeley.edu (Marco Molinaro) Tue, 16 Jan 1996 15:50:44 -0800 To: emartz@microbio.umass.edu, STAFFORD@bbri.harvard.edu Subject: RE: rotation and writing pdb files Hi Walter, >> I had a question about manipulating structures and writing out new >> PDB coordinates. I have a molecule I would like to bend in the middle and >> then write its new coordinates into a pdb file. With our enhanced version, if you can get the conformation you desire through the bond rotate command then you can save it as a new pdb file. Be warned that the molecule will not come up in the same view when you re-open it. >>Also I would like to take >> 2 structures, dock them and then write out their new pdb coordinates >> relative to each other instead of to their respective centers of mass. I >> have been using the UBC-1.3 version of RasMac-2.5. It looks hopeful (as >> thought not a great deal would be required to make it do that), but when >> it writes the files it forgets the new coordinates. I have purused the >> help file but could not find anything. We are still working on more realistic docking with use of perspective as well as real depth (currently there is no way of moving one molecule relative to the other in the Z dimension). We have not implemented any way to remember coordinates and docking of two molecules but we are working on a movie feature that would allow you to do this in a round about way. >> I have been using a program >> called MIDAS on an SGI machine to do this but would like to able to do it >> on the MAC. I don't blame you. Good luck and feel free to ask more questions directly if needed. I look forward to receiving feedback. Thanks for using our program. Regards, Marco Molinaro _________________________________ Dr. Marco Molinaro molinaro@cchem.berkeley.edu MultiCHEM - Director of Multimedia Development Department of Chemistry University of California, Berkeley Berkeley, Ca. 94720-1460 VOX: (510) 643-1003 FAX : (510) 643-1471 /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 17 Jan 1996 11:13:05 -0500 (EST) From: Eric Martz Subject: Non-html tutorials for our web page. To: rasmol@noc1.oit.umass.edu Thusfar, the items I've linked to our RasMol home page under 'Educational Applications' are WEB PAGES associated with courses at various universities. However, it is becoming apparent that RasMol or similar software is being used in a number of courses with traditional paper tutorials, rather than an html document as the primary starting point. Therefore, I'd like to start a new branch under 'Educational Applications' for RasMol (or other software) -based tutorials which are provided as plain text/non-html documents. This is an invitation to submit such documents to me to make publically available on our web page, to allow others to see and build upon what is already being done. Please include complete identification of the authors and institution, email address to contact, etc. Provide the document in any form you think most suitable, e.g. plain text, Postscript, etc. Short documents could be emailed to me as plain text. I can also handle binhexed or uuencoded enclosures by email. However, I would prefer that you put the document by anonymous ftp into /incoming at marlin.bio.umass.edu. Note that you will not be able to list the filenames, lengths, etc. of files in /incoming at this site to confirm receipt (a security precaution). Just email to let me know you've put something there, and best to include the byte length of the file so I can verify that it was all received. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 17 Jan 1996 14:53:55 -0500 (EST) From: "Dabney W. Dixon" To: rasmol Subject: Video Tape I am on the Chemistry faculty at Georgia State University in Atlanta. We have been using Rasmol and Mage in teaching biochemistry. We are now funded by the State of Georgia to make chemistry and biochemistry resources more accessible in the State. We are planning to make a video tape (informal, not polished) and distribute it to the colleges in Georgia. The tape would give a hands-on demonstration of how to use Rasmol and Mage, largely for folks who are not familiar with the Web and its resources. Does anyone know of another such video tape that is already available? Thanks. Dabney Dixon ddixon@gsu.edu >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 23 Jan 1996 09:48:23 -0500 (EST) From: Eric Martz Subject: New Tutorial To: rasmol@noc1.oit.umass.edu Some time ago, Andrew Coulson kindly provided a tutorial which he uses at the University of Edinburgh. Belatedly and at last I have gotten around to linking it into the RasMol home page in the educational section. It is designed for students with no prior RasMol experience, so introduces the basic use of RasMol. It goes through structural features of a number of globular proteins. I've provided direct links to Brookhaven so these PDB files can be gotten conveniently. Indeed, one could follow the tutorial text in the web browser window while doing the tutorial in a separate RasMol window (provided RasMol is configured as a web viewer)! Others who have written tutorials are invited to provide them to me so they can similarly be made publically available. Visitors to the RasMol pages exceeded 100/day last week. There was only 9% overlap with the visitors during the previous week. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 23 Jan 1996 22:38:45 -0500 To: rasmol@noc1.oit.umass.edu From: Conrad Bleul HELP! In the introduction to RASMOL, in the section "What Can RasMol do?" they say that RasMol can display bond distances and angles! How do I do that???? Thanx (c)onrad Conrad Bleul 38 Harris Str. #4 Brookline, MA 02146 USA """""" """""""" O O -----oOOo--^---oOOo----- >>>>------>------>------>------>------>------>------>------>------>------> Date: Tue, 23 Jan 96 20:17:52 PST To: rasmol@noc1.oit.umass.edu From: Duane Sears Subject: Re: Dear Dr. Bleul, To measure atomic distances, at the RasMol> prompt in the RasMol version 2.6 Command Line window, enter the following command: RasMol> set picking monitor When you click on two atoms, the distance is displayed on the image with a connecting dashed line. The following commands sent the information about distance, angle or torsion to the RasMol Command Line window: RasMol> set picking distance RasMol> set picking angle RasMol> set picking torsion To return the mouse action back to the atom identification mode, type the command RasMol> set picking ident The display of interatomic distances with a dashed line can also be accomplished with a script file. For example, a dashed line with the corresponding distance between between atoms #1374 and #1500 in a pdb file will be displayed if the following lines are embedded in ascript file: set monitors on monitor 1374 1500 I hope this helps. Duane Sears At 10:38 PM 1/23/96 -0500, you wrote: >HELP! >In the introduction to RASMOL, in the section "What Can RasMol do?" they say >that RasMol can display bond distances and angles! >How do I do that???? >Thanx >(c)onrad >Conrad Bleul >38 Harris Str. #4 >Brookline, MA 02146 >USA > > """""" > """""""" > O O > -----oOOo--^---oOOo----- > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Duane W. Sears Professor of Immunology and Biochemistry Department of Molecular, Cell, and Developmental Biology University of California Santa Barbara Santa Barbara, CA 93106 Telephones: Office: 805-893-3499 (answering machine) Lab: 805-893-4272 FAX: 805-893-4724 Internet addresses: Faculty: sears@lifesci.lscf.ucsb.edu Academic: bioimages@lifesci.lscf.ucsb.edu WWW homepage: http://lifesci.ucsb.edu/MCDB/courses/108a/108ahome.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 24 Jan 1996 00:11:24 -0800 To: rasmol@noc1.oit.umass.edu From: molinaro@lcbvax.cchem.berkeley.edu (Marco Molinaro) Subject: distances from Rasmol Another option is to use the UCB enhanced version - look for it at http://hydrogen.cchem.berkeley.edu:8080/Rasmol/. Extracting distances should be self explanatory. PS - we've only released the enhanced version for Mac thus far Regards, Marco _________________________________ Dr. Marco Molinaro molinaro@cchem.berkeley.edu MultiCHEM - Director of Multimedia Development Department of Chemistry University of California, Berkeley Berkeley, Ca. 94720-1460 VOX: (510) 643-1003 FAX : (510) 643-1471 >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 24 Jan 1996 00:53:49 -0800 (PST) From: Ryan Hung Subject: Resolution and colors To: rasmol@noc1.oit.umass.edu Hi, I've been trying to produce high resolution and truecolor images in Rasmol. I've tried several strategies, but all have failed for various reasons. I'll outline these here, and I'd appreciate if anybody could help me with any of these: 1. Try to find way of making Rasmol write higher resolution (greater # of pixelsxpixels) exported graphics files (i.e. ppm), but Rasmol seems to insist on producing output the size of its display window, either in MS windows or in X Windows (under Linux). In X Windows, with the -nodisplay option, Rasmol produces output of the default window size for the current screen resoltuion. Also, in X Windows, the display window can only be resized to slightly larger than the screen size, even with virtual consoles in fvwm. 2. Try to recompile Windows version of Rasmol to support 16bpp mode. Doesn't seem to work. 3. Try to run 32bpp version of Rasmol in X Windows while in 8bpp mode, with the -nodisplay option set. This way, I could increase the screen resolution, and still (hopefully) write images in truecolor. However, Rasmol complains of no suitable display detected, even with -nodisplay set. 4. Run 32bpp version of Rasmol in X windows at 640x480 in 32bpp mode. While the images display fine, because of the problem in 1., the display window cannot be resized to the full size of the virtual console. 5. Compromise with a 16bpp compile of Rasmol in X Windows. Unfortunately, the display window is not displayed correctly (on the command line, it indicates [24 bit] rather than 16 bit), with the colours all garbled. Ryan. _/ \__/ \__/ \__/ \__/ \__/ \_rhung@freenet.vancouver.bc.ca__/ \__/ Apoptosis=programmed cell death__/ \rwhung@netinfo.ubc.ca \__/ \__/ \__ _/--you can't live without it!_/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \_My words Copyright (C) 1995 \__/ \__ >>>>------>------>------>------>------>------>------>------>------>------> Date: Wed, 24 Jan 1996 16:50:49 -0600 From: George Helmkamp To: rasmol@noc1.oit.umass.edu Subject: To obtain bond distances, use the Geometry tool and click on the specific atoms of interest. I find it best to project as ball-and-stick and then enlarge the image. George Helmkamp, University of Kansas Medical Center >>> Conrad Bleul Tuesday, 23 January 1996 >>> HELP! In the introduction to RASMOL, in the section "What Can RasMol do?" they say that RasMol can display bond distances and angles! How do I do that???? Thanx (c)onrad Conrad Bleul 38 Harris Str. #4 Brookline, MA 02146 USA """""" """""""" O O -----oOOo--^---oOOo----- >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 25 Jan 1996 12:53:47 +0000 (GMT) From: Sayle Dr R A To: rasmol@noc1.oit.umass.edu cc: Ryan Hung Subject: Re: Resolution and colors Dear Ryan, >> Yesterday, Ryan Hung wrote: > I've been trying to produce high resolution and truecolor images in > Rasmol. I've tried several strategies, but all have failed for various > reasons. Thanks very much for your e-mail. Your e-mail highlights some of the deficiencies of RasMol that are actively being worked on. For example, the 16bit mode within RasMol (#define SIXTEENBIT) is still highly experimental and hasn't even been tested. Fortunately, I recently installed the latest version of the XFree X Windows server on Linux and should for the first time have access to a 16bit X display. However, it isn't recommend for anyone but X windows developers. > 3. Try to run 32bpp version of Rasmol in X Windows while in 8bpp mode, > with the -nodisplay option set. This way, I could increase the screen > resolution, and still (hopefully) write images in truecolor. However, > Rasmol complains of no suitable display detected, even with -nodisplay > set. I've just tried this. You should find that normally you get a "No suitable display detected!" and with -nodisplay, a "Display window disabled!". After both of these warnings, you should still get the RasMol command line and this will allow you to generate 24bit/pixel images on any UNIX machine. Its also relatively straight forward to increase the default screen size in RasMol. On about line 18 of "graphics.h", the UNIX values of "InitialWide" and "InitialHigh" are both defined to be 576. Editting the file to make these much larger, e.g. 2048x2048, should allow you to produce a version of RasMol to produce extremely high resolution 24bit images. Remember that GIF images can't be stored at this depth, so write the file as a PPM, PICT, SUN rasterfile or PostScript. Hopefully, the next version of RasMol with contain a "resize" command to allow the screen to be resized from the command line on all platforms. I'm also workin on a way of generating output files at resolutions x2 and x4 the current display resolution. I hope this helps. Please let me know how you get on. Roger -- Roger Sayle INTERNET: ras32425@ggr.co.uk Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line) Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082 ============================================================================ p.s. I tried generating cartoons of crambin (1CRN) at 2048x2048 resolution and had problems with rounding errors in ribbons due to scaling a protein up so large, but bigger proteins, such as 1GD1, looked fine. Be warned that, for the time being, your mileage may vary at very high resolutions. >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 25 Jan 96 14:31:35 PST To: rasmol@noc1.oit.umass.edu From: Duane Sears Subject: Duane Sears -- INTRODUCTION Dear RasMolers (and other incisors of molecular structure), By way of introduction, I have taught Biochemistry and Immunology courses at UC Santa Barbara for several years by projecting manipulatable computer-generated images in lectures given to fairly large classes (ranging up to 250 students). In 1990, I began by using the Chem-X program in order to create structures for these courses. For classroom projection, this program ran on a remote Vax linked by the campus broadband to a Mac at the front of the class; acting as a terminal, the Mac collected calculated coordinate and graphic information from the Vax and redirected it to a Sony Data projector for image projection on a large screen in front of the class. When I learned how to use the first version of RasMol, I immediately switched while maintaining the same basic hardware setup, except that the very slow broadband connection was replaced with a much faster ethernet connection. However, the major student complaint accompanying these early efforts was that image movement was far too slow and often fragmented, particularly with large spacefilled structures like hemoglobin; this problem stemmed both from computer speed and the necessity for networking two computers over long distances. Fortunately, these limitations give way to the speed of the new PowerMacs (and Pentum chips, which I don't have) and the versions of RasMol that run efficiently on either personal computer platform. Now, I conduct all of my classroom computer activities with a stand-alone PowerMac. The increased computing power led me to institute a computer lab for my biochemistry students. Last Fall, I attempted to create a series of weekly, hands-on computer activities with the expectation that each of the 200 students in my biochemistry course would dutifully go through these exercises at a computer facility equipped with 30 PowerMacs. To help maintain student interest, I also developed computer-graded "homework tests" that each student was required to take and their grades on these counted toward their final grade in the course. Not stopping to anticipate what a crazy ambitious project this would be, I only partially succeeded at what I set out to accomplish (and lost a lot of sleep in the process). Any of you wishing to know more about the rather rough-edged results of this endeavor may find my biochemistry web page of interest (comments and suggestions are welcome and would be much appreciated): http://www.mcl.ucsb.edu/classes/biol108a/108ahome.htm. In my research life, my primary interests lie in the area of IgG antibody Fc receptors (Fc-gamma R). Even though we are very interested in the structure/function relationships of these molecules (of which not much is known), RasMol has not played much of a part in our research. Recent studies from my lab have focussed on the genes encoding these molecules and the organization of their structures, particularly in rats and mice. Past and current studies aim more at the cell biology and immunology of these molecules as they participate in immunological processes, particularly those mediated by macrophages and natural killer cells. I look forward to the exchange of information created by the RasMol server. Hats off to Eric for making this splendid idea work. There are some capabilities I would like implemented in the RasMol program and I plan to bring some of these up in future correspondance in order to find out whether others might find certain features useful. Of course, any changes would ultimately rest on the program developers, and particularly Roger, without whose vision and generosity we simply would not be here. Thanks. Duane ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Duane W. Sears Professor of Immunology and Biochemistry Department of Molecular, Cell, and Developmental Biology University of California Santa Barbara Santa Barbara, CA 93106 Telephones: Office: 805-893-3499 (answering machine) Lab: 805-893-4272 FAX: 805-893-4724 Internet addresses: Faculty: sears@lifesci.lscf.ucsb.edu Academic: bioimages@lifesci.lscf.ucsb.edu WWW homepage: http://lifesci.ucsb.edu/MCDB/courses/108a/108ahome.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>------>------>------>------>------>------>------>------>------>------> Date: Thu, 25 Jan 96 16:06:47 PST To: rasmol@noc1.oit.umass.edu From: Duane Sears Whoops, I got my web site address wrong. It's http://www.mcl.ucsb.edu/classes/biol108/108ahome.htm Several of the Web links here are pdb files. I assume most of you with Web servers will have them configured to launch RasMol and display .pdb files downloaded from my Web page, so no need to relate this information here. If you are using a Mac, you can also launch RasMol, display a .pdb file, AND have it scripted by a script (.spt) file if you configure Netscape (v1.1) as follows: Under the Options/Preferences/Helper Applications menu, add a new Mime type = application; Subtype = x-spt; Extensions = spt; and File type = RSML. Browse to the RasMol folder and select the RasMac program for launching. A few of the URLs in my WebPage link to .spt script files. If you click on these, RasMac will launch and display the scripted version of a PDB file, IF the PDB file is ALREADY IN THE SAME DIRECTORY AS THE RASMAC PROGRAM. The script files include load commands, e.g., load 1mbo.pdb, and thus to view scripted versions of these structures, it is necessary to have the pdb file in the RasMol folder. ++++++++++++++++++++++++++++++++++++ I HAVE A QUESTION FOR ROGER or anyone else who knows. How do you accomplish the same feat with Windows? I can't figure out how to set up the Web server and Netscape preferences so that a script file launches RasMol and displays a scripted structure in the same way. In the Windows version of Netscape v1.1, I don't see a file type option and I'm stumped. ++++++++++++++++++++++++++++++++++++ Those visiting my Web page may be interested in viewing my Excel spreadsheets as well. Configure Netscape as follows: Under the Options/Preferences/Helper Applications menu, add a new Mime type = application; Subtype = excel; Extensions = xls; and File type = XLS. Browse to the Excel (v 5.0) folder and select the Excel program for launching. WARNING. Excel on a Mac is a big memory eater and if you have less than about 16 MB of memory you will need to have virtual memory on, and even this may not work if too many files are open on your system. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Duane W. Sears Professor of Immunology and Biochemistry Department of Molecular, Cell, and Developmental Biology University of California Santa Barbara Santa Barbara, CA 93106 Telephones: Office: 805-893-3499 (answering machine) Lab: 805-893-4272 FAX: 805-893-4724 Internet addresses: Faculty: sears@lifesci.lscf.ucsb.edu Academic: bioimages@lifesci.lscf.ucsb.edu WWW homepage: http://lifesci.ucsb.edu/MCDB/courses/108a/108ahome.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>------>------>------>------>------>------>------>------>------>------> Date: Fri, 26 Jan 96 11:37:08 PST To: h.rzepa@ic.ac.uk (Rzepa,Henry), rasmol@noc1.oit.umass.edu From: Duane Sears Subject: Re: MIME types for PDB etc Cc: ras32425@ggr.co.uk Dear Henry, Thank you for your following note regarding MIME types. ========================================================= At 09:02 AM 1/26/96 +0000, you wrote: >Dear Duane, > >I came across this from a cross posting by a colleage >Re:http://www.mcl.ucsb.edu/classes/biol108/108ahome.htm >">>>>>Under the Options/Preferences/Helper Applications menu, add a new >Mime type >>>>>>= application; Subtype = x-spt; Extensions = spt; and File type = RSML. >>>>>>Browse to the RasMol folder and select the RasMac program for launching. >" > >It struck us two years ago that international standards were needed in >prcisely this area. We have gone through IETF and now IUPAC with a >proposal to standardise "chemical" content types; > >http://www.ch.ic.ac.uk/chemime2.html >and http://www.ch.ic.ac.uk/hypermail/chemime/ > >Perhaps you re not familiar with this effort. At any rate, it has been adopted >by many chemical sites, including journals, NIH, etc etc. > >In this context, I wonder if you have considered using the >currently accepted chemical/x-pdb instead of a specific proposal. >I rather fear that if everyone choses their own type, then >confusion will reign. > >Best wishes ============================================================================ I was not aware of the specific efforts you mention for standardization, but I am aware of the chemical/x-pdb standard itself. This standard is used by all of us who download pdb files for displaying RasMol (Kinemage, etc.) images. Thus, I didn't specifically mention the standard in my posting because I assumed everyone would be familiar with it already. The reason I raised the issue of MIME type/subtypes is that the RasMol program treats or handles the raw data PDB files differently than the script files which contain an embedded series of RasMol commands. The command displays a chemical coordinate file with a series of default image settings. As you know, with the chemical/x-pdb MIME type/subtype configuration setting for a Web browser, the RasMol load command is effectively executed when a pdb file is downloaded. However, I have also wanted the Web browser to be configured so that RasMol will launch and a script file will execute when such files are downloaded through the Web. As my posting indicates, I've figured out how to do this with a Mac but not a Windows machine. I noticed with the latest RasMol version for the Mac, RasMac v2.6, creates a non-text file when one saves a script file from the Command Line Window using the command . If one double-clicks on such a file, RasMac is launched AND the script file is executed. Thus, I realized it must be possible to set Netscape up so that when a script file is downloaded, it will automatically launch RasMol and execute. With the help of someone who knows much more about computers than I do, we figured out how to do this by adding application/x-spt to the MIME type/subtype settings and selecting the RSML file type for the configuration files on the Web server as well as Netscape. However, with the Windows version of Netscape 1.1, the same configurations don't work. I can't find a "file type" option in the Helper Applications configuration of the Windows version of Netscape 1.1. Moreover, in contrast to RasMac v2.6, Raswin v2.6 creates a text file when the command is issued, indicating to me that the PC and Mac versions of RasMol are not "symmetrical" in this regard. This may explain why the Web browser works differently with RasMol script files on the two platforms. It's also possible that I don't know how to set up my Web browser correctly. However, I suspect (with RasMol at least) that part of the difference might stem from differences in the way RasMol handles these two file types on a Windows machine as I discovered with one of Roger Sayle's earlier versions of RasMol, called Rasmenu. Rasmenu featured increased menuing options with pull-down menu options for the load (File/Open) as well as the script (File/Script) commands. The load (Open) command always functioned normally but the script command always created a fatal conflict with Windows. If I remember my correspondence with Roger on this, it had something to do with an "unfixable" problem with one of the DLL files. I apologize if my reasoning above sounds a little fuzzy; I'm not a "computer person" (whatever that is). However, I completely agree with the need to establish standards in this area. In fact the chemical/x-pdb standard is highly appreciated. I would like to extend such a standards to the script file application of RasMol (and perhaps other features). It would be very useful download RasMol script files via Web browsers so that RasMac or Raswin is launched and the script file is executed; the added bonus is that the script file would downloaded on the user's computer and could easily be saved for posterity. Perhaps others endorse this concept and might have better ideas for how to implement such standards. Thanks again for raising these issues for discussion. Duane ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Duane W. Sears Professor of Immunology and Biochemistry Department of Molecular, Cell, and Developmental Biology University of California Santa Barbara Santa Barbara, CA 93106 Telephones: Office: 805-893-3499 (answering machine) Lab: 805-893-4272 FAX: 805-893-4724 Internet addresses: Faculty: sears@lifesci.lscf.ucsb.edu Academic: bioimages@lifesci.lscf.ucsb.edu WWW homepage: http://lifesci.ucsb.edu/MCDB/courses/108a/108ahome.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>------>------>------>------>------>------>------>------>------>------> From: Ryan Hung Subject: Re: Resolution and colors Date: Sat, 27 Jan 1996 03:09:48 -0800 (PST) To: rasmol@noc1.oit.umass.edu On Thu, 25 Jan 1996, Sayle Dr R A wrote: > Thanks very much for your e-mail. Your e-mail highlights some of the You're welcome. And thanks very much for all the effort that you've put into creating, maintaining, and updating Rasmol. It's an excellent job! > deficiencies of RasMol that are actively being worked on. For example, > the 16bit mode within RasMol (#define SIXTEENBIT) is still highly > experimental and hasn't even been tested. Fortunately, I recently > installed the latest version of the XFree X Windows server on Linux > and should for the first time have access to a 16bit X display. > However, it isn't recommend for anyone but X windows developers. I got a bunch of compile errors while trying to compile with #define SIXTEENBIT. Something to do with lines 1490-1494 in x11win.c. > > 3. Try to run 32bpp version of Rasmol in X Windows while in 8bpp mode, > > with the -nodisplay option set. This way, I could increase the screen > > resolution, and still (hopefully) write images in truecolor. However, > > Rasmol complains of no suitable display detected, even with -nodisplay > > set. > > I've just tried this. You should find that normally you get a "No > suitable display detected!" and with -nodisplay, a "Display window > disabled!". After both of these warnings, you should still get the > RasMol command line and this will allow you to generate 24bit/pixel > images on any UNIX machine. You're right, it does work! > Its also relatively straight forward to increase the default screen > size in RasMol. On about line 18 of "graphics.h", the UNIX values > of "InitialWide" and "InitialHigh" are both defined to be 576. Editting > the file to make these much larger, e.g. 2048x2048, should allow you > to produce a version of RasMol to produce extremely high resolution > 24bit images. Remember that GIF images can't be stored at this depth, > so write the file as a PPM, PICT, SUN rasterfile or PostScript. > Hopefully, the next version of RasMol with contain a "resize" command > to allow the screen to be resized from the command line on all platforms. > I'm also workin on a way of generating output files at resolutions x2 > and x4 the current display resolution. Here's some hacking I did to rasmol.c and graphics.h to get two new command line parameters, [-width nnnn] and [-height nnnn], which define the starting display window size, whether or not -nodisplay is used: In line 143 of rasmol.c, after the other declarations, I added: static int DispWidth; static int DispHeight; In the static void DisplayUsage() declaration, I changed to: static void DisplayUsage() { fputs("usage: rasmol [-nodisplay] [-script scriptfile] ",OutFp); fputs("[-width nnnn] [-height nnnn] ",OutFp); fputs("[[-format] file]\n formats: -pdb -nmrpdb ",OutFp); fputs("-mopac -mdl -mol2 -xyz -alchemy -charmm\n\n",OutFp); exit(1); } In static void ProcessOptions(argc,argv), I initialized the DispWidth and DispHeight after the two register statements: register char *ptr; register int i,j; DispWidth = 576; DispHeight = 576; In static void ProcessOptions(argc,argv), after the processing of the script option, I added: } else if( !strcmp(ptr,"script") ) { if( i != argc-1 ) { ScriptNamePtr = argv[++i]; } else DisplayUsage(); } else if( !strcmp(ptr,"width") ) { if( i != argc-1 ) { DispWidth = abs(atoi(argv[++i])); } else DisplayUsage(); } else if( !strcmp(ptr,"height") ) { if( i != argc-1 ) { DispHeight = abs(atoi(argv[++i])); } else DisplayUsage(); In graphics.h, I changed the definitions after #ifndef InitialWide to: #define InitialWide DispWidth #define InitialHigh DispHeight After recompiling, rasmol -h now shows: usage: rasmol [-nodisplay] [-script scriptfile] [-width nnnn] [-height nnnn] [[-format] file] formats: -pdb -nmrpdb -mopac -mdl -mol2 -xyz -alchemy -charmm I was able to successfully run the 24bit Rasmol with these modifications to generate a 2400x1800 high quality output of a TSST-1 (toxic syndrome toxin 1) molecule. I.e., rasmol.32bpp -nodisplay -width 2400 -height 1800. To generate the output, I had to first create and test a script at lower resolutions (so I could actually see what was happening). When I was satisfied with the script, I then ran Rasmol as above, and exported several large (12MB) ppm files. A word of advice to anyone attempting this: make sure you have enough memory. I have a 486DX4-100 with 16MB RAM, and I'm using a 32MB swap partition for Linux, and I still used about 24MB of the swap partition while generating the image. This leads me to one further suggestion, and that is, Roger, it would be very helpful to have some other 24bit formats available, especially compressed formats. One I would suggest looking at is TIFF, since there are already library files available for that format. BTW, Roger, thank you very much for your help. I really appreciate it. Ryan. _/ \__/ \__/ \__/ \__/ \__/ \_rhung@freenet.vancouver.bc.ca__/ \__/ Apoptosis=programmed cell death__/ \rwhung@netinfo.ubc.ca \__/ \__/ \__ _/--you can't live without it!_/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \__/ \_My words Copyright (C) 1995 \__/ \__ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: RE: announcement of rmscript for mac/rmscop for unix Date: Sun, 28 Jan 1996 20:28:19 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear Tim: I finally got around to putting two links to SCOP on the RasMol page, under molecules galore, and also under educational resources. Let me know if I've oversimplified or missed the point. The RasMol page got visits from 100 new people per DAY last week! The list now has about 65 subscribers. And I'm close to getting the list history on the web. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: Tim HUBBARD, that was ... Date: Sun, 28 Jan 1996 20:31:53 -0500 (EST) To: rasmol@noc1.oit.umass.edu That last message from me was for Tim Hubbard. Yup, even I who should know better autoreplied to the list instead of to the sender. Watch out for that! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: Antibody script fixed (we hope) Date: Mon, 29 Jan 1996 19:14:01 -0500 (EST) To: rasmol@noc1.oit.umass.edu Bill Huntsman in Wisconsin US, Nigel Lindsey in Bradford UK, and Jose Miguel Fernandez Fernandez in Granada ES all reported that RasMol crashed with an 'unhandled exception' or 'general protection fault' when running my script ANTIBODY.TOP at the point of trying to put up the very fat yellow disulfide bonds. (I never saw this in dozens of runs here, but finally today it happened to me.) Roger Sayle has come to the rescue and identified the bug -- I made my yellow sausages just TOO fat, apparently. So I've changed two 'ssbonds 300' commands to 'ssbonds 200'. Hopefully this will cure the problem. The file AB1ZIP.EXE on the RasMol home page now has these fixed, or you can simply edit the ssbonds commands in files S-S.SCR and IGG1-A.SCR. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: Re: Plea for sleep() Date: Tue, 30 Jan 1996 21:05:02 -0500 (EST) To: jhowell@emedia.net Cc: rasmol@noc1.oit.umass.edu In message Tue, 30 Jan 1996 18:02:03 -0500, "James M. Howell" writes: > Have you thought of using an external driver program instead of the > script? This would resemble the Rasmenu program and feed keystrokes > to either Rasmol or to the command line. I have constructed > such a program using Visual Basic and > putting timing into it would not be be difficult. It does offer much > more flexibility than the script approach. Timing of an > actual command probably can be done as well. > > Regards > J M Howell Dear James: Thanks for your offer. Andrew Coulson is also working on what I believe is a similar approach using Visual Basic. He pointed out to me that the communication employed between his program and RasWin is unique to Windows -- will not work on the Mac, unix, VMS. My present scripts work fine on all platforms, except for the timing and cancellation problems. So the reason I made my plea for sleep() is that I'd like to retain the support for all platforms. Since the scripts are primarily for educational use, I think Windows and the Mac are particularly important. So, my plea remains active ... /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: <75904.emartz@microbio.umass.edu> >>>>------>------>------>------>------>------>------>------>------>------> From: Thomas Andrew Manderfield Subject: Re: Plea for sleep() Date: Tue, 30 Jan 1996 21:51:34 -0500 (EST) To: rasmol@noc1.oit.umass.edu Excerpts from mail: 30-Jan-96 Re: Plea for sleep() by Eric Martz@microbio.umas > In message Tue, 30 Jan 1996 18:02:03 -0500, > "James M. Howell" writes: > > > Have you thought of using an external driver program instead of the > > script? This would resemble the Rasmenu program and feed keystrokes > > to either Rasmol or to the command line. I have constructed > > such a program using Visual Basic and > > putting timing into it would not be be difficult. It does offer much > > more flexibility than the script approach. Timing of an > > actual command probably can be done as well. > > > > Regards > > J M Howell > > Dear James: Thanks for your offer. Andrew Coulson is also working > on what I believe is a similar approach using Visual Basic. He > pointed out to me that the communication employed between his program > and RasWin is unique to Windows -- will not work on the Mac, unix, VMS. > My present scripts work fine on all platforms, except for the timing > and cancellation problems. So the reason I made my plea for sleep() is that > I'd like to retain the support for all platforms. Since the scripts > are primarily for educational use, I think Windows and the Mac are > particularly important. So, my plea remains active ... > Well between everyone on this list, we may have every platform covered. Because of Rasmols great open interface and scriptability, I began some time ago to create a similar program for controlling RasMol. I am not fluent in C, but have recently developed an AppleScript application to create PDB animations with Rasmol. My goals are to have the capability to go with and without Rasmol as a final destination for these animations. I will have to put off tinkering with it for a while, for the project's deadline is approaching and it does enough for now. I have spent a lot of time, setting the tool up to work for my project as well as a general use tool for others on a Mac. For those out there using a Macintosh, you can check out the following URL for more information on it: http://berget.bio.cmu.edu/tom/rasmol.html This really doesn't meet your needs, Eric, and the capability you seek would be better for everyone rather then resulting to external coding like it seems so much of us are doing. I thought I would mention it though to see if there is any interest in pursuing it on the Macintosh side (since that is all I am able to do). My own solution juggles many factors of creating animations where pauses are just a lot of extra code that doesn't do anything (or show up in quicktime), but I regret that I am not capable of creating any better of a solution but one limited to my own platform. sincerely, Tom Manderfield ()-----------------------/#/\\----------------------------() / // \\\ // / | ()-------------------------------------------------------() | | | | /| Thomas Manderfield Footlocker Project | =/] [=| Graphic Commnctns Management Biological Sciences |=]/ | Carnegie Mellon Mellon College of Science | () | 412.688.8313 412.268.5647 | / | |/ ()_______________________________________________________() X-Vms-To: SMTP%"rasmol@lists.umass.edu" >>>>------>------>------>------>------>------>------>------>------>------> From: moreaut@univ-tours.fr Subject: Help: Hbonds problems Date: Mon, 5 Feb 1996 11:54:51 +0200 To: rasmol@noc1.oit.umass.edu dear Rasmol users: I have tried to visualize hydrogen bonds within the aprotinin-trypsin complex. (2ptc.pdb entry). The interchain (i.e between aprotinin and trypsin) Hbonds are not found. The same thing happens in a peptide-HLA complex, no Hbonds are found between the peptide and the protein. In fact we know that Hbonds are present at the interface.The Hbonds between residues of a same chain are found but not those between two chains. So what is wrong ??? Is there a trick or a way to visualize the interchain H-bonds anyway?? Thanks for your help. *------------------------------------------------------------------* | Dr. Thierry MOREAU | | | | Laboratoire d'Enzymologie et Chimie des Proteines | | | | URA CNRS 1334 Phone: (33) 47 36 62 06 | | 2bis, Bd Tonnelle Fax: (33) 47 36 60 46 | | 37032 TOURS cedex Email: moreaut@univ-tours.fr | | FRANCE | | | *------------------------------------------------------------------* X-Envelope-To: rasmol@lists.umass.edu >>>>------>------>------>------>------>------>------>------>------>------> From: Michael.Vork@FYS.RULIMBURG.NL Subject: introduction new subscriber Date: Mon, 05 Feb 1996 12:21:09 +0100 (MET) To: rasmol@noc1.oit.umass.edu Maaastricht, februari 5 1996 Hi members of rasmol discussion group, In response to the Eric's request I herby send a short resume about my activities. I have been working within the field of physiology and biochemistry for almost eleven years at the university of Limburg, The Netherlands. For my Ph.D. thesis I studied the fatty acid-binding protein in cardiac muscle, a small (15 kD) protein involved in intracellular fatty acid transport. During a subsequent post-doc project I studied heat shock protein 70, which is thought to be involved in the proper folding of proteins during translation at ribosomal sites. Therefore, I am particularly interested in tertiary protein structures and folding mechanisms. For this purpose I find rasmol very educational. What I am really interested in is question whether tertiary structure can be predicted from primary protein structure in an aqueous environment or in crystals. I guess it takes a giant computer to calculate all the interactions. Is anyone of this group involved in the protein folding simulation ? If so, I like to hear from you. One small question remains. Does anybody use the stereo option within the rasmol program ? I found out that it is not possible to give the command "set stereo 5", in which 5 indicates the angle between the two images. Rasmol responds with a syntax error message. I've tried the 16 bit and the 32 bit version 2.6. No luck. Hope to hear from you all. >>>>------>------>------>------>------>------>------>------>------>------> From: Andrew Coulson Subject: Re: Help: Hbonds problems Date: Mon, 5 Feb 1996 14:16:20 +0000 To: rasmol@noc1.oit.umass.edu Rasmol doesn't do a general search for hydrogen bonds. For proteins, it implements the algorithm used by Kabsch and Sander to define backbone-to-backbone hydrogen bonds (as the first part of the process of defining secondary structures). For nucleic acids, it simply has a list of the H-bonds in Watson-Crick base pairs. Andrew Coulson >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: Stereo Date: Mon, 05 Feb 1996 12:51:55 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Mon, 05 Feb 1996 12:21:09 +0100 (MET), Michael.Vork@FYS.RULIMBURG.NL writes: > One small question remains. Does anybody use the stereo option within the > rasmol program ? The stereo option is not fully implemented in the presently available RasMol 2.6 beta test version. The image is split, but the two images are not yet rotated relative to each other. Therefore one cannot actually see an image in 3D yet. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: hbonds between chains Date: Mon, 05 Feb 1996 13:00:45 -0500 (EST) To: rasmol@noc1.oit.umass.edu Thierry Moreau asked if there was a way for RasMol to display hbonds between chains, and Andrew Coulson replied that it cannot do so at present. In my script mhc1.top (available at the web site) one of the segments shows the closest atoms in the MHC and peptide, using the RasMol 'within' command. I made the peptide backbone a wireframe, spacefilled the closest peptide atoms, and made the MHC closest atoms spacefilled but a small, constant diameter so one can tell which chain each atom belongs to. The atoms are colored CPK. The result is that one can immediately see (i) that there are no interchain bonds in the middle of the peptide, only at the ends, and (ii) all of the close atom pairs are hydrogen/oxygen (this is a theoretical model containing some hydrogens, 1ROG) except one which is hydrogen/nitrogen. Perhaps it would be worthwhile to implement a new command in RasMol which would show lines between the closest atoms? In X-ray crystal structures, however, where the hydrogens are missing, it would take a more sophisticated algorithm. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: More publicity Date: Tue, 06 Feb 1996 11:24:41 -0500 (EST) To: rasmol@noc1.oit.umass.edu When Roger Sayle released RasMol 2.5 in October, 1994, he announced it on several newsgroups. I'm not set up to send to them. Would someone on this list like to send a short announcement of the RasMol home page to the newsgroups? (If you wish I can write a few sentences.) Namely: bionet.software bionet.announce sci.bio sci.chem comp.graphics.visualization bionet.xtallography sci.techniques.xtallography During the week ending February 5, 1996, the RasMol web site was visited by 969 people. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: New items on RasMol web site Date: Tue, 06 Feb 1996 11:41:18 -0500 (EST) To: rasmol@noc1.oit.umass.edu Items recently added to the RasMol web site (http://www.umass.edu/microbio/rasmol) include: Sources of PDB files for lipid bilayers (Helmut Heller). Gallery images of lipid bilayers (don't miss '5 bakers dancing': go to molecules galore, lipid bilayers). Link t