>>>>------>------>------>------>------>------>------>------>------>------> 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/