>>>>------>------>------>------>------>------>------>------>------>------> 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 to VMD (Visual Molecular Dynamics) software and gallery. The 3 Martz scripts packaged for Macs (thanks to Tom Manderfield!). Willy Wriggers' Hingefind script for X-PLOR. Bill Guilford's Cell Movement site (Univ Vermont) Other/Gallery link to the Theoretical Biophysics Group, Beckman Institute, U Illinois Urbana-Champaign, where are immobilized artificial membranes, phospholipase A2 interacting with the membrane surface, and actin. Let me know what else you find that should be linked! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: <42080."Eric Martz" > >>>>------>------>------>------>------>------>------>------>------>------> From: Thomas Andrew Manderfield Subject: Re: New items on RasMol web site Date: Tue, 6 Feb 1996 13:09:28 -0500 (EST) To: rasmol@noc1.oit.umass.edu Excerpts from mail: 6-Feb-96 New items on RasMol web site by Eric Martz@microbio.umas > 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 to VMD (Visual Molecular Dynamics) software and gallery. > The 3 Martz scripts packaged for Macs ^^^^^^^^ One situation I have been unable to work around: directories. When I first re-archived these scripts for the Macintosh, I examined this and was unable to coerce rasmol into using another directory. Just today, I found a control panel for setting default directories for any application. It didn't work. I had also failed at creating a symbolic link via aliases, even in conjunction with the Control Panel. I did discover, from a troubleshooting FAQ for the Default Directory Control Panel, that System 7.5.(?)'s General Control Panel does handle *some* directory control. I fiddled with it and to no avail, but have not tried every permutation of General Control/Default Directory Control/Alias use/and restarts (if even needed?). Has anyone accomplished this? If so what are your General Control Panel settings, in case that is the reason my end doesn't do it? Another note, to my over descriptive exploration: The 'load' command does read in some, if not all file types via an absolute reference. This does not help to much on portability, not sure if this can be relative either? Actually, I think at one point I was able to access a particular directory via absolute address (maybe from the command line?), and then continue with the scripts realtive addresses. (I changed my higher level directories to one letter names years ago for similar reasons). Tom >>>>------>------>------>------>------>------>------>------>------>------> From: mxc@iris.bioc.uvic.ca (Michael Conway) Date: Tue, 6 Feb 1996 09:59:30 -0800 To: rasmol@noc1.oit.umass.edu We have just started using rasmol to display some zinc finger domains for comparison. I would like to know how to get higher resolution diplay from the program, particularly for gif files to be exported from the SGI we run rasmol on to a MacIntosh. Right now the SGI is running the 8 bit version of rasmol 2.6, we didn't seem to be able to copile the 32 bit version. Is the display on the 32 bit version in a higher resolution? Would it be better to increase the image pixels in the graphics.h file and squeeze the gifs on the MacIntosh? It would be very usefull if some of the instructions for this sort of thing were listed at the Rasmol website. Perhaps a Rasmol FAQ could be assembled if one does not already exist. Thanks Michael Conway >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: RasMol FAQ Date: Tue, 06 Feb 1996 14:07:02 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Tue, 06 Feb 1996 09:59:30 -0800, mxc@iris.bioc.uvic.ca (Michael Conway) writes: > It would be very usefull if some of the instructions > for this sort of thing were listed at the Rasmol website. > Perhaps a Rasmol FAQ could be assembled if one does not > already exist. Because of our local configuration etc., I had to go to considerable effort here to get the email list history on the web. That, at least, has finally been accomplished. I cannot spare the time to create/maintain a FAQ, and of course once Roger Sayle updates the documentation for 2.6 some of what might go into a FAQ today may be unnecessary. If someone else wishes to contribute and maintain a RasMol FAQ, I'll be happy to put it up on the web page or link to it. Meanwhile, I remind you that it is not difficult to search the email history for keywords, using your web browser's "find" (or the slash syntax in lynx). That's why I made the all-history file. If you search 'all' and 'current' you've searched the entire history. For example, searching for the word 'resolution' in the file 'current' finds Ryan Hung's 1/27/96 reply to Roger Sayle's reply to Ryan's inquiry about high resolution output. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Ryan Hung Subject: Re: your mail Date: Tue, 6 Feb 1996 22:27:19 -0800 (PST) To: rasmol@noc1.oit.umass.edu On Tue, 6 Feb 1996, Michael Conway wrote: > We have just started using rasmol to display some zinc finger > domains for comparison. > I would like to know how to get higher resolution diplay from > the program, particularly for gif files to be exported from the > SGI we run rasmol on to a MacIntosh. > Right now the SGI is running the 8 bit version of rasmol 2.6, > we didn't seem to be able to copile the 32 bit version. Is > the display on the 32 bit version in a higher resolution? > Would it be better to increase the image pixels in the > graphics.h file and squeeze the gifs on the MacIntosh? As Eric mentioned, Roger and I discussed this a few weeks ago, so if you haven't already, try to look these up in the archive, as they may prove to be helpful--Roger's response was certainly helpful to me. Incidently, what was the error message returned when you tried to compile the 32 bit version? The display window can be resized up to the screen resolution using the window manager. If you need resolutions larger than that, e.g. for high resolution output, you'll have to recompile with the initial height and wide set larger in graphics.h, and do without a display window. You could also try out the code that I posted to this mailing list which allows the display window size to be set when Rasmol is run. Roger has mentioned that future revisions will implement display window resizing from the Rasmol command line. 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: Sayle Dr R A Subject: Re: Double bonds? Date: Wed, 7 Feb 1996 16:51:31 +0000 (GMT) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear Eric, > I am having no luck getting RasMol 2.6-beta-32-bit to display two lines > for a double bond. I have a PDB for phosphatidyl choline from Helmut > Heller with one double bond in a fatty acid, between atoms 33 and 34. > So I added to the PDB file: > CONECT 33 34 > CONECT 33 34 > and loaded it and did 'set bonds on' but it's still a single line. I'm sorry to take so long to reply, but I've been attending a conference for the last few days. My appologies if someone has already answered this question. The problem is that version 2.6beta only respects PDB connect records, if there are more bonds than atoms in a PDB file. This prevents problems where partial connectivity is stored in a PDB file, but also allows the complete specification of connectivity and bond order in a small molecule. The answer is to add the appropriate single bonds to the PDB file as well as the double bond between 33 and 34. This is an area that is actively being improved within RasMol. For version 2.6, the "set bonds" command will default to "on", displaying bond order information if its in the file. I may also change the rules about ignoring CONECT records in PDB files. 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 >>>>------>------>------>------>------>------>------>------>------>------> From: toni@athe.wustl.edu (Toni Kazic) Subject: Re: Double bonds? T)) To: rasmol@noc1.oit.umass.edu Cc: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu Roger, > This is an area that is actively being improved within RasMol. For > version 2.6, the "set bonds" command will default to "on", displaying > bond order information if its in the file. I may also change the > rules about ignoring CONECT records in PDB files. Great! I believe this might help quite a bit with occasional odd bonding we see in proteins with ligands (e.g. triangular oxygen-centered bonds). Regards, Toni Kazic Institute for Biomedical Computing Washington University >>>>------>------>------>------>------>------>------>------>------>------> From: Duane Sears Subject: A problem with RasMol and disulfide bond connectivity Date: Wed, 7 Feb 96 11:01:27 PST To: rasmol@noc1.oit.umass.edu Cc: Sayle Dr R A Dear Roger and other RasMol users, I believe the problems I am about describe are somehow related to recent questions regarding the methods for displaying double bonds (but I'm not completely sure). In attempting to display the pdb file for a neutrophil defensin (1dfn.pdb), I noticed that the disulfide bonds are not shown to be connected when the file is loaded into RasMol. In the pdb file itself, these disulfides are specified by CONECT statements. I have not discovered a command that will connect them when the complete structure file is loaded. If I issue a save pdb command, creating a new pdb file, the resulting file still does not produce a disulfide-bonded structure. Having noticed on other occassions that this "trick" will sometimes solve connectivity problems, I tried restricting the structure to sidechains (i.e., restrict sidechains) and then I issued a save pdb command. This procedure (either with a RasMac or Raswin) creates a file containing only sidechain atom information. When this file is loaded into RasMol, the disulfides are correctly connected! However, I still can't figure out how to get disulfides connected when the two complete polypeptide chains of this structure are present. I have had a seemingly similar problem with the vandate complex of Ribonuclease A (6rsa.pdb). Only 4 of the 5 oxygens pentacovalently coordinated to the vanadate ion are shown to be connected when this structure is loaded into RasMol. I have not found a way to get the fifth oxygen metal chelation bond displayed. Thanks for considering these nuances. 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 homepages: http://www.mcl.ucsb.edu/classes/biol108/108ahome.htm http://www.mcl.ucsb.edu/classes/biol123/123home.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: Re: Double bonds? Date: Wed, 07 Feb 1996 16:33:58 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear Roger: Thanks for the clarification on double bond display. I vote for a RasMol command to make it obey all CONECT records in the PDB file, since I don't seem to have any way to add the CONECT records for all bonds to a file which lacks them. (I tried loading a tryptophan PDB which lacks CONECT's, doing the RasMol connect command [it reported 28 bonds], then saving as pdb, but RasMol 2.6beta doesn't write out the CONECT records.) So I believe an 'obey connect' command would allow me to manually supply just the connect records for double bonds, or inter-chain bonds, and have them displayed. Along this line, I was looking at the PDB for the entire IgG molecule which is available on our web page from Eduardo Padlan. Using RasMol's incredibly useful 'within' command (incidentally 'help within' denies the existence of this command in 2.6beta) I found what I think are the atoms covalently bonded from carbohydrate chain to an amino acid. Of course, RasMol doesn't show this interchain bond, and of course I couldn't get it to do so by adding a lone CONECT record. In message Wed, 07 Feb 1996 16:51:31 +0000 (GMT), Sayle Dr R A writes: > > Dear Eric, > >> I am having no luck getting RasMol 2.6-beta-32-bit to display two lines >> for a double bond. I have a PDB for phosphatidyl choline from Helmut >> Heller with one double bond in a fatty acid, between atoms 33 and 34. >> So I added to the PDB file: >> CONECT 33 34 >> CONECT 33 34 >> and loaded it and did 'set bonds on' but it's still a single line. >> > > I'm sorry to take so long to reply, but I've been attending a conference > for the last few days. My appologies if someone has already answered > this question. > > > The problem is that version 2.6beta only respects PDB connect records, > if there are more bonds than atoms in a PDB file. This prevents problems > where partial connectivity is stored in a PDB file, but also allows the > complete specification of connectivity and bond order in a small molecule. > > The answer is to add the appropriate single bonds to the PDB file as > well as the double bond between 33 and 34. > > This is an area that is actively being improved within RasMol. For > version 2.6, the "set bonds" command will default to "on", displaying > bond order information if its in the file. I may also change the > rules about ignoring CONECT records in PDB files. > > 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 > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Lipid bilayers Date: Wed, 07 Feb 1996 18:00:59 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've slightly improved the text in the lipid bilayer figures I put on the web yesterday (thanks to suggestions from Helmut Heller, who made the simulations). If anyone downloaded copies you may wish to get the improved versions. Also, I've provided versions with white backgrounds for printing, and a version of '5 bakers dancing' in black and white. Higher resolution versions are in preparation. I'm now looking for PDB files of model bilayers which include cholesterol and/or ethanolamine or serine headgroups in addition to choline -- any suggestions? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: IGG PDB's improved Date: Wed, 07 Feb 1996 18:54:34 -0500 (EST) To: rasmol@noc1.oit.umass.edu There were some minor problems with the PDB's on the RasMol web site for whole/intact IgG1 molecules. I believe I've fixed them. Details and the new versions are on the web site. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Problems getting scripts w/ Mac Date: Thu, 08 Feb 1996 10:56:12 -0500 (EST) To: timp@vt.edu Cc: rasmol@noc1.oit.umass.edu In message Thu, 08 Feb 1996 08:28:24 -0500, timp@vt.edu writes: > I have recently discovered your Rasmol collection (wonderful resource) and > am running into trouble trying to obtain some of the files. Perhaps you > can offer some suggestions. I am interested in some of the scripts, and > have tried to download antibody.sea.hqx and mch1.sea.hqx. I need the > Macintosh versions. In about 6 different attempts, I have failed every > time. I am using Netscape 2.0 on a IIci with 8 meg of ram. When I click > on the __.hqx link address, Netscape opens a text page which displays the > file in ascii. Download then starts, but in every case but one, part way > through I get an error message saying Netscape is out of memory and the > download terminates. I am not running any other applications, and have > downloaded much larger files, although not with this version of Netscape, > which I have only had for a few days. Do you know if there are any bugs > in the Mac versions of your script files? I have never before seen the > files opened into a text page before beginning the down load. > > Any suggestions will be appreciated. Thanks. > > =*=*=*=*=*=*=*=*=*=*=*=*=*=*= > Dr. Timothy L. Pickering, Assistant Director > NSF Center for Polymeric Adhesives & Composites > Virginia Tech > 201A Hancock Hall > Blacksburg, VA 24061-0257 > Tel. (540) 231-4443, FAX: (540) 231-9452 > E-Mail: timp@vt.edu > URL http://www.vt.edu:10021/research/stc/STC.Home.Page.html > =*=*=*=*=*=*=*=*=*=*=*=*=*=*= > Dear Tim: I can't diagnose your Mac problems as I never use Macs. I've had plenty of problems with web browsers under Windows, also. In response to your plight, I've made all the files in the rasmol/distrib directory available by anonymous ftp in /pub/shareware/rasmol/distrib on marlin.bio.umass.edu. I'll put a note to that effect on the scripts page at the web site. I hope this will allow you to work around the browser problems. I'm also copying this message to the RasMol Email list in case a Mac user there has suggestions. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Thomas Andrew Manderfield Subject: RasMac 2.5 -- 24bit color Date: Thu, 8 Feb 1996 19:48:37 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: Court Demas Hello Rasmol List, Court Demas, a collegue of mine recently recompiled RasMol 2.5 for 24bit color on the Macintosh. If you would like a copy, please see http://www.dhp.com/~court for more information. Is 2.6's source available before it leaves beta? I would like to have it recompiled to 24 bit in its present state for the Cartoon/trace/"save in script" features to finish up a project as soon as possible. Thanks for the help, Tom PS: If you try to download the 24bit version of RasMac 2.5 from Court Demas' page, the server has not been updated to send .hqx files properly. (similar to mac scripts on the Rasmol Page). This will be corrected soon, in the meantime, if you really want/need it, click on the link and drag till you get the 'save link as...' option, if you use Netscape. Save as text, and manually open with a debinhexer. Again, the server will be updated shortly. ()-----------------------/#/\\----------------------------() / // \\\ // / | ()-------------------------------------------------------() | | | | /| Thomas Manderfield Footlocker Project | =/] [=| Graphic Commnctns Management Biological Sciences |=]/ | Carnegie Mellon Mellon College of Science | () | 412.688.8313 412.268.5647 | / | |/ ()_______________________________________________________() >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: New additions to web site Date: Sat, 10 Feb 1996 18:57:40 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've added the following to the RasMol web site: On the Classroom page, a link to a great tutorial on Ferritin from the Washington U St Louis Chemistry Dept. High(er) resolution versions of the "5 bakers dancing" image of phospholipids from a bilayer, including white background and black and white versions. All the lipid bilayer PDB files (crystall, gel, fluid) from the Heller, Schaefer and Schulten 1993 study (because from the USA and some sites in Europe the link to Heller's ftp server in Munich is extremely slow). The PDB files for the subsets of molecules from the above lipid bilayers which were used to generate the images on the bilayer page, along with some documentation of how they were extracted. Some trivial DOS PDB-manipulating C programs in a package called PDBTOOLS, for PDB amateurs like me who lack commercial tools. These I created to assist in, for example, extracting the waters for one leaflet in the same X range as the subset of phospholipids, and in assembling the whole immunoglobulin PDB from the chain files provided to me by Eduardo Padlan. They're under "RasMol Accessories". /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: One more makes 80 Date: Sat, 10 Feb 1996 19:02:57 -0500 (EST) To: rasmol@noc1.oit.umass.edu The subscribership of this list is now one short of eighty! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Stephen Koch Subject: Rasmenu for version 2.6 Raswin Date: Sat, 10 Feb 1996 20:59:53 -0500 To: rasmol@noc1.oit.umass.edu Is there a rasmenu program which can be used with the Raswin32 version 2.6 for Windows. Thanks. Stephen Koch 516-632-7944 (7931) Koch@sbchem.sunysb.edu Fax 516-632-7960 Department of Chemistry, SUNY,Stony Brook, NY 11794-3400 Bioinorganic WWW Server: http://sbchm1.sunysb.edu/koch/biic.html >>>>------>------>------>------>------>------>------>------>------>------> From: Eric Martz Subject: Stereo Now Date: Mon, 12 Feb 1996 11:55:54 -0500 (EST) To: rasmol@noc1.oit.umass.edu I realized that it is already possible to make a true stereo image in RasMol. (The present 2.6-beta version has a stereo option which splits the image, but doesn't rotate the images relative to each other, so one cannot see any depth.) The trick is to use the Univ California Berkeley-enhanced RasMac (promised soon in RasWin form). You can display the same molecule twice, translate one left, one right, to split the image. Then rotate the right image with a 'rotate y 3' command. A positive rotation between 3-5 degrees of the right image produces correct depth for crossed eyes. Then click on 'rotate all' (to rotate both molecules together). With eyes crossed, beholding the glory of true 3D, one can then, with caution, rotate the image with the mouse. This works for small X rotations, but soon the eyes complain, because this is not the right type of rotation to keep the 3D effect, especially Y rotations. Fun! I found that I could see excellent depth for a relatively simple protein backbone. However, I had trouble with a complex image like the spacefilled surface of a mass of water. I suspect this is because at the 640 x 480 pixels I was using, there are substantial differences between the two images due to the way the image falls on the pixels. I hope that at 1024 x 768, this would be cured, but I haven't tried it. (RasMac UCB is linked to http://www.umass.edu/microbio/rasmol) (In the UCB-RasMol test version I was using, after selecting one of the loaded molecules from the menu on the right, one must click on the command window, then reselect the graphics window, in order to get the program to accept a typed command such as 'translate x -20'.) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Mutation example Date: Mon, 12 Feb 1996 11:57:35 -0500 (EST) To: rasmol@noc1.oit.umass.edu Can someone direct me to an example or two of PDB files which illustrate how a single amino acid mutation can make a large difference in structure and function? I need an example to use in a lower lever undergrad class which touches on basic genetic concepts. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Why does RasMol change XYZ? Date: Mon, 12 Feb 1996 12:01:30 -0500 (EST) To: rasmol@noc1.oit.umass.edu Using RasWin 2.6-beta-32bit, I noticed that if I open a PDB file, and without any further operations 'write pdb filename', the XYZ values are shifted. When read back in from the new PDB, the image looks identical. Rotating or translating the image before writing has no effect on the values written, as I expected. Does someone know why RasMol changes the absolute coordinates? Just curious. (The file I tested was large, 16,000 atoms in water, phospholipids, and protein. I did not test a small file.) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Selective cutaway strategy Date: Mon, 12 Feb 1996 12:20:09 -0500 (EST) To: rasmol@noc1.oit.umass.edu This is primarily a question for Roger, but others may be interested in this strategy. I'm working with images of a large structure including a phospholipid leaflet, a protein, and about 5,000 molecules of water. I want to cut away portions of these masses, e.g. the water or the leaflet. (I can do this with the DOS CORSEL utility which I recently put on the RasMol home page, but I have to make take apart and reassemble a separate PDB for each cutaway, rather tedious.) I can come close to doing what I want by placing* a fake hetero atom off to one side, and using the 'within' command (producing a spherical cutaway surface). However, the 'within' command seems to have an upper limit of 40 Angstroms which it will accept. If this limitation could be removed, this strategy would work much better. Is there any reason why removing this limit would wreak havoc? (* By 'placing', I mean manually editing an atom onto the end of the PDB file with coordinates such as 0, 99, 0.) In the future, perhaps RasMol can be enhanced to accept commands based on XYZ coordinates. Particularly useful would be 'set picking' to report the coordinate position (XYZ values) of an atom, and the ability to select/restrict with coordinate inequalities, e.g. 'select X < 6.9 and X > -6.9'. Such cutaways are similar to slabbing, but for selected parts of a structure, and allowing rotation of the resulting cutaway image (whereas the slab command keeps the slab plane vertical when the molecule is rotated). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Script translate bug in 2.6-beta Date: Mon, 12 Feb 1996 12:06:07 -0500 (EST) To: rasmol@noc1.oit.umass.edu There appears to me to be a bug in RasWin-2.6beta-32bit. When a manually created script file loads a PDB and performs a series of operations before the first 'refresh', translate Y operations are ignored (I'm not sure about X). If a 'pause' is substituted for the 'refresh', subsequent translate operations in the script execute correctly. Does anyone know a workaround which will make the translate command perform without requiring user intervention in the form of a pause command? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Sayle Dr R A Subject: Re: Why does RasMol change XYZ? Date: Mon, 12 Feb 1996 18:34:55 +0000 (GMT) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear Eric, > Using RasWin 2.6-beta-32bit, I noticed that if I open a PDB file, and > without any further operations 'write pdb filename', the XYZ values are > shifted. When read back in from the new PDB, the image looks identical. RasMol repositions the molecule towards the cartessian origin. Some PDB files, for example viral capsid proteins, are stored in a crystallographic co-ordinate system, with the protein tens to hundreds of Ansgtroms away from (0,0,0). Writing re-centered files allows RasMol to write file formats that are in a range that can be read by other molecular graphics software (at the risk of corrupting the crystal symmetry, which is stripped from the PDB file anyway!). 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 >>>>------>------>------>------>------>------>------>------>------>------> From: Sayle Dr R A Subject: Re: Rasmenu for version 2.6 Raswin Date: Mon, 12 Feb 1996 19:33:03 +0000 (GMT) To: Koch@sbchm1.chem.sunysb.edu Cc: rasmol@noc1.oit.umass.edu Stephen, > Is there a rasmenu program which can be used with the Raswin32 > version 2.6 for Windows. Thanks. You should find that the existing version of RasMenu (for version 2.5) should work perfectly with RasWin32 version 2.6. The only caveat is that raswin32.exe needs to be renamed raswin.exe and placed in the same directory as rasmenu.exe. When RasMenu starts up it simply tries to execute the file "raswin.exe" in the same directory and passes all menu options as DDE requests to the running program. I hope this answers your question. 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 >>>>------>------>------>------>------>------>------>------>------>------> From: Sayle Dr R A Subject: Re: RasMac 2.5 -- 24bit color Date: Mon, 12 Feb 1996 19:40:01 +0000 (GMT) To: Thomas Andrew Manderfield Cc: rasmol@noc1.oit.umass.edu, Court Demas Dear Thomas & Court, > Is 2.6's source available before it leaves beta? I would like to have > it recompiled to 24 bit in its present state for the Cartoon/trace/"save > in script" features to finish up a project as soon as possible. The full source code for RasMac version 2.6beta is available, its just not included in the Macintosh distribution of the beta-test release. All the major source files (including rasmac.c and applemac.c) are included in the UNIX distribution, and if unpacked may be transfered to a Mac. The only missing file is the "RasMac.rc" resource file that may be extracted from the Mac executable by cutting and pasting the required resources with ResEdit, from the RasMac 2.6 binary executable. 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 >>>>------>------>------>------>------>------>------>------>------>------> From: Brian Haas Subject: rasmenu Date: Fri, 16 Feb 1996 09:16:39 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dr. Martz, I am a new user of Rasmol and have recently subscribed to the discussion list. I find Rasmol to be quite interesting and a great tool for protein viewing. I do have a number of questions regarding the program and any response would be greatly appreciated. I remember a message regarding rasmenu activation with RASWIN32. It was stated that renaming Raswin32 - raswin.exe and placing rasmenu.exe in the same directory would allow the 2.6 version to operate under rasmenu. I gave this a try and had no success. Rasmenu works just fine under the 2.5 16 bit version of rasmol, but the 32 bit 2.6 test version will not bring up the rasmenu. After exiting the 32 bit version, an error message is displayed "can't find raswin.exe". This seems unusual because the program runs just fine even though it was booted throught the rasmenu.exe command, and the error message is displayed on exiting the program. Do you think that the rasmenu is not set up for 32 bit operation, but will only work with the 16 bit version? In that case, I'll just do away with the 32 bit version and download raswin16 2.6. I love that distances and angles can now be calculated with the 2.6 version. One problem that I have is that the "set monitor on" command will not allow distances to be displayed on the modelling screen; only the command window displays the distances. The set stereo [-] (value) seems not to work either. Could this result from not having the finished 2.6 version? Is the finished version available yet? Backbone dihedral angles can be calculated when the protein is rendered as wireframe. It is difficult to calculate dihedral angles efficiently in this manner because the sidechains clutter the view. In insightII, the backbone command shows a full trace of the backbone (n,ca,c,o) whereas in rasmol the backbone is an alpha carbon trace and dihedral angles cannot be calculated. Does Dr. Sayle have any plans to install a command in future versions which will display all backbone atoms without the sidechains, or is there an indirect way to show this display in the present version which I am unwarare of? Brian Haas Graduate Student of Molecular Biology State University of Albany, New York. X-Vms-To: SMTP%"rasmol@lists.umass.edu" >>>>------>------>------>------>------>------>------>------>------>------> From: moreaut@univ-tours.fr Subject: Re: rasmenu Date: Fri, 16 Feb 1996 15:30:31 +0200 To: rasmol@noc1.oit.umass.edu Brian Haas writes: > I remember a message regarding rasmenu activation with RASWIN32. It >was stated that renaming Raswin32 - raswin.exe and placing rasmenu.exe in the >same directory would allow the 2.6 version to operate under rasmenu. I gave >this a try and had no success. Rasmenu works just fine under the 2.5 16 bit >version of rasmol, but the 32 bit 2.6 test version will not bring up the >rasmenu. After exiting the 32 bit version, an error message is displayed >"can't find raswin.exe". This seems unusual because the prog ram runs just >fine even though it was booted throught the rasmenu.exe command, and the error >message is displayed on exiting the program. Do you think that the rasmenu is >not set up for 32 bit operation, but will only work with the 16 bit version? >In th at case, I'll just do away with the 32 bit version and download raswin16 >2.6. I also got a problem with RasWin32 vers2.6: it works on a PC (80386) under Windows3.1 with WIN32S(a microsoft module) it also works on a PC under Windows NT but only with a Pentium processor but not with a 80486? The 16 bit version runs with both processor? What can be the problem?? At the SwissProt site, they say that PCs users have probably to use vbrun300.ddl ??? does somebody have additionnal informations? > > I love that distances and angles can now be calculated with the 2.6 >version. One problem that I have is that the "set monitor on" command will not >allow distances to be displayed on the modelling screen; only the command >window displays the distances. The set stereo [-] (value) seems not to work >either. Could this result from not having the finished 2.6 version? Is the >finished version available yet? please read carefully the manual or the 2.6 release notes To have distances (or angles or dihedral) displayed on the screen use the following commands: set picking distance set picking monitor to remove the distance: monitor off to disabled picking : set picking none to enabled picking : set picking on that's great!!!! I know there is a problem with the stereo option: there was a discussion on the list on this topic recently. See the archive list. > Backbone dihedral angles can be calculated when the protein is rendered >as wireframe. It is difficult to calculate dihedral angles efficiently in this >manner because the sidechains clutter the view. In insightII, the backbone >command shows a full trace of the backbone (n,ca,c,o) whereas in rasmol the >backbone is an alpha carbon trace and dihedral angles cannot be calculated. though RasMol is not InsightII, you can display only the mainchain atoms for both proteins and nucleic acids use the command: select mainchain please read the manual...and have fun *------------------------------------------------------------------* | 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 | | | *------------------------------------------------------------------* >>>>------>------>------>------>------>------>------>------>------>------> From: i-baianu@uiuc.edu (Ion Baianu) Subject: Re: Date: Mon, 19 Feb 1996 16:30:43 -0600 To: rasmol@noc1.oit.umass.edu Attn. of Prof. Duane W. Sears: Hope I have my link address correct to your URL in my Cyberspace Tour of Molecular Modeling Facilities on the Web! The URL address for the outline of my tour is: http://www.ag.uiuc.edu/~fs401/MOL-MOD-ITINERARY.html It can also be reached as a link from our course gome page at the URL address: http://www.ag.uiuc.edu/~fs401/FS401Home.html Regards, I. C. Baianu, Professor, ACES, FSHN Dept., Coordinator of the AFC--NMR Facility >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 >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>>------>------>------>------>------>------>------>------>------>------> From: i-baianu@uiuc.edu (Ion Baianu) Subject: Re: NEW Molecular Modeling Tour in CyberSpace Date: Mon, 19 Feb 1996 16:34:55 -0600 To: rasmol@noc1.oit.umass.edu Attn. of Prof. Duane W. Sears: Hope I have the correct link address to your URL in my "Cyberspace Tour of Molecular Modeling Facilities on the Web!" The URL address for the outline of my tour is: http://www.ag.uiuc.edu/~fs401/MOL-MOD-ITINERARY.html It can also be reached as a link from our course home page at the URL address: http://www.ag.uiuc.edu/~fs401/FS401Home.html Regards, I. C. Baianu, Professor, ACES, FSHN Dept., Coordinator of the AFC--NMR Facility >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 >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: RasMol source? Date: Wed, 21 Feb 1996 09:00:17 -0500 (EST) To: genehsu@umich.edu Cc: rasmol@noc1.oit.umass.edu In message Tue, 20 Feb 1996 18:19:59 -0500 (EST), Gene Hsu writes: > Do you know where to find the source for the macintosh version of RasMol > 2.6? I'd like to try to recompile it with more features. > > -- Gene Dear Gene: Please subscribe to the RasMol email list if you have not already done so. Instructions are on the web at http://www.umass.edu/microbio/rasmol If you can't access that, let me know and I'll email instructions to you. Before you 'add more features', check out Berkeley-enhanced RasMac (link on the web site). You can find Marco Molinaro's email address there. Tom Manderfield has also recompiled RasMac (manderman+@cmu.edu). Roger Sayle plans to release RasMol 2.6 'real soon' with quite a few enhancements not present in 2.6-beta. Browse the email history at the web site for a message Feb 12, subject '24bit color', from Sayle to Manderfield which explains how to get the source code. Let me know if I can be of further help. I'm sure the 80+ people on the email list would like to know what enhancements you have in mind if you care to share your thoughts. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: toni@athe.wustl.edu (Toni Kazic) Subject: other input formats? Date: Wed, 21 Feb 1996 10:09:38 -0600 To: rasmol@noc1.oit.umass.edu Greetings RasMoleans, Roger, I was wondering if you planned to add CXF and CIX inputs to RasMol soon? Regards, Toni Kazic Institute for Biomedical Computing Washington University ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: other input formats? Date: Wed, 21 Feb 1996 18:05:06 +0000 (GMT) To: Toni Kazic Cc: rasmol@noc1.oit.umass.edu Dear Toni, > Roger, I was wondering if you planned to add CXF and CIX inputs > to RasMol soon? Thanks very much for your e-mail. I must admit that this is the first request I've received for CXF or CIX formats. What little I do know about CXF is that it is based upon self-defining data-types and aritrary tagged data on each atom/bond/molecule. The good news is that I have been looking at data structures and algorithms for manipulating this class of file formats. Other notable members include mmCIF (the proposed sucessor to the PDB format), MIF, MODEL, STAR, ASN.1 (NCBI's mmDB database), ISIS sketch, CAChe and CEX. This work is currently at an early experimentation stage and done in collaboration with several other molecular graphics groups, including the author's of "babel". However, it is still too soon to say when these parsers/generators will be available and what form they'll come in. If you have an immediate need for CXF or CIX let me know and I'll investigate them further. 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 X-Vmsmail-To: SMTP%" rasmol@lists.umass.edu" ++++------+------+------+------+------+------+------+------+------+------+ From: OSTERHOUT@RISVAX.ROWLAND.ORG Subject: Rasmol stereo Date: Thu, 22 Feb 1996 17:57:04 -0500 (EST) To: rasmol@noc1.oit.umass.edu Hi, I recently obtained RasMol v2.6 for the Mac. I notice that the stereo option displays two images but the images are identical. Hence, no stereo effect. I cannot find any documentation about controlling image rotation or separation. Are there any internal program parameters controlling these options? Sincerely, John Osterhout ****************************************************************************** John J. Osterhout osterhout@risvax.rowland.org Protein Folding and Design http://titan.rowland.org:1125/johno.html The Rowland Institute for Science (617) 497-4683 100 Edwin H. Land Blvd (617) 497-4627 (FAX) Cambridge, MA 02142 Manifestly Important and Nearly Impossible ****************************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Rasmol stereo Date: Fri, 23 Feb 1996 10:45:50 -0500 (EST) To: rasmol@noc1.oit.umass.edu You are correct. The stereo option is not fully implemented in the 2.6-beta version. There is a way to do stereo on UCB-RasMac. Use your browser to search for 'stereo' in the email 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: EDTA PDB? Date: Tue, 27 Feb 1996 18:49:53 -0500 (EST) To: rasmol@noc1.oit.umass.edu Does anyone know where I can get a PDB for EDTA complexed to calcium ion? (real or theoretical) Of course, why not EGTA while we're at it? (I don't see either at KLOTHO.) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: toni@athe.wustl.edu (Toni Kazic) Subject: Re: EDTA PDB? Date: Tue, 27 Feb 1996 18:04:25 -0600 To: emartz@microbio.umass.edu Cc: rasmol@noc1.oit.umass.edu No, we don't have it in Klotho (for one thing CONCORD won't --- for good reason --- calculate complexes!). I just checked Laura Walsh's Annotated PDB Guide for the 1994 --- a wonderful resource -- but didn't find anything. I'm in the midst of tracking Laura down now. Toni ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Scientific Plotting Software Date: Tue, 27 Feb 1996 19:34:30 -0500 (EST) To: rasmol@noc1.oit.umass.edu I spent several months trying out various general purpose scientific plotting/graphing packages, and finally decided to buy Prism. I found it hard to identify the best packages on the market and find out where to contact the vendors. And there are almost no published comparative reviews. So, I set up a web page. So far it has only my opinion based on very limited experience -- I hope that Windows users on this list will contribute additional opinions to put up for public view on the web site, and I hope that SOMEONE ELSE will start a similar page for Macintosh packages so I can link my page to it. The URL is: http://www.umass.edu/microbio/sciplot /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: "Christopher Hogue" Subject: RasMol and Kinemage Services from WWW-Entrez Date: Wed, 28 Feb 1996 11:24:09 -0500 To: rasmol@noc1.oit.umass.edu Hi All. Christopher Hogue, Visiting fellow, National Center for Biotechnology Information, joining the RasMol list. By way of introduction, I have been spinning biomolecular structures since 1988 on my PC using a little-known program called AcroSpin, way before Kinemage and RasMol ever appeared. But I had to write lots of programming to convert PDB files into the AcroSpin format. But more on AcroSpin later... I use RasMol and Kinemage on almost all their supported platforms, often to test our 3D structure services, but also to do research on structures. I'm the principal "structure" software developer at the National Center for Biotechnology Information, which you may know as a "sequence" database (GenBank). I'm writing programs which use ASN.1 formatted MMDB structure data. MMDB is the Molecular Modelling Data Base, which is the entire PDB database "reincarnated" into an ASN.1 data file format. Among other things, I'm working on MMDB-API, an optimized C applications programming interface for molecular modelling that speaks ASN.1. MMDB-API is great at generating other file formats like PDB files and Kinemage renderings. I'm also working on a new generation of structure viewers for MMDB, all destined for the public domain and made to simultaneously deliver cross-platform support (Win, Mac, Unixes, etc). You can read more about MMDB at http://www.ncbi.nlm.nih.gov/Structure OR You can do a structure query using WWW-Entrez at http://www.ncbi.nlm.nih.gov/ The Entrez service provides an integrated database such that you can find related sequences, structures and read MEDLINE abstracts on-line. NCBI provides a number of primary services that numerous other database and query services link to, the MEDLINE abstracts being amongst the most popular. You may have already been in the Entrez service without realizing it. If you want to find information, sequences and abstracts on-line about research related to a 3D-structure that is *more recent* than the structure file itself - check out WWW-Entrez's neighboring facilities. Want to know if there is a structure related to a known sequence in the database? You can find it with WWW-Entrez, starting from the sequence or even from a MEDLINE article talking about the sequence. WWW-Entrez's structure services can make PDB files at various levels of resolution, (i.e. alpha-carbon only, one XYZ per atom only, or the full PDB dataset) and is fully enabled for MIME-type launching of RasMol or Kinemage. WWW-Entrez can also make Kinemage files from any PDB entry in up to 4 different rendering styles - Colored by chain/molecule; Colored by secondary structure & residue type; Colored by element; Colored by temperature factor. The buttons sets made by WWW-Entrez for Kinemage allow you to pick a virtual-backbone, actual-backbone or a full residue structure image from one file. The coolest feature of WWW-Entrez is its ability to automatically make Kinemage *animations* out of any multiple-model NMR structure in the structure database, as well as out of correlated-disorder (i.e. when one atom shows up in two different XYZ locations in the crystal). Check out the accessions 125D, 1AKE or 5HVP from Entrez's structure query page and see the resulting Kinemage files - then hit the animate button! Currently I working on more services and software that I hope you will find interesting. Now, about AcroSpin... AcroSpin was a $35 program entirely coded in machine language by David B. Parker. It would spin large vector wireframes/point clouds in real-time on just about any PC with a graphics. If anyone wants access to the following structures in AcroSpin format for showing structures on PC compatible that is in the speed range between a PCjr up to a 386-16 - write me - and I'll send you the files you need and tell you how to get AcroSpin from its author. I have AcroSpin files for: Insulin, Myoglobin, Azurin, Cytochrome C peroxidase; and a nearly complete set of structures representing the family of small EF-hand calcium binding proteins: Calmodulin, Parvalbumin, Tropoinin-C, Calbindin D9K, and Oncomodulin. The reason I'm distributing this information about AcroSpin is because I know there are some educational computer labs with slower computers that are not well-suited for running Windows applications. These files can comprise a nice introduction to molecular structure if you are limited by the hardware in your computer lab. Write me if you want these - or forward my address to anyone you may know who is in need of such access. Cheers, Christopher Hogue Visiting Fellow, National Center for Biotechnology Information. Bldg 38A, NIH. 8600 Rockville Pike, Bethesda MD 20894 (301)-496-2475 (301)-435-2433 (fax) hogue@ncbi.nlm.nih.gov Disclaimer: The opinions expressed herein are not necessarily representative of those of NCBI or the US government. ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Laura Walsh's annotated PDB (EDTA-metal complexes) Date: Wed, 28 Feb 1996 13:23:41 -0600 To: rasmol@noc1.oit.umass.edu The August 1994 edition is it ---- she needs funding to continue! You can get it at http://www.scs.uiuc.edu/~lwalsh/ and there's no more information on ED/GTA - metal complexes. Toni "Laura Walsh's annotated PDB (EDTA-metal complexes)" (Feb 28, 1:23pm) References: <9602281923.AA18000@athe.wustl.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: (EDTA-metal complexes) Date: Wed, 28 Feb 1996 14:53:01 -0500 To: rasmol@noc1.oit.umass.edu Hi all. Using WWW-Entrez, I found two immunoglobins with EDTA-like chelated metal complexes in their binding sites: 1INE, and 1IND. The first is an iron complex, the second an indium complex, but they are pretty much the same. Note that the chelator is an EDTA derivative, not EDTA proper. Try this: http://www3.ncbi.nlm.nih.gov:80/htbin-post/Entrez/query?uid=1348&form=6&db=t&Dopt=s or: http://www3.ncbi.nlm.nih.gov:80/htbin-post/Entrez/query?uid=1347&form=6&db=t&Dopt=s Hit the View button to launch RasMol or Kinemage to see the structures. In Kinemage, hitting the "Virtual" button on the side will leave the metal-ion complex on-screen and turn off the protein. WWW-Entrez makes Kinemages that by default show every ion as a colored ball on screen (e.g. Fe is orange, Cl is green, Ca is pink, Mg is magenta, etc) This helps to highlight the biologically significant active sites of metalloenzymes and other ion-bound structures. Chris Hogue. NCBI ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Acorn Archimedes RISC OS Date: Wed, 28 Feb 1996 16:30:24 -0500 (EST) To: rasmol@noc1.oit.umass.edu I pass this on in case anyone is interested. -Eric ------------------------------ Wed, 28 Feb 1996 19:55:38 +0100 (MEZ) From: Stefan Wuerthner To: Eric Martz [snip] My brother did a port of RasMol for Acorn Archimedes running RISC OS, so the whole is working under RISC OS :-)) [snip] /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Fw: RE: rasmol scripts Date: Wed, 28 Feb 1996 16:33:05 -0500 (EST) To: rasmol@noc1.oit.umass.edu In case anyone else has the same question ... ------------------------------ Wed, 28 Feb 1996 19:55:38 +0100 (MEZ) From: Stefan Wuerthner Subject: RE: rasmol scripts To: Eric Martz By the way, would it be ok to distribute your scripts together with the RISC OS port of RASMOL? (that would mean: upload to a german and a british ftp server). ------------------------------ My reply: Please do not distribute copies of the scripts from other servers; rather, please link the other servers to my scripts page. All script files are plain text, hence OS-independent. The reason I ask this is so that when I improve or fix bugs in the scripts, your link will immediately point to the latest version. For the same reason, when someone else writes a script, I will link my page to their server rather than offering a copy. Thanks. http://www.umass.edu/microbio/rasmol/scripts.htm /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Visits to web plateau Date: Thu, 29 Feb 1996 13:50:41 -0500 (EST) To: rasmol@noc1.oit.umass.edu The number of visitors to the RasMol web site at UMass has been nearly constant for the past month. There are about 1,000 visitors per week (about 15,000 document fetches). The visitors continue to be about 90% new each week. Since the site was created in November, 1995, it has been visited by about 7,000 people (distinct Internet addresses) from 49 countries. This email list now has 93 subscribers. For the 4 week period 1/15-2/12, 11% of the visitors visited 2 or more times: 14 visited weekly, 66 visited 3 of 4 weeks, 275 visited 2 of 4 weeks, and the remaining 2,985 visited only once during that month. The country-breakdown of the 6,164 machine addresses which I've kept might be of interest: USA: 1852-edu 603-com 380-net 86-gov 48-org 10-mil 35-us Over 30: 224-de 192-uk 173-jp 172-ca 97-nl 88-se 84-fr 77-dk 45-ch 43-it 38-no 36-es 33-fi 31-be 5-15: kr br at pl il pt cz mx nz gr za tw ar si ie hk 1-4: ru my hu tr sg is cl ve in cr th su ro ph ee co cn Does anyone know where, on the web, one can look up a two-letter country code? I recognize only about half of these! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 Subject: Re: Visits to web plateau Date: Thu, 29 Feb 96 14:57:17 EST To: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu >Does anyone know where, on the web, one can look up a two-letter >country code? I recognize only about half of these! Path: senator-bedfellow.mit.edu!faqserv >From: o.crepin-leblond@imperial.ac.uk (Olivier M.J. Crepin-Leblond) Newsgroups: comp.mail.misc,comp.mail.uucp,news.newusers.questions,alt.internet.services,alt.internet.access.wanted,alt.answers,comp.answers,news.answers Supersedes: Followup-To: poster Lines: 597 Approved: news-answers-request@MIT.Edu Expires: 11 May 1995 22:19:54 GMT NNTP-Posting-Host: bloom-picayune.mit.edu Summary: This posting gives a list of country codes with email accessibility. It is helpful in finding-out if a country has easy access to email and internet facilities and is aimed at general email and internet users. X-Last-Updated: 1995/03/25 Originator: faqserv@bloom-picayune.MIT.EDU Xref: senator-bedfellow.mit.edu comp.mail.misc:22604 comp.mail.uucp:15398 news.newusers.questions:55874 alt.internet.services:47136 alt.internet.access.wanted:25495 alt.answers:8351 comp.answers:10903 news.answers:40848 ++++------+------+------+------+------+------+------+------+------+------+ Subject: FAQ: International E-mail accessibility Date: 28 Mar 1995 22:20:47 GMT Archive-name: mail/country-codes Last-modified: 1995/03/24 Based on International Standard ISO 3166 Names Compiled by Olivier M.J. Crepin-Leblond E-mail: Release: 95.03.2 Release Notes: a. Sierra Leone (SL) with UUCP (*) b. World Wide Web (WWW) version available This document is Copyright 1995 by Olivier Crepin-Leblond. No part of this document may be reproduced in any commercial publication by any means - graphic, electronic, or mechanical, including photocopying, recording, taping, or storage in an information retrieval system without prior written permission of the copyright holder. It may however be freely redistributed in its entirety provided that this copyright notice, its headers "Archive-name", "Last-modified", and "Release" are not removed. Every now-and-then there are enquiries on the net regarding E-mail to a distant country. The question is often of the type "has that country got E-mail access ?". The following table is a guide of country codes, showing the countries which have access to Internet or general E-mail services. The country codes have been derived from the International Organization for Standardization standard ISO 3166. A country code is taken as a top level domain once it is registered at rs.internic.net so *not* all country codes listed are top level domains. At the bottom of the table, there is also a section of general top level domains, based on the information available at rs.internic.net. NOTES: 1. Description of codes: FI stands for FULL INTERNET access. This includes 'telnet', 'ftp', and internet E-mail. B stands for BITNET access although the address may be in internet DNS (Domain Name System) format. * (Asterisk) means that the country is reachable by E-mail. If this is not preceded by FI or B, it means that the connection may be a UUCP connection. An asterisk is included after FI or B for consistency. PFI stands for a provisional full internet connection.(+) P stands for provisional connection. (+) (+) This is used when one or more of the following is true: - address not verified or lack of address - UUCP dialup not active - net connection possible but not officially announced - premature official announcement of connection F stands for a country that is connected to Internet only via means of the FIDOnet network. It is assumed that the FIDO connection in this case is stable and reliable. 2. Networks which are not included: Networks such as MILNET (U.S. Military's unclassified portion of the DDN - Data Defense Network) have computers all around the world. It is generally possible to assume that wherever there is a U.S. military base, there will be a node reachable through gateways. Private company networks such as for DEC (Digital Equipment Corp.), or Sun Microsystems, for example, have nodes in many exotic locations. However the connection may take place via UUCP and cost a lot of money. Those networks have therefore not been included. In addition, those are PRIVATE networks. Many companies ( like U.S. Sprint, for example ) offer commercial services to many countries which are not readily available on the Internet. The service is VERY COSTLY, usually takes place via UUCP or X.400 connections. X.400 E-mail is usually charged to someone and if the telecommunication carrier cannot find someone to pay for the message transfer, it will reject it. As a result, those types of network have not been included in the list. Although a user may RECEIVE E-mail from a user on those networks, one may not be able to reply to it. 3. Updates: The situation changes from day to day. The growth in international networking is such that the information contained in this document may be out of date by the time it reaches you. If you have any update (i.e. knowledge that a new country is connected), please send a message to , including an example address from the country reached so that it can be verified. Furthermore, if you are a connection provider or could provide a low cost connection in a country, and are not listed as a provider in that country (see "FURTHER INFORMATION" section), please notify either Randy Bush or me. NOTE: This doesn't include providers for North America. If you are a North American provider, then please DON'T contact us. 4. .US sites While there are several hundreds of BITNET nodes in USA, none have a name in the format `.US'. That's why the .us domain is only FI and *. 5. .edu, .com, etc. The domains in this section are special in that some of them are used in more than one country. The domains which have full internet access are marked accordingly. However, this doesn't mean that *all* of those domains have full internet access. For example, only a small proportion of .mil sites have full internet access. The same is true for .com sites, for example. 6. UK and GB domains There are two codes for United Kingdom, namely UK and GB. While UK is used for addressing of most domains in DNS format, the field GB is used mainly in the X.400 addressing of United Kingdom sites. However, there is an increasing trend in some United Kingdom sites being directly connected to Internet under the GB domain. The GB domain is hence a perfectly suitable Internet top level domain. When looking for further information, it is worth looking at both UK and GB for United Kingdom. 7. Further information column This column contains information as follows: - E-mail address of a contact from which further information may be obtained and/or - Details of a gopher system that can be queried for further information in this case, look at Section 8: Where to find further information or - If no other information available: nameserver details, if any. This is the main nameserver as listed in the rs.internic.net database. Those often change as the network grows, and it is hard to keep track of all nameservers, but they should usually work. Nameservers can be queried by users using nslookup. 8. Where to find further information A number of sites run on-line information databases, mail-servers, and gopher information systems where further information can be found. - rs.internic.net Part of this site, the InterNIC database services, contains the Internet "white pages". The "whois" section of the "white pages" has registration records for top level domains. "whois" can be accessed by connecting interactively (telnet rs.internic.net), or via gopher (gopher rs.internic.net) or using the "whois" command available on some computer systems (whois -h rs.internic.net). Registration records for a domain are sometimes useful since they provide Administrative and Technical Contacts for this domain and those may hence be able to provide further information. - gopher.ripe.net This is a gopher system run by ripe.net, the co-ordinator for European Internet nodes. It contains a lot of information regarding European IP, etc. It may be accessed either as "gopher gopher.ripe.net" or "telnet gopher.ripe.net" and logging-in appropriately. It also has a "whois" database. - GNET: an Archive and Electronic Journal This is co-ordinated by Larry Press Archived documents are available by anonymous ftp from the directory global_net at dhvx20.csudh.edu (155.135.1.1). To conserve bandwidth, the archive contains an abstract of each document, as well as the full document. In addition to the archive, there is a moderated GNET discussion list. To submit a document to the archive or subscribe to the moderated discussion list, use the address gnet_request@dhvx20.csudh.edu. - BITNIC Bitnet Network Information Center Bitnet LISTSERVs contain files which list all BITNET sites around the world. For a listing of all BITNET sites, in country code order, send a message to LISTSERV@Bitnic.educom.edu (or LISTSERV@BITNIC for BITNET folks), no subject, and the command: GET NODES INFO3 in the body of the message. A very long file of information on all international BITNET sites can be ftp'ed from Bitnic.educom.edu and is called BITEARN.NODES . It is more than 2Mb long. - gopher.psg.com This gopher system, maintained by the Network Startup Resource Center and PSGnet/RAINet contains perhaps the most comprehensive collection of information about country connectivity. It may be accessed as "gopher gopher.psg.com". For the gopher client impaired, one can telnet to gopher.psg.com and login as gopher. An important feature is an E-mail interface to access the information in the gopher system. Send E-mail to: server@gopher.psg.com any subject, and in the body of the message: send country/ Example: if you want further information about Brazil (country code BR) send country/BR Many thanks to Randy Bush and to John Klensin for setting-up this site and this collaborative effort. 9. Archiving Once released, this document is archived in a number of archive sites around the world. Amongst them: ftp://rtfm.mit.edu:/pub/usenet/news.answers/mail/ ftp://lth.se:/pub/netnews/news.answers/mail/ #ftp://ftp.uu.net:/usenet/news.answers/mail/ #ftp://unix.hensa.ac.uk:/pub/uunet/usenet/news.answers/mail/ #ftp://grasp.insa-lyon.fr:/pub/faq/mail/ (#) those may not be accessible via Bear access or direct PC access in some cases. Via E-mail request as follows: mail ftpmail@grasp.insa-lyon.fr open [mime] get pub/faq/mail/country-codes quit Subject: no one cares where [ ] = optional All FAQs are also available via listserv@cc1.kuleuven.ac.be or listserv@blekul11.bitnet . For an index of all FAQs available, put the command GET NETFAQS FILELIST in the body of your message. The document is also retrievable by E-mail from rtfm.mit.edu by sending an E-mail to mail-server@rtfm.mit.edu , blank subject line and the command: send usenet/news.answers/mail/country-codes The up-to-date, pre-release document is also available using an experimental simple mail-server that I have setup from my account. Send E-mail to: with a subject: archive-server-request and the command: get mail/country-codes in the body of your message. The document is also distributed automatically once a month on a mailing list. To subscribe to that mailing list, send a message to: listserver@ic.ac.uk with the command in the body of the message: SUBSCRIBE country-codes where "" is your real name. 10. New World-Wide-Web (WWW) document An experimental (i.e: under construction) WWW version of this document is available as: http://www.ee.ic.ac.uk/misc/country-codes.html This is currently experimental, so its reference may change at short notice, and some of the links in the document are currently not working. HTTP references for Top-Level information servers for a particular country should be sent to . ISO 3166 Codes + Top level domains. WARNING: The link to some countries marked as being connected to Internet via UUCP or FIDO is often an expensive telephone dialup link. The people in those countries pay dearly for every byte of information sent to them. It is therefore not advised to send an electronic mail to a remote node in such a country asking "how's the weather there". When it comes to money, people take things very seriously, especially since funds are scarce. It is a matter of net etiquette to keep this in mind. Junk mail sent to any node that has to pay a lot for its telephone connection will clearly be dealt with HARSHLY and evasive action may well be taken against those not respecting this notice. Code Country Conn Notes Further information ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ AD Andorra AE United Arab Emirates P Apparently dead ns.uu.net AF Afghanistan(Islamic St.) AG Antigua and Barbuda * upr1.upr.clu.edu AI Anguilla AL Albania P gwd2i.cnuce.cnr.it AM Armenia FI * Ex-USSR AN Netherland Antilles AO Angola (Republic of) * gopher gopher.psg.com AQ Antarctica FI * intermittent luxor.cc.waikato.ac.nz AR Argentina FI B * Uni. de Buenos Aires gopher gopher.psg.com AS American Samoa AT Austria FI B * gopher gopher.ripe.net telnet ns.ripe.net AU Australia FI * munnari.oz.au AW Aruba * gopher gopher.psg.com AZ Azerbaijan FI B * Ex-USSR gopher gopher.psg.com BA Bosnia-Herzegovina BB Barbados * upr1.upr.clu.edu BD Bangladesh F BE Belgium FI B * gopher gopher.ripe.net telnet ns.ripe.net BF Burkina Faso * gopher gopher.psg.com BG Bulgaria FI B * Daniel Kalchev BH Bahrain B * Gulfnet BI Burundi BJ Benin BM Bermuda FI * BN Brunei Darussalam BO Bolivia * gopher gopher.psg.com BR Brazil FI B * gopher gopher.psg.com BS Bahamas * upr1.upr.clu.edu BT Bhutan BV Bouvet Island BW Botswana * gopher gopher.psg.com BY Belarus FI * Ex-USSR gopher gopher.psg.com BZ Belize * gopher gopher.psg.com CA Canada FI B * relay.cdnnet.ca CC Cocos (Keeling) Isl. CF Central African Rep. CG Congo * gopher gopher.psg.com CH Switzerland FI B * gopher gopher.ripe.net telnet ns.ripe.net CI Ivory Coast * gopher gopher.psg.com CK Cook Islands CL Chile FI B * gopher gopher.psg.com dcc.uchile.cl CM Cameroon FI * in .fr domain gopher gopher.psg.com CN China FI * ns.cnc.ac.cn gopher gopher.psg.com CO Colombia FI B * gopher gopher.psg.com cunixd.cc.columbia.edu CR Costa Rica FI B * gopher gopher.psg.com CS Czechoslovakia ******** not a top-level domain anymore ******** CU Cuba * gopher gopher.psg.com CV Cape Verde CX Christmas Island CY Cyprus FI B * gopher gopher.ripe.net CZ Czech Republic FI B * gopher gopher.ripe.net telnet ns.ripe.net DE Germany FI B * gopher gopher.ripe.net telnet ns.ripe.net gopher gopher.psg.com DJ Djibouti DK Denmark FI B * gopher gopher.ripe.net telnet ns.ripe.net DM Dominica * upr1.upr.clu.edu DO Dominican Republic * gopher gopher.psg.com DZ Algeria FI * gopher gopher.psg.com EC Ecuador FI B * gopher gopher.psg.com EE Estonia FI * Juhan Poeldvere EG Egypt FI B * gopher gopher.psg.com EH Western Sahara ER Eritrea F gopher gopher.psg.com ES Spain FI B * gopher gopher.ripe.net telnet ns.ripe.net ET Ethiopia F gopher gopher.psg.com FI Finland FI B * gopher gopher.ripe.net telnet ns.ripe.net FJ Fiji FI * FK Falkland Isl.(Malvinas) FM Micronesia FO Faroe Islands FI * danpost.uni-c.dk FR France FI B * gopher gopher.ripe.net telnet ns.ripe.net gopher gopher.psg.com FX France (European Ter.) ??? GA Gabon GB Great Britain (UK) FI * X.400 & IP ns1.cs.ucl.ac.uk GD Grenada P upr1.upr.clu.edu GE Georgia * Ex-USSR ns.eu.net GF Guyana (Fr.) * gopher gopher.psg.com GH Ghana * gopher gopher.psg.com GI Gibraltar GL Greenland FI * gopher gopher.psg.com GM Gambia F gopher gopher.psg.com GN Guinea PFI * dial-IP GP Guadeloupe (Fr.) P gopher gopher.psg.com GQ Equatorial Guinea GR Greece FI B * gopher gopher.ripe.net telnet ns.ripe.net GS South Georgia and South Sandwich Islands GT Guatemala * ns.uu.net GU Guam (US) FI * in US domains gopher gopher.psg.com GW Guinea Bissau GY Guyana HK Hong Kong FI B * hp9000.csc.cuhk.hk HM Heard & McDonald Isl. HN Honduras * ns.uu.net HR Croatia FI * dns.srce.hr HT Haiti P gopher gopher.psg.com HU Hungary FI B * gopher gopher.ripe.net telnet ns.ripe.net gopher gopher.psg.com ID Indonesia FI * gopher gopher.psg.com ns.uu.net IE Ireland FI B * gopher gopher.ripe.net telnet ns.ripe.net IL Israel FI B * relay.huji.ac.il IN India FI B * gopher gopher.psg.com sangam.ncst.ernet.in IO British Indian O. Terr. IQ Iraq IR Iran FI B * Ali Shokoufandeh Ebrahim Mashayekh Akbar Behzadi IS Iceland FI B * gopher gopher.ripe.net telnet ns.ripe.net IT Italy FI B * gopher gopher.ripe.net telnet ns.ripe.net JM Jamaica FI * gopher gopher.psg.com JO Jordan JP Japan FI B * gopher gopher.psg.com jp-gate.wide.ad.jp KE Kenya * gopher gopher.psg.com KG Kyrgyz Republic Ex-USSR KH Cambodia * KI Kiribati KM Comoros KN St.Kitts Nevis Anguilla P upr1.upr.clu.edu KP Korea (North) P KR Korea (South) FI B * ns.kaist.ac.kr KW Kuwait FI * No BITNET gopher gopher.psg.com KY Cayman Islands KZ Kazachstan FI * Ex-USSR LA Laos LB Lebanon FI * gopher gopher.psg.com LC Saint Lucia * upr1.upr.clu.edu LI Liechtenstein FI * gopher gopher.ripe.net telnet ns.ripe.net LK Sri Lanka FI * intermittent gopher gopher.psg.com LR Liberia LS Lesotho * gopher gopher.psg.com LT Lithuania FI * Ex-USSR aun.uninett.no LU Luxembourg FI B * gopher gopher.ripe.net telnet ns.ripe.net LV Latvia FI * Ex-USSR lapsene.mii.lu.lv LY Libya MA Morocco PFI * FI late'94/'95 gopher gopher.psg.com MC Monaco MD Moldova FI * intermittent MG Madagascar (Republic of) * gopher gopher.psg.com MH Marshall Islands MK Macedonia (former Yugo.) * gopher gopher.psg.com ML Mali * gopher gopher.psg.com MM Myanmar MN Mongolia * gopher gopher.psg.com MO Macau FI * hkuxb.hku.hk MP Northern Mariana Isl. MQ Martinique (Fr.) MR Mauritania MS Montserrat MT Malta P ns.iunet.it MU Mauritius * gopher gopher.psg.com MV Maldives MW Malawi F MX Mexico FI B * gopher gopher.psg.com mtecv1.mty.itesm.mx MY Malaysia FI B * mimos.my MZ Mozambique * gopher gopher.psg.com NA Namibia * gopher gopher.psg.com NC New Caledonia (Fr.) * gopher gopher.psg.com NE Niger * in .fr domain gopher gopher.psg.com NF Norfolk Island NG Nigeria F gopher gopher.psg.com NI Nicaragua FI * gopher gopher.psg.com NL Netherlands FI B * gopher gopher.ripe.net telnet ns.ripe.net NO Norway FI B * gopher gopher.ripe.net telnet ns.ripe.net NP Nepal * gopher gopher.psg.com NR Nauru NU Niue NZ New Zealand FI * truth.waikato.ac.nz OM Oman * PA Panama FI B * gopher gopher.psg.com PE Peru FI * gopher gopher.psg.com PF Polynesia (Fr.) * gopher gopher.psg.com PG Papua New Guinea * munnari.oz.au PH Philippines FI * ns.uu.net PK Pakistan * Imran Anwar PL Poland FI B * gopher gopher.ripe.net telnet ns.ripe.net gopher gopher.psg.com PM St. Pierre & Miquelon PN Pitcairn PR Puerto Rico (US) FI B * sun386-gauss.pr PT Portugal FI B * gopher gopher.ripe.net telnet gopher.ripe.net PW Palau PY Paraguay * ns.uu.net QA Qatar RE Reunion (Fr.) FI * In .fr domain inria.inria.fr RO Romania FI B * roearn.ici.ac.ro RU Russian Federation FI B * Ex-USSR RW Rwanda F gopher gopher.psg.com SA Saudi Arabia FI B * dial-ip gopher gopher.psg.com SB Solomon Islands SC Seychelles * gopher gopher.psg.com SD Sudan F SE Sweden FI B * gopher gopher.ripe.net telnet ns.ripe.net SG Singapore FI B * gopher solomon.technet.sg gopher gopher.psg.com SH St. Helena SI Slovenia FI * gopher gopher.ripe.net telnet ns.ripe.net SJ Svalbard & Jan Mayen IsFI * in .no domain SK Slovakia (Slovak Rep) FI B * gopher gopher.ripe.net telnet ns.ripe.net SL Sierra Leone * gopher gopher.psg.com SM San Marino SN Senegal * gopher gopher.psg.com SO Somalia SR Suriname * upr1.upr.clu.edu ST St. Tome and Principe SU Soviet Union FI B * Still used. gopher gopher.psg.com SV El Salvador gopher gopher.psg.com SY Syria SZ Swaziland * gopher gopher.psg.com TC Turks & Caicos Islands TD Chad TF French Southern Terr. TG Togo * gopher gopher.psg.com TH Thailand FI * gopher gopher.psg.com chulkn.chula.ac.th TJ Tadjikistan Ex-USSR TK Tokelau TM Turkmenistan * Ex-USSR in .su domain TN Tunisia FI B * gopher gopher.psg.com alyssa.rsinet.tn TO Tonga TP East Timor TR Turkey FI B * gopher gopher.psg.com knidos.cc.metu.edu.tr TT Trinidad & Tobago * gopher gopher.psg.com TV Tuvalu TW Taiwan FI B * gopher gopher.psg.com TZ Tanzania F gopher gopher.psg.com UA Ukraine FI * UA Network Enq. UG Uganda F gopher gopher.psg.com UK United Kingdom FI B * ISO 3166 is GB telnet news.janet.ac.uk gopher news.janet.ac.uk UK Network Enq. gopher gopher.psg.com UM US Minor outlying Isl. US United States FI * see note (4) venera.isi.edu UY Uruguay FI B * gopher gopher.psg.com UZ Uzbekistan Ex-USSR VA Vatican City State VC St.Vincent & Grenadines P upr1.upr.clu.edu VE Venezuela FI * nisc.jvnc.net VG Virgin Islands (British) VI Virgin Islands (US) * VN Vietnam * gopher gopher.psg.com VU Vanuatu * gopher gopher.psg.com WF Wallis & Futuna Islands WS Samoa YE Yemen YT Mayotte YU Yugoslavia B * effectively cut-off completely ZA South Africa FI * gopher gopher.psg.com ZM Zambia FI * intermittent gopher gopher.psg.com ZR Zaire ZW Zimbabwe FI * gopher gopher.psg.com See Note [5] for the next top level domains (rs.internic.net): ARPA Old style Arpanet * alias still works ns.nic.ddn.mil COM Commercial FI * telnet whois.internic.net EDU Educational FI B * telnet whois.internic.net GOV Government FI * telnet whois.internic.net INT International field FI * used by Nato ns1.cs.ucl.ac.uk MIL US Military FI * ns.nic.ddn.mil NATO Nato field * soon to be deleted ??? NET Network FI * telnet whois.internic.net ORG Non-Profit OrganizationFI * telnet whois.internic.net +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ DISCLAIMER: while every effort is made to provide accurate information, this list is not guaranteed to be accurate. This document is in NO WAY an official document. The information given should not be used as a basis for routing tables but only as general end-user information. This is a voluntary effort. I would appreciate greatly if errors/omissions could be pointed out to me and they would be corrected in the next release. The information included in this document implies no view whatsoever regarding questions of sovereignty or the status of any place listed. Affiliation to Imperial College is given for identification purposes only. -- Olivier M.J. Crepin-Leblond, Digital Comms. Section, Elec. Eng. Department Imperial College of Science, Technology and Medicine, London SW7 2BT, UK Mobile (GMT): +44 (0)956 84 111 3 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Scripts, Bilayers added to web site Date: Mon, 04 Mar 1996 18:24:26 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've added the following to our web site: 1. A new script: -Hemoglobin, with pauses, designed for a lecture projection to discuss elementary protein structure, mutation, sickle hemoglobin. 2. Enhanced scripts: -DNA3: with pauses, designed for a lecture projection to show basic DNA structure. Now includes ATP, replication, and mutation. -AB2: Antibody:antigen. Enhanced to include the whole IgG1 structure and generally polished a bit. -DNA2: Runs unattended (no pauses); a slower version than DNA1 for faster computers and/or fast RasWin32. 3. New Gallery Images -Roger Sayle's favorite 4, showing RasMol at its best. -Cutaway views of lipid bilayers in crystal, gel, fluid modes (built on the molecular dynamics simulation PDB's kindly provided by Heller, Schaefer, and Schulten). 4. A bibliography page (lists the 3 TIBS articles on free molecular visualization software). Do you know of others I should add? 5. Summary of visiting stats (7,000 people so far ...) 6. A 'what's new' log so you can find new additions easily. The Windows and plain text versions of the new/enhanced scripts are now available. sea.hqx packages for Macs will be provided soon. Reminder: these scripts work on all platforms (Windows, Mac, unix, VMS). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Fix for all-blue when color by group wanted Date: Mon, 04 Mar 1996 22:50:14 -0500 (EST) To: rasmol@noc1.oit.umass.edu Perhaps some of you have seen the same puzzling 'all blue' chain I have when you requested a 'color by group'. I discovered how to avoid this. It happens when you have restricted the display such that it does not show the first chain in a multi-chain molecule. Therefore, if you issue the color by group command before you restrict the display to omit early the early chain, the coloring works properly. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Stuart Green Subject: Contour data in rasmol Date: Tue, 5 Mar 1996 09:15:28 +0000 (GMT) To: RasMol List RasMol folks, Has anyone extended RasMol to visualise 3D contour data (electrostatic potentials, connelly surfaces, orbitals etc.) along with the molecular rendering. If not, does anyone think that incorporating the marching cube algorithm to generate the mesh of points, then feeding this data to rasmol's graphics routines would be a problem? Any experiences, hints or tips 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: RasMol scripts -Reply Date: Wed, 06 Mar 1996 09:24:54 -0500 (EST) To: ghelmkam@kumc.wpo.ukans.edu Cc: rasmol@noc1.oit.umass.edu, eap@vger.niddk.nih.gov (Eduardo Padlan) In message Tue, 05 Mar 1996 13:17:06 -0600, George Helmkamp writes: > Eric, Thanks for the advice on running the scripts. They are up and > running. I particularly like your Hemoglobin unit - very instructive and > interactive. The pauses to permit rotation, etc. are great for going > beyond what is in the basic unit. I think the "sticky patches" in the HbS > section may be a bit difficult for many students to follow. Perhaps those > areas of the tetramers could be exagerated and more clearly identified. > The generation of a long polymer of HbS tetramers may also be included, > since this is what probably happens in the erythrocyte and contributes to > the shape change and eventual lysis of sickled cells. I really appreciate > your efforts. And I do plan to use some of this in my medical > biochemistry lectures next fall. Dear George: Be advised that I know nothing about Hb except what I read in Victor Rodwell's article in the Lange Biochem overview! And precious little about protein structure! Of course you could improve the script if you wish and I'd be happy to distribute the improved version. I wrote the Hb script for two colleagues here who teach Biotech 200 to fresh/soph, about 100+ students. It seemed to go over well. Lange says the deoxy patch is on the alpha chain. I didn't expect to be able to show aggregation at all in RasMol, but was delighted to find that the sickle Hb was dimerized in the X-rayed crystal, and that it appears to be sticking at the sickle mutant valine 6. I haven't read the paper which describes this crystal analysis yet so I don't know Padlan's interp. Anyway, polymerization beyond dimers would be a tough assignment for RasMol (were at nearly 10,000 atoms at the dimer!). What I did is project overheads from the Rodwell's article (see ref in script). He has a nice diagram of polymerization, and a good scanning EM of a sickled RBC. I'm delighted to hear you plan to use the script in a class. Keep me posted. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: christer@biokemi.su.se (Christer Jansson) Subject: Rasmol and Alchemy formats Date: Thu, 7 Mar 1996 06:54:31 +0100 To: rasmol@noc1.oit.umass.edu Dear Rasmolians! There is a site with amino acid structures at http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html The structures shown are in an Alchemy format with the suffix .mol (i.e. ala.mol). I cannot open these files with Rasmac. Is that because Rasmol does not recognize this format or is it because I'm using Rasmol for Macintosh? Is there another application that one can use to view these files? I would appreciate any comments. Kind regards, Christer Jansson Christer Jansson Professor of Biochemistry Biochemistry Dept, Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden E mail: christer@biokemi.su.se Fax: +46 8 153679 Phone: +46 8 162592 amino acid structures ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Rasmol and Alchemy formats// Availability of standard Date: Thu, 7 Mar 96 08:48:20 PST To: rasmol@noc1.oit.umass.edu At 06:54 AM 3/7/96 +0100, you wrote: >Dear Rasmolians! >There is a site with amino acid structures at >http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html >The structures shown are in an Alchemy format with the suffix .mol (i.e. >ala.mol). I cannot open these files with Rasmac. Is that because Rasmol >does not recognize this format or is it because I'm using Rasmol for >Macintosh? Is there another application that one can use to view these >files? > >I would appreciate any comments. > >Kind regards, > >Christer Jansson > >Christer Jansson >Professor of Biochemistry >Biochemistry Dept, Arrhenius Laboratories, Stockholm University, S-10691 >Stockholm, Sweden >E mail: christer@biokemi.su.se >Fax: +46 8 153679 >Phone: +46 8 162592 --------------------------------------------------------------- Standard amino acid structures for Rasmolians, Christer, I can't answer you questions about how to view Alchemy format files but I can offer all of you access to my web page with links to files in pdb format for all 20 of the standard amino acids. http://www.mcl.ucsb.edu/classes/biol108/weeks/week02.htm If your Web server is suitably configured, when you click on the icons for any of these text-based files, they will be downloaded onto your computer (usually with a cryptic name). Rename the file and it is yours. I'm sorry I haven't had the time to generate a single compressed file for distribution containing all 20 structures, but the files are tiny and it should only take a few minutes to download and rename all 20. Duane P.S. These files were created with the biopolymers module of Sybyl. All covalently linked hydrogens have been added to the structures. All alpha-amino groups, the epsilon-amino group of Lys, and the quanidinium group of Arg are protonated (charge = +1). All alpha-carboxyl groups, the beta-carboxyl group of Asp, and the gamma carboxyl group of Glu are deprotonated (charge = -1) to give an accurate representation of the AA ionization states at physiological pH values. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 homepages: http://www.mcl.ucsb.edu/classes/biol108/108ahome.htm http://www.mcl.ucsb.edu/classes/biol123/123home.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: RasMol ver. 2.6 beta Date: Mon, 11 Mar 1996 10:21:33 -0500 (EST) To: jkerns+@pitt.edu Cc: rasmol@noc1.oit.umass.edu In message Sun, 10 Mar 1996 21:54:25 -0800, Jeff Kerns writes: > Can you tell me who is developing the new version of RasMol? Roger Sayle, the creator of RasMol, is currently working on the next full release of RasMol, version 2.6. Roger is an employee of Glaxo Wellcome; the company offers RasMol free to the world, as did Roger prior to becoming employed there. Marco Molinaro at U Cal Berkeley is working on an enhanced version of RasMol 2.6. His enhanced 2.5 is available (see www.umass.edu/microbio/rasmol for link). Others are considering various enhancements, and have ported RasMol to various platforms. Consult the history of the RasMol mailing list (above web site) for these. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: RasMol for NEXTSTEP Date: Mon, 11 Mar 1996 11:11:21 -0500 (EST) To: windemut@cumbnd.bioc.columbia.edu Cc: rasmol@noc1.oit.umass.edu, heller@attila.imo.physik.uni-muenchen.de In message Fri, 08 Mar 1996 13:36:36 -0500, Andreas Windemuth writes: > A while back I made available a NEXTSTEP Application version > for RasMol, called RasMol.app, which I whipped up when Roger > visited our lab. RasMol.app uses RasMol 2.6 and keeps RasMol > source modifications to a minimum. I asked Roger if he could > include it into the official rrelease, but I suspect he didn't get > araound to that. RasMol.app can be found at the following > locations: > > RasMol-src.tar.gz: The source > > "ftp://next-ftp.peak.org/pub/next/sources/science/RasMol-src.tar.gz" > RasMol-NI16.tar.gz: Binary for Intel and NeXT with 16 bit graphics > > "ftp://next-ftp.peak.org/pub/next/binaries/science/RasMol-NI16.tar.gz" > RasMol-NI2.tar.gz: Binary for Intel and NeXT with 2 bit > graphics > > "ftp://next-ftp.peak.org/pub/next/binaries/science/RasMol-NI2.tar.gz" > Andreas Windemuth > > +-------------------------------------------------------------------- > |Columbia University, Department of Biochemistry and Biophysics > |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail > |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu > +-------------------------------------------------------------------- I will link these to the RasMol web site soon. -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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Group coloring problems continue Date: Mon, 11 Mar 1996 15:27:15 -0500 (EST) To: rasmol@noc1.oit.umass.edu I'm having trouble with group coloring in RasWin 2.6-beta-32bit. Earlier I realized that in some cases group coloring fails if an early protein chain is hidden with a restrict command before the color group command is issued. But even avoiding this [which makes the visible chain all-blue] I'm still having a problem. With some PDB's, the protein color starts with blue but stops at green instead of going all the way to red (despite having nearly 200 residues). In one case I noticed the waters in the crystal were colored from green to red, evidently continuing the colors, and being considered as part of the 'chain'. How do I get RasWin to recognize the end of the chain for group-coloring purposes? Here is an excerpt from the problem PDB file. I inserted TER records to no avail. ATOM 1 CB ASP A 6 8.044 26.448 -22.991 1.00 33.58 [...] ATOM 1491 OT2 LYS A 189 0.505 32.248 -22.077 1.00 22.29 TER 1492 LYS A 189 ATOM 1493 MG IUM 201 -13.883 7.616 -5.838 1.00 9.37 REMARK ***1493 OH2 TIP 202 -3.965 27.054 -21.494 1.00 17.39 HETATM 1494 OH2 TIP 204 -12.017 0.226 -3.149 1.00 18.58 [...] HETATM 1566 OH2 TIP 308 -19.012 17.157 -23.488 1.00 27.40 END ***I sacrificed this one water because I didn't want to bother to renumber the atoms from here forward after inserting the TER record. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: Downloading PDB's from BNL Date: Mon, 11 Mar 1996 15:30:57 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've never figured out how to get Netscape to save a PDB file from BNL. After getting the entire PDB file to display as plain text in the Netscape browse window, I select File, Save-as, and what I get is a file named send-tex which does not contain the PDB. I've been able to get the PDB only by sneaking out into a DOS window, copying the cached file in DOS, outside of Netscape, and editing it to strip out non-PDB lines. Surely there's a better way! Will someone please enlighten me? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ amino acid structures ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Re: Rasmol and Alchemy formats// Availability of standard Date: Mon, 11 Mar 1996 14:37:52 -0600 To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu They are also on Klotho (http://ibc.wustl.edu/klotho/), and work with Rasmol. Toni Kazic Institute for Biomedical Computing Washington University "Downloading PDB's from BNL" (Mar 11, 3:30pm) References: <55859.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: Downloading PDB's from BNL Date: Mon, 11 Mar 1996 18:01:25 -0500 To: emartz@microbio.umass.edu Cc: rasmol@noc1.oit.umass.edu This must be a platform-dependent problem - what is your OS? Have you tried copying the text from Netscape to the clipboard and pasting it into a text editor? I know some of these are big, but this works if you have enough memory. One can use the BNL FTP site to get the file from a query, without double downloading, if you know its PDB code, as follows: The BNL search page at http://www.pdb.bnl.gov/cgi-bin/browse returns the PDB code at the bottom of a search, prior to fetching an entry. Take this code and find the file on the FTP site. ftp://pdb.pdb.bnl.gov/fullrelease/uncompressed_files/ That way you only have to transfer it to your system once. Another way to solve the problem was discussed on the MIME-types discussion list. Apparently the Brookhaven site uses the fetch script: http://www.pdb.bnl.gov/cgi-bin/get-pdb-entry?id=****&type=view&encoding=none where **** is the PDB code (lowercase letters only) gets you the PDB file with the MIME-type tag . If you replace '&type=view' with '&type=text', and open the file then it is delivered with the plain text MIME type instead, which you should be able to see and save, without any embedded HTML. Try this: http://www.pdb.bnl.gov/cgi-bin/get-pdb-entry?id=1omd&type=text&encoding=none A third solution is to use Molecules-R-Us or Entrez to get the data. These offer a number of save options with and without embedded HTML/MIME tags. Chris Hogue NCBI >On Mar 11, 3:30pm, Eric Martz wrote: > Subject: Downloading PDB's from BNL > I've never figured out how to get Netscape to save a PDB file from > BNL. After getting the entire PDB file to display as plain text > in the Netscape browse window, I select File, Save-as, and what > I get is a file named send-tex which does not contain the PDB. > I've been able to get the PDB only by sneaking out into a DOS window, > copying the cached file in DOS, outside of Netscape, and editing it to > strip out non-PDB lines. Surely there's a better way! Will someone please > enlighten me? > > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > 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 > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >-- End of excerpt from Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Downloading PDB's from BNL Date: Tue, 12 Mar 1996 09:36:40 -0500 (EST) To: rasmol@noc1.oit.umass.edu (Forwarded to rasmol@noc1.oit.umass.edu by Eric Martz) From: rmsmith@amherst.edu Indeed, there is a simpler method, although I didn't find it very obvious. This is complements of Dave Ratner. If you have used the Search template under PDB WWW Browser set up at BNL to get a list of PDB files you can do the following: select the file you want to download, select 'Fetch Entry'. At this point you get the text of the PDB file in the window. One of the options there is 'View the file, e.g., with RasMol' or something like that. When I select this, I get the message 'Viewer not configured' and am presented with the further option to 'Save to disk' (it does this in PDB format). I am not sure if you will be presented with that choice if you have RasMol configured to run from Netscape. (The part I didn't find obvious is selecting 'View...' since I knew that I didn't have RasMol configured to run through Netscape.) Rob rmsmith@amherst.edu --------------------------------------------------------------------------- Department of Chemistry a Program in Molecular and Cellular Biology Amherst College n University of Massachusetts Amherst, MA 01002 d Amherst, MA 01003 --------------------------------------------------------------------------- /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: toni@athe.wustl.edu (Toni Kazic) Subject: Re: Downloading PDB's from BNL Date: Tue, 12 Mar 1996 11:25:47 -0600 To: emartz@microbio.umass.edu Cc: rasmol@noc1.oit.umass.edu Eric, I just tried essentially the same thing and it worked fine on my unix machine with Netscape 2.0. After retrieving the file, I clicked on the BNL button saying "send entire text", got the result, and then saved that to a file using netscape save-as and selecting the text option. I did change the name of the output file to "test.pdb" just so I could immediately view it in RasMol. Worked fine. Toni Kazic Institute for Biomedical Computing Washington University ++++------+------+------+------+------+------+------+------+------+------+ From: Aidan Dysart Subject: Re: Downloading PDB's from BNL Date: Tue, 12 Mar 1996 13:28:23 -0500 (EST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu > I've never figured out how to get Netscape to save a PDB file from > BNL. After getting the entire PDB file to display as plain text > in the Netscape browse window, I select File, Save-as, and what > I get is a file named send-tex which does not contain the PDB. > I've been able to get the PDB only by sneaking out into a DOS window, > copying the cached file in DOS, outside of Netscape, and editing it to > strip out non-PDB lines. Surely there's a better way! Will someone please > enlighten me? if you hold Option while clicking on the link (on a mac) netscape will save the file as a text file without displaying it. Aidan Dysart ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Group coloring problems continue Date: Thu, 14 Mar 1996 16:24:28 +0000 (GMT) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear All, > With some PDB's, the protein color starts with blue but stops at green > instead of going all the way to red (despite having nearly 200 residues). > In one case I noticed the waters in the crystal were colored from green to > red, evidently continuing the colors, and being considered as part of the > 'chain'. How do I get RasWin to recognize the end of the chain for > group-coloring purposes? Here is an excerpt from the problem PDB file. I > inserted TER records to no avail. I'm sorry to take so long to reply to your message, but unfortunately I've been away from my e-mail in the US for the last three weeks. I apologise for any inconvenience this may have caused. When RasMol performs group colouring it decides the range of colours it uses from the residue numbering given in the PDB file. Hence the lowest residue number is displayed in blue and the highest residue number is displayed as red. Unfortunately, if a PDB file contains a large number of hetatoms, such as water molecules, that occupy the high residue numbers, the protein is displayed in the blue-green end of the spectrum and the waters in the yellow-red end of the spectrum. This is aggrevated by there typically being many more water molecules than amino acid residues. The solution to this problem is to use the command "set hetero off" before the "colour group" command. This can also be achieved by toggling "Hetero" on the "Options" menu, before selecting "Group" on the "Colour" menu. This command instructs RasMol to only use non-hetero residues in the group colour scaling. I hope this solves your problem. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Aidan Dysart Subject: AN interesting use of RasMol and the Web... Date: Thu, 14 Mar 1996 23:01:29 -0500 (EST) To: rasmol list I upt up somthing on my web page that I think all of you might enjoy. However, you must you Netscape 2.0 to view it (sorry!). Go to the URL that is listed in my .sig file below, and click on { biochemitsy } on the left hand side. That will take you to my meager biochem page, but awaiting is a nice animation of Adenosine Deaminase (not sure of the species). I created this animation in the same way that I created my name animation, but ot get each individual frame, I used RasMac, and exported still shots as GIFs. I just clicked the scollbar once between each frame. so, what do you think. If any of you are Professors (which I imagine at least some of you are) this might be a useful tool for online papers, class notes, etc. Instead of just a still shot you get an active document. You could also do this in stereo mode in RasMol 2.6. Wouldn't that be cool! Anyway, check it out. ___________________________________________________________________________ / Aidan Dysart \Through the darkness of future past \ | The University of Michigan \the magician longs to see | | adysart@umich.edu \one chants out between two worlds | | http://www-personal.umich.edu/~adysart \'Fire walk with me.' | \__________________________________________\________________________________/ "AN interesting use of RasMol and the Web..." (Mar 14, 11:01pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: AN interesting use of RasMol and the Web... Date: Fri, 15 Mar 1996 10:54:27 -0500 To: rasmol@noc1.oit.umass.edu Hi Aidan, I had a look at your animation. On my 90 MHz pentium it is doing two rotations per second - way too fast for it to be useful. This is an old problem from computer game design - simply put - animation to be timed on the local CPU. This is why MIME-type launching of a local 3D viewer is a better solution - unless you can set up a local JAVA timimg script. You might be able to get away with another trick from film animation - that is to repeat each frame 2-3 times. Also, I could barely read the blue hot-linked text on that black background. Chris Hogue. Visiting Fellow hogue@ncbi.nlm.nih.gov Disclaimer: The views expressed here are not necessarily representative of NCBI or the US government. >On Mar 14, 11:01pm, Aidan Dysart wrote: > Subject: AN interesting use of RasMol and the Web... > > I upt up somthing on my web page that I think all of you might enjoy. > However, you must you Netscape 2.0 to view it (sorry!). Go to the URL > that is listed in my .sig file below, and click on { biochemitsy } on the > left hand side. That will take you to my meager biochem page, but > awaiting is a nice animation of Adenosine Deaminase (not sure of the > species). I created this animation in the same way that I created my name > animation, but ot get each individual frame, I used RasMac, and exported > still shots as GIFs. I just clicked the scollbar once between each frame. > > so, what do you think. If any of you are Professors (which I imagine at > least some of you are) this might be a useful tool for online papers, > class notes, etc. Instead of just a still shot you get an active > document. You could also do this in stereo mode in RasMol 2.6. Wouldn't > that be cool! Anyway, check it out. > > ___________________________________________________________________________ > / Aidan Dysart \Through the darkness of future past \ > | The University of Michigan \the magician longs to see | > | adysart@umich.edu \one chants out between two worlds | > | http://www-personal.umich.edu/~adysart \'Fire walk with me.' | > \__________________________________________\________________________________/ > >-- End of excerpt from Aidan Dysart ++++------+------+------+------+------+------+------+------+------+------+ From: merckel@max.mpibp.uni-frankfurt.de Subject: Re: AN interesting use of RasMol and the Web... Date: Mon, 18 Mar 1996 11:23:25 EST To: rasmol@noc1.oit.umass.edu Hi, Regarding the local speed of Aidans JAVA applet, maybe it would be possible to get it to operate interactively, ala the applets you may find at: Indiana University Molecular Structure Center - Crystallography http://www.iumsc.indiana.edu/ The applets there, e.g. Buckminsterfullerene, are interactive. Left mouse button does a rotation and middle mouse does a zoom. I have not tried out JAVA programming yet, maybe someone at that site could give a few pointers. I do like Aidans effort !!! Keep it up ! Mike ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Kerns Subject: Rasmol text Date: Mon, 18 Mar 1996 19:48:19 -0500 (EST) To: rasmol@noc1.oit.umass.edu Can anyone tell me if it is possible to add text within the Rasmol viewing area? I would like to customize the molecules I'm working with so I can give handouts to students so adding titles, headers, etc. would be most useful. Also, is there a convenient way of labelling amino acid residues? Currently I've been selecting one atom of a residue and labelling that atom. The problem I've run into however, is that if I change the color of the text it of course changes the color of the atom. Any suggestions would be most welcomed. Thanks in advance Jeff ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: RE: RasMol scripts -Reply Date: Tue, 19 Mar 1996 18:24:01 +0000 (GMT) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu In a recent post from Eric: > Anyway, polymerization beyond dimers would be a tough assignment for > RasMol (were at nearly 10,000 atoms at the dimer!). For those of you interested in such things, the current RasMol record is 308,514 atoms of a viral capsid, by Aaron Halpern of the Human Papillomavirus Database Project, at Los Alamos National Labs, NM. Any takers for a new record? 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: RasMol Help file Date: Tue, 19 Mar 1996 18:22:58 -0500 (EST) To: dkk@welchlink.welch.jhu.edu Cc: rasmol@noc1.oit.umass.edu In message Mon, 18 Mar 1996 19:49:32 -0800, Piotr Kosicki writes: > Hello! My mother is a biochemist and I have been downloading RasMol and > .PDB images from the Internet for her to use in her work. When I try to > use help in RasMol, Windows tells me it cannot find the help file. Could > you tell me where I can get the Help file? Thanks a lot! 1. In order to call up help within RasWin, the files you need are RASMOL.HLP and RASWIN.HLP. These files come with RasWin 2.5 (full release) but not with 2.6-beta (for which the help files have not yet been updated). You can get the files from http://www.umass.edu/microbio/rasmol/getras.htm as a self-extracting compressed file RASMAN.EXE. Then you must put copies of these files in the _same_ directory you have specified as the Working Directory in the Windows Program Item Properties dialog box. By default, RasMol looks for all files here, including scripts and help files. 2. Help for RasWin 2.6-beta is in the form of a plain text file, RELEASE.TXT, which you can get at the same web site listed above. This you must display outside of RasMol with a file viewer, or print. Let me know if you still have problems. I will add more information on this on the web site to make it more clear for others. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Joseph J. Grabowski" Subject: Posting pdb's to the Web Date: Wed, 20 Mar 96 06:52:02 EST To: rasmol@noc1.oit.umass.edu Hi. I am a new user of RASMOL and am incorporating it on the WWW pages for my sophmore level bio-organic chemistry course. Installation as a helper file for NetScape and use to download files from various databases works quite well. The problem I have is when I create my own RASMOL file (in this case, just the active site residues of an enzyme) and then ftp this file from my PowerMac to the campus server for incorporation into our Web pages. When the appropriate image is selected from a browser set to our Web page, the RASMOL file is sent back to my PowerMac - now as a text file, rather than as a file that automatically launches RASMOL. This has to be a problem with the file I posted, since I can automatically have RASMOL launched when I select images from other web pages. I don't mind reading to find the answer - if you could just point me in the right direction. I am using RasMac v25.-ucb1.3, but I suspect (for no reason) that somehow the "identifiers" (sorry, I really don't know the correct computer terms) that specify the creator for the RASMOL file is being corrupted/changed when I ftp the file up to the Web computer. Incidentally, the text file that comes back can be opened, providing the correct image, from within RASMOL. The only problem, the file is not identified as RASMOL and does not automatically launch RASMOL. Any help and/or hints would be appreciated. ---------------------------------------------------------------------------- Joseph J. Grabowski joeg+@pitt.edu Associate Professor Office: 624-8632 Department of Chemistry Lab: 624-8383 University of Pittsburgh Fax: 624-8552 ---------------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: rlevine@nih.gov (Rod Levine) Subject: Where's the Center ? Date: Tue, 19 Mar 1996 19:17:30 -0500 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu (RasMol List) Dear RasMol'ers, If I understand correctly, the default location for the Centre command is the center of gravity of the molecule. Is there a way to determine where that is located? I'd like to be able to measure distances from that center of gravity to specific atoms. Thanks, Rod Levine --------- NIH Bldg 3, Room 106 MSC 0320 Bethesda, MD 20892-0320 email: rlevine@nih.gov voice: 1 (301) 496-2310 fax: 1 (301) 496-0599 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fw: Re: Leading space in label, echo Date: Wed, 20 Mar 1996 13:58:50 -0500 (EST) To: rasmol@noc1.oit.umass.edu Here's the answer for anyone else who wants to know. -Eric ------------------------------ Wed, 20 Mar 1996 17:12:45 +0000 (GMT) From: Sayle Dr R A Subject: Re: Leading space in label, echo To: Eric Martz Eric inquired: > Often I want to include leading spaces in a label (to get the label > spaced away from the molecule onto the black background) or in an > echo'd legend line (e.g. to set up a small table or center something). > RasMol evidently strips out leading whitespace on label and echo > lines. I would prefer that the leading white space be retained in > these two commands. My workaround is to put a period before the spaces, > but that is slightly ugly. Dear Eric, You'll be pleased to hear that I'm still working through the outstanding e-mails.... The secret is to place the comments in a string, i.e. delimit them with either apostrophes or double quotes. For example, label " 123" or even echo " It is possible" echo "to indent the beginnings" echo "of paragraphs." The same also applies to filenames. By placing the filename within quotes you can specify a filename on a Macintosh or UNIX box that begins with (or contains) a space. I hope this helps. Roger Dear Roger: YES it certainly does. Thanks! -Eric /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ "Posting pdb's to the Web" (Mar 20, 6:52am) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: Posting pdb's to the Web Date: Wed, 20 Mar 1996 15:03:13 -0500 To: rasmol@noc1.oit.umass.edu Hi Joseph, Simple problem. You just need to insert the MIME-type tag at the beginning of the PDB file that your server is emitting. That's the tag that tells Netscape to launch RasMol, which is associated with this MIME-type (Multipurpose Internet Mail Extension). To learn more about MIME-types, visit http://www.ch.ic.ac.uk/chemime/ Chris Hogue NCBI. >On Mar 20, 6:52am, Joseph J. Grabowski wrote: > Subject: Posting pdb's to the Web > Hi. > > I am a new user of RASMOL and am incorporating it on the WWW pages for > my sophmore level bio-organic chemistry course. Installation as a helper > file for NetScape and use to download files from various databases works > quite well. The problem I have is when I create my own RASMOL file (in > this case, just the active site residues of an enzyme) and then ftp this > file from my PowerMac to the campus server for incorporation into our > Web pages. When the appropriate image is selected from a browser set > to our Web page, the RASMOL file > is sent back to my PowerMac - now as a text file, rather than as a file > that automatically launches RASMOL. This has to be a problem with the file > I posted, since I can automatically have RASMOL launched when I select > images from other web pages. > > I don't mind reading to find the answer - if you could just point me > in the right direction. I am using RasMac v25.-ucb1.3, but I suspect > (for no reason) that somehow the "identifiers" (sorry, I really don't know > the correct computer terms) that specify the creator for the RASMOL file > is being corrupted/changed when I ftp the file up to the Web computer. > Incidentally, the text file that comes back can be opened, providing the > correct image, from within RASMOL. The only problem, the file is not > identified as RASMOL and does not automatically launch RASMOL. Any help > and/or hints would be appreciated. > > ---------------------------------------------------------------------------- > Joseph J. Grabowski joeg+@pitt.edu > Associate Professor Office: 624-8632 > Department of Chemistry Lab: 624-8383 > University of Pittsburgh Fax: 624-8552 > ---------------------------------------------------------------------------- >-- End of excerpt from Joseph J. Grabowski ++++------+------+------+------+------+------+------+------+------+------+ From: jsb2@camsci.com Subject: Re: Posting pdb's to the Web Date: Wed, 20 Mar 96 22:07:09 EST To: rasmol@noc1.oit.umass.edu >Simple problem. You just need to insert the MIME-type tag > >at the beginning of the PDB file that your server is emitting. Careful! This hs no right to work. If it does happen to work with your WWW server software and you ever change your server, it will most likely stop working. The proper way to do this is NOT to modify the individual files but to configure chemical/x-pdb as a "known" MIME type to your WWW server. You generally must be the server administrator to do this, and the exact procedure varies greatly (but is always simply and straightforward) from server to server. Check your manuals. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Hogue Subject: Re: Posting pdb's to the Web Date: Wed, 20 Mar 1996 23:57:50 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Hi all, Jonathan is absolutely right, thanks!. My mistake - I didn't quite understand that it was a property of the server software. This underscores the importance of getting the chemical MIME-types standardized, so that the typical sytem administrator dosen't have to do a special set-up for every person who wants to make WWW-based courses using these MIME-types. This is a problem likely to come up again and again. I found it very difficult to find information about this before Jonathan pointed it out. Not surprising, because in the eyes of "WWW standards", the use all the chemical/x-... MIME-types we are interested in are considered non-standard! If you are using a local file (i.e. file://), (like I was when I tried my ill-advised advise) Netscape launches RasMol only if the extention of the file (e.g. "pdb" or "ent") matches one of the extentions already registered together with the helper-app and mime-type within Netscape. It ignores the tag at the top (ouch), and appears to work. Christopher Hogue NCBI On Wed, 20 Mar 1996 jsb2@camsci.com wrote: > >Simple problem. You just need to insert the MIME-type tag > > > >at the beginning of the PDB file that your server is emitting. > > Careful! This hs no right to work. If it does happen to work with your > WWW server software and you ever change your server, it will most likely > stop working. > > The proper way to do this is NOT to modify the individual files but to > configure chemical/x-pdb as a "known" MIME type to your WWW server. > You generally must be the server administrator to do this, and the exact > procedure varies greatly (but is always simply and straightforward) from > server to server. Check your manuals. > > Jonathan Brecher > CambridgeSoft Corporation > jsb@camsoft.com > ++++------+------+------+------+------+------+------+------+------+------+ From: "Boris Steipe" Subject: Re: Posting pdb's to the Web Date: Thu, 21 Mar 96 09:29:10 +0100 To: rasmol@noc1.oit.umass.edu > The problem I have is when I create my own RASMOL file and then ftp this > file from my PowerMac to the campus server for incorporation into our > Web pages. When the appropriate image is selected from a browser set > to our Web page, the RASMOL file > is sent back to my PowerMac - now as a text file, rather than as a file > that automatically launches RASMOL. As far as I understand, the problem is with the Web-server, which has to be configured to serve the correct MIME-type with files of ending .PDB or .ENT . Browsers should not try to interpret file.extensions but use MIME type information to pass the file to the correct helper application. (I use chemical/X-pdb, but I am not sure if that has progressed from the X-something to a recognized standard in the meantime). You have to talk to your Webmaster about this. It is definitely not a problem of your files. best wishes Boris Steipe +---Dr. Boris Steipe---------------+ | Genzentrum | | Wuermtalstr. 221 Tel.: +49 (89) 74017 - 417 | | 81375 Muenchen, Germany Fax.: - 448 | +------+ ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Re: Posting pdb's to the Web T)) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu There is an ongoing effort to standardize chemical MIME types, and a discussion group. See http://www.ch.ic.ac.uk/hypermail/chemime/ CHEMIME archive by thread for progress and to participate! Toni ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Pedro, our 117th Date: Thu, 21 Mar 1996 22:38:52 -0500 (EST) To: rasmol@noc1.oit.umass.edu A special welcome to the 117th subscriber to the RasMol email list, Pedro M. Coutinho. Some of you will recognize Pedro as the creator of one of the most extensive bioscience indexes on the web, Pedro's BioMolecular Research Tools (http://www.public.iastate.edu/~pedro/research_tools.html). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "SUZANNE W. SLAYDEN" Subject: RasMol Introduction Date: Fri, 22 Mar 1996 09:51:36 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear RasMolers, As some of you have done, I'd like to introduce myself and express my delight in finding a list dedicated to discussion of one of my favorite programs. I teach (primarily) undergraduate Organic Chemistry at George Mason University. I'm fortunate that I teach my large lecture section in a "high tech" classroom, equipped with a Pentium and a ceiling-mounted RGB monitor display projector. It's a wonderful performance space in which to use RasMol to demonstrate organic structure and stereochemistry. I used "Molecules 3D" software to generate structure files of all the compounds I talk about in the first half of the course. RasMol and these files are also on the servers in the student computer labs and I give the files to any student who wants to work at home. If any of you are attending the ACS meeting next week in New Orleans, please come to the Frugal Chemists Software Symposium, organized by the Division of Computers in Chemistry, Tuesday afternoon. I'll be speaking on "Dynamic Display of Structure and Stereochemistry in the Organic Chemistry Course", showing how to draw molecules with the very inexpensive (~$30), yet versatile, "Molecules 3D" and then exporting them to RasMol. And I'm looking forward to using the many ideas I've learned about from this list. By the way, do any of you know why I can't get ver. 2.6 to run on my Thinkpad laptop? Ver. 2.5 works just fine. Suzanne Slayden |---------------------------| | Suzanne W. Slayden | | Chemistry Department 3E2 | | George Mason University | | Fairfax, VA 22030-4444 | | sslayden@gmu.edu | |---------------------------| ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: User Colors Date: Fri, 22 Mar 1996 15:47:15 -0500 (EST) To: dbeecher@facstaff.wisc.edu, rasmol@noc1.oit.umass.edu Douglas Beecher writes: >Can anyone tell me how to assign colors to amino acids in RasMol? >Specifically, I'd like to assign red to K, R, and H; blue to D and E; green >to all hydrophobic residues, and some other color to polar aa's. Help for >User colours indicates that RasMol can use color schemes stored in the PDB >file and mentions Raster3D, but it isn't specific about how to go about >properly apending the PDB file. > >Douglas J. Beecher, Ph.D. >University of Wisconsin-Madison >Dept. Food Microbiology and Toxicology >1925 Willow Dr. >Madison, WI 53706 > >608/263-1177 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - I don't know how to put the colors in the PDB file, but I think a more versatile way would be to create a plain ASCII text file named COLORAA.SCR containing (as per your request): BEGIN SCRIPT FILE define temp selected select temp and (lys or arg or his) color red select temp or (asp or glu) color blue select temp and hydrophobic color green select temp and polar color magenta select temp refresh END SCRIPT FILE The BEGIN and END lines should NOT be included in the script file. This is versatile because you can issue the command 'script coloraa.scr' regardless of what molecule or what subset of AA's is selected, and it will always work. The 'temp' maneuver causes it to return without changing the subset selected before the script was executed. If you want gray (e.g. for hydrophobic, looks like carbon's CPK color) color [180,180,180] Another cute trick (if you're displaying side groups) is along this line. It colors only the side groups, leaving the backbone innocuous (here, dark gray): select backbone color [150,150,150] select temp and (lys or arg or his or asp) and not backbone color red For consistency, it may be useful to follow the CPK colors, coloring acidic AA's red, nitrogenous ones blue, hydrophobic ones gray, and polor ones pink ('not quite red'), i.e. [255,180,180]. Such scripts will work equally well on all platforms (Windows, Mac, unix). Windows: The script file must reside in the same directory indicated as the working directory in the RasWin icon's properties box (with icon selected, click on File, Properties). Mac: wish I knew! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ "Re: Group coloring problems continue" (Mar 14, 4:24pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "S Sridharan" Subject: printing from rasmol Date: Tue, 26 Mar 1996 16:54:43 -0500 To: rasmol@noc1.oit.umass.edu Dear Roger, When you were in Barry Honig's lab you showed us how rasmol uses printer resolution when creating postscript files. I guess you used the write ps comand. I have been trying to do the same on some model systems with a mixture of ribbons and cpk. I printed it on the same kodak color printer. It looks like it is coming out at screen resolution (the jaggies are visible). I tried both the write ps command and the export IRIS rgb (and open it in Showcase for printing) Is there something that I overlooked? I am using an 8 bit INDY. thanks Sridhar Dept. Biochem & Mol. Biophys. Columbia Univ. ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: printing from rasmol Date: Wed, 27 Mar 1996 20:14:32 +0000 (GMT) To: S Sridharan Cc: rasmol@noc1.oit.umass.edu Dear Sridhar, > When you were in Barry Honig's lab you showed us how rasmol uses printer > resolution when creating postscript files. I guess you used the write ps > comand. I have been trying to do the same on some model systems with a > mixture of ribbons and cpk. Thanks very much for your e-mail. The answer to the problem is to use the RasMol command "write vectps" rather than "write ps" to generate Vector PostScript output at printer resolution rather than Raster PostScript output at screen resolution. Unfortunately, Ribbons, cartoons, strands and trace representations are not currently supported in Vector PostScript output. However, it is hoped that MolScript quality output will be available in the near future. An alternative solution has also been discussed on the RasMol mailing lists URL, "http://klaatu.oit.umass.edu:80/microbio/rasmol/raslist.htm". This requires making a simple two or three line change to the RasMol source code. > 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 > images, using "rasmol -nodisplay -script ". 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Correct RasMol URL Date: Wed, 27 Mar 1996 15:58:17 -0500 (EST) To: rasmol@noc1.oit.umass.edu > An alternative solution has also been discussed on the RasMol mailing > lists URL, "http://klaatu.oit.umass.edu:80/microbio/rasmol/raslist.htm". The CORRECT address for the RasMol web site is http://www.umass.edu/microbio/rasmol The klaatu.oit address is the present actual machine, but this will likely change in the future. It is unfortunate that the machine address often ends up being used in web links, because these will all break when the machine changes, while the logical address www.umass is guaranteed to remain functional. If any of you maintain web links to the RasMol site, please use the logical address. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Francis M.J. Hsieh" Subject: Can't Copy from Command Line Window.... Date: Thu, 28 Mar 1996 14:43:50 +0800 To: rasmol@noc1.oit.umass.edu Dear Netters. I found I can't copy the word display in the Command Line Window = using My RasWin32 2.6 .... Can I solve it? Sincerely Yours. -- Francis M. J. Hsieh, NTHU, Taiwan. (=C1=C2=A9s=E8=FB=A1A=A5x=C6W=B2M=B5=D8= =A4j=BE=C7) ++++------+------+------+------+------+------+------+------+------+------+ From: "Boris Steipe" Subject: Stereo ?? Date: Thu, 28 Mar 96 14:50:53 +0100 To: rasmol@noc1.oit.umass.edu Dear Rasmol users, I admire anyone who really can make sense of a jumbled wireframe display without using stereo, but I have the impression that most of those who accept mono have just never had the experience of viewing molecules in true 3D. For me, split screen stereo is the *single* *most* *important* feature of any molecular display program. Granted, it does take a little practice (in my experience with students usually only a few half-hour sessions). Still, I feel the results are so convincing, that I dont understand why not everybody in the field uses stereo all the time (and some even resort to epensive and unwieldy hardware solutions with inferior display qualities). I am completely puzzled that most people seem to be happy getting 3D cues from rotating flat projections, instead of looking at 3D objects. Enough proselytizing, but does anybody know how to make RasMac stereo *work* ? Both 2.6b and UCB 2.6 on my Mac produce a split screen image with two objects, but a stereo angle of 0. Thus the object remains frustratingly flat. The syntax set stereo [-] described in release.txt only produces input errors. When will stereo be available ? Can I hold my breath and wait ? It seems such a trivial thing to implement. And it is so important. Please ? Best wishes, Boris +---Dr. Boris Steipe---------------+ | Genzentrum | | Wuermtalstr. 221 Tel.: +49 (89) 74017 - 417 | | 81375 Muenchen, Germany Fax.: - 448 | +------+ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Stereo ?? Date: Thu, 28 Mar 1996 13:29:36 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear Boris: Please look at the history of this email list at http://www.umass.edu/microbio/rasmol and you will find all the answers. Search for 'stereo'. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Orjan Hansson" Subject: Lecture on Visualization of Biomolecules Date: Mon, 1 Apr 1996 15:44:13 GMT+0100 To: rasmol@noc1.oit.umass.edu Dear RasMol Users, Recently, I gave a short lecture at our department about "Visualization of Biomolecules", mainly using RasMol and Mage. The overhead slides were in the form of HTML documents which I presented to the audience with an overhead projector connected to a PC running Netscape. I had configured Netscape to start RasMol or Mage whenever I clicked a PDB or KIN file. With these rather simple means you get an impressive result: From the overhead slides you can jump directly to a molecular graphics program and visualize the molecules with rotations in "real time", etc. I am now planning to use this technique in our basic biochemistry courses. If you would like to read the above mentioned lecture notes, look at the following URL (Netscape 2.0 recommended): http://www.lundberg.gu.se/bcbp/edu/inet96/molvis/index.html Any comments are highly appreciated! With best regards, Orjan Hansson Orjan Hansson E-mail: Orjan.Hansson@bcbp.gu.se Dept. of Biochemistry & Biophysics or: bcbpoh@lundberg.gu.se Lundberg Institute Tel: +46 31 773 39 29 Goteborg University and Fax: +46 31 773 39 10 Chalmers University of Technology WWW: http://www.lundberg.gu.se Medicinaregatan 9C, S-413 90 Goteborg (Sweden) ++++------+------+------+------+------+------+------+------+------+------+ From: mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) Subject: Scripts and the Web Date: Mon, 1 Apr 1996 15:26:54 +0000 To: rasmol@noc1.oit.umass.edu Dear all, I'm a newbie to this list so this may be a FAQ. I want to use Rasmol (RasMac actually) with the WWW for teaching. I have produced some scripts which load pdb files and display molecules to highlight certain aspects of structure, and I use the echo command to annotate these. These scripts are stored on a Novell server. Users log on via the Macs (PowerMac 7100/66, System 7.5), launch Netscape, click on links to the scripts on a WWW page, which launches a script (*.rsml, configured in Netscape to launch RasMac) via a URL of the type file:///. This part works, the script is opened the pdb file opened, but: 1. Even though each script starts with "zap" if the user returns to Netscape and clicks on another link to a script, RasMac crashes the Mac. Quitting RasMac first is necessary. 2. If I use the "pause" command this works fine if I open the script from RasMac's command line (script ......), but not at all if the same script is launched via Netscape. The script stops at the pause, but does not continue when the space bar is pressed, that just enters a space! 3. 2 is a downer, because I thought it might alleviate 1, one script could show all the features I wanted with the same pdb file without multiple scripts and multiple quits. 4. It doesn't seem possible to include a "Quit" command in a RasMac script, which could overcome users forgetting to do this. I don't know if the same behaviour occurs with RasWin/RasMol, possibly on those systems you get multiple copies of Rasmol loading? Anyone any ideas? The WWW and Rasmol together can make a great teaching tool if I can get around this. You can't really on the average user to quit from Rasmol after each script. (I suppose a Rasmol "plug-in" is the answer.) TIA ------------------------------------------------------------------------ Fergus Doherty, PhD. Department of Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH. U.K. Internet: Fergus.Doherty@nottingham.ac.uk Tel: (0)115 970 9366 FAX: (0)115 942 2225 Mail by Eudora 1.5.1 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Scripts and the Web Date: Mon, 01 Apr 1996 16:47:02 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Mon, 01 Apr 1996 15:26:54 +0000, mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) writes: > launch Netscape, click on > links to the scripts on a WWW page, which launches a script (*.rsml, > configured in Netscape to launch RasMac) via a URL of the type file:///. I'd appreciate knowing in detail how you do this. Enough detail for a person who works with a Mac about once a year to follow! (That is changing ...) > 1. Even though each script starts with "zap" if the user returns to > Netscape and clicks on another link to a script, RasMac crashes the Mac. I've seen a similar bug in Berkeley-enhanced RasWin, but here the crash (kills Windows!) is on the first instance of a zap in a script. (A manually typed zap followed by running a zap-less script works fine). I've never seen this in plain RasWin 2.6-beta but I'm not starting the script the same way you are. > 2. If I use the "pause" command this works fine if I open the script from > RasMac's command line (script ......), but not at all if the same script > is launched via Netscape. The script stops at the pause, but does not > continue when the space bar is pressed, that just enters a space! I reported this bug some time ago to Roger Sayle. It is also present in RasWin 2.6 beta. The failure occurs when the Windows properties command line uses a parameter to make RasWin run a script upon startup. > 3. 2 is a downer, because I thought it might alleviate 1, one script > could show all the features I wanted with the same pdb file without > multiple scripts and multiple quits. Why not just have the students run each script manually? All they have to type is 'script scriptname'; surely that would be workable. When one script finishes ('RasMol>' prompt returns in command line window) they could run another one. > 4. It doesn't seem possible to include a "Quit" command in a RasMac > script, which could overcome users forgetting to do this. Again, running the scripts manually would avoid the need to quit. A problem with RasWin 2.6-beta is that there is no way to stop a script before it finishes short of shutting down RasWin. Shutting down be done with a double click in the upper left at a pause, but if the script doesn't pause, a Ctrl-Alt-Delete reboot is the only way to stop. For example, at a recent small local retreat, I ran four pause-less scripts in sequence over and over for hours. Once I got it set up right, it worked like a charm. But if a curious onlooker wants to stop at a particular image and explore manually, no can do. And of course the first three times I started the 3-hour sequence, I misadjusted one or another part of the windows, so I had to reboot and start over again. Roger says Ctrl-C stops a RasWin script in 2.6-full-release (not yet available). I have lots of ideas for enhancing RasMol's script management capabilities, and am thinking seriously about getting into the source code myself. I would be very interested to run your scripts and, if you are willing, to make them available thru my RasMol web site. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: ++++------+------+------+------+------+------+------+------+------+------+ From: Thomas Andrew Manderfield Subject: Re: Scripts and the Web Date: Mon, 1 Apr 1996 23:54:03 -0500 (EST) To: rasmol@noc1.oit.umass.edu Fergus, Have you looked into using AppleScript? There is a plugin for Netscape to allow scripts to be embedded into html pages. This may be helpful to have netscape quit Rasmol. Further it could also be used to make client side helper apps to set Rasmol up, and even further, with certain utilities it can enter the text into RasMols line command directly to avoid any conflicts (like saving in 2.5) I could answer your questions more directly, but the 'file:///' reference threw me off. Are you not sending the scripts via http? ++++------+------+------+------+------+------+------+------+------+------+ From: mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) Subject: Re: Scripts and the Web Date: Tue, 2 Apr 1996 09:26:18 +0000 To: rasmol@noc1.oit.umass.edu Thomas, Thanks for your prompt reply to my RasMac/Netscape script problem. I think there is a bug/incompatibility here which may be tricky to work around. However your suggesttion of AppleScript did ocurr to me. Perhaps you could point me to the plug-in? And any sources of useful AppleScripts to do this? >Have you looked into using AppleScript? There is a plugin for Netscape >to allow scripts to be embedded into html pages. This may be helpful to >have netscape quit Rasmol. Further it could also be used to make client >side helper apps to set Rasmol up, and even further, with certain >utilities it can enter the text into RasMols line command directly to >avoid any conflicts (like saving in 2.5) > >I could answer your questions more directly, but the 'file:///' >reference threw me off. Are you not sending the scripts via http? No. the file:/// URL is like using the "open file" command in Netscape, so it is opening a file from a server (Novell Netware as it happens but that doesn't matter) to which the user must obviously be connected. The extra slash (/// rather than //) is necessary to get Netscape to go to the top level directory ie desktop, then you can describe the file path eg. MBN1.USER/TEACHING/CALFILES/Year3/ub.rsml, where MBN1.USER is a mounted server volume. This works OK (except for the problems I outlined), it allows me to include a "load pdb" command in the script which points to a pdb file on the server for the script to open. Obviously no good for those who can't log on to our server. Eventually I may move on to using the Web server to deliver these scripts. In that case the pdb file will have to be loaded first via a link, followed by the RasMac script. Would I use the http:// URL or ftp:// for this? Then another link would load the RasMac script. But I would have to have a MIME type configured on the WWW server for both .pdb and .rsml (script) files, which is why I did it the way I have, it was easier. ------------------------------------------------------------------------ Fergus Doherty, PhD. Department of Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH. U.K. Internet: Fergus.Doherty@nottingham.ac.uk Tel: (0)115 970 9366 FAX: (0)115 942 2225 Mail by Eudora 1.5.1 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PdbAlign/PdbDist Date: Fri, 05 Apr 1996 15:18:54 -0500 (EST) To: rasmol@noc1.oit.umass.edu I would like to link PdbAlign/PdbDist as Pedro requests (below), but first I'd like to have a clue what they do. More importantly, I'd like to be able to describe what they do in terms understandable to nonspecialists for the link on the web site. Can someone please send me a simplified description of what these programs do (avoiding technical jargon)? ------------------------------ Thu, 21 Mar 1996 13:47:21 -0600 (CST) From: Pedro M Coutinho To: emartz@microbio.umass.edu Cc: pedro@iastate.edu In the Rasmol Accessories liost could you point out to the PdbAlign-PdbDist -DistAlign group of programs available at ftp://ftp.ebi.ac.uk/pub/software/unix/pdbalign AC BC00466 NAME PdbAlign - PdbDist - DistAlign DOMAIN Molecular modelling and graphics DESCRIPTION Given a GCG multiple sequence alignment file (a GCG MSF file), DESCRIPTION which a includes a sequence of known structure, the program DESCRIPTION pdbalign maps the sequence variability onto the known structure. DESCRIPTION The central premise is of course, that for a closely related DESCRIPTION family of proteins (sequence ID > 40%) the 3-D structures will DESCRIPTION not be significantly different. DESCRIPTION usage: pdbalign [options] [] DESCRIPTION options: -entropy -zvelebil -conservation -pairwise DESCRIPTION where the -zvelebil option refers to the measure of variability DESCRIPTION used in M.Zvelebil, G.J.Barton, W.R.Taylor, M.J.E.Sternberg, DESCRIPTION "Pediction of Protein Secondary Structure and Active Sites using DESCRIPTION the Alignment of Homologous Proteins",J.Mol.Biol, (1987), 195, DESCRIPTION p.957-961. Color by temperature (eg in RasMol) can be used to DESCRIPTION display the output. DESCRIPTION The usage for pdbdist is DESCRIPTION usage: pdbdist [-ligand ] [outfile] DESCRIPTION without the -ligand option (default) HETATM records are used, DESCRIPTION where the definition of ligand is that used by RasMol (ie the DESCRIPTION set of non solvent HETATMs). A given residue can be used as the DESCRIPTION ligand eg. -ligand THR36. pdbdist calculates the distance from DESCRIPTION each atom in the pdb file to each atom in the ligand and records DESCRIPTION the minimum in the temperature field for that atom record. AS DESCRIPTION before, color by temperature (eg in RasMol) can be used to DESCRIPTION display the output pdb file. DESCRIPTION The usage for distalign is DESCRIPTION usage: distalign [-threshold ][-entropy] [-zvelebil] DESCRIPTION distalign reads the output from pdbdist and also the original DESCRIPTION GCG MSF file and produces an MSF file annotated with a measure DESCRIPTION of sequence variability and the distance of the residue at that DESCRIPTION position (of the sequence of known structure) from the ligand. DESCRIPTION Positions of high variabiity but close to the ligand can be DESCRIPTION immediately highlighted. AUTHOR Sayle R., Saqi M.A.S., Weir M.P., Lyall A. RA Sayle R., Saqi M.A.S., Weir M.P., Lyall A.; RT "PdbAlign,PdbDist and DistAlign: Tools to aid in RT relating sequence variability to structure."; RL Comput. Appl. Biosci. 11(5):571-573. ADDRESS Dr. Mansoor Saqi, Bioinformatics Group ADDRESS Dept. of Biomolecular Structure ADDRESS Glaxo Group Research ADDRESS Greenford, Middlx, UK. CONTACT ras32425@ggr.co.uk OR mass15599@ggr.co.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE C /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew B. Sparks" Subject: RasMol on Mac PPC 7500 Date: Sun, 07 Apr 1996 12:23:22 -0500 To: rasmol@noc1.oit.umass.edu Hi RasMolarians- I have toyed around at work with RasMol v 2.5, 2.6, and the Berkeley 2.6/1.0 on a Mac Quadra for a couple of days. I now want to run RasMol at home on my Mac PPC 7500/100. I have downloaded any tried each of the three aforementioned versions on my machine, and I am having a seriously frustrating problem with all of them. The program launches allright, but when I try to open a PDB file that opens fine at work, the command line interface tells me "Error: File 'Hard Drive:Applications:RasMol:1srl.pdb not found!'" Now, the path is correct, and I get this message even after I double-click on the PDB file and that launches RasMol. Further, the file works on the machines at work, the RasMol GetInfo window correctly identified the machine as a PP601, and the command line interface tells me the RasMol version is PPC native, 8-bit. I'm usually not a computer idiot, but this has me stumped. Any ideas out there? Andrew Sparks UNC-CH Dept. Biology Chapel Hill NC absparks@email.unc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol on Mac PPC 7500 Date: Tue, 9 Apr 1996 16:41:19 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: absparks@email.unc.edu Dear Mac RasMol Programmers, > The program launches allright, but when I try to open a PDB file that > opens fine at work, the command line interface tells me "Error: File > 'Hard Drive:Applications:RasMol:1srl.pdb not found!'" Now, the path is > correct, and I get this message even after I double-click on the PDB > file and that launches RasMol. Further, the file works on the machines > at work, the RasMol GetInfo window correctly identified the machine as a > PP601, and the command line interface tells me the RasMol version is PPC > native, 8-bit. I'm usually not a computer idiot, but this has me > stumped. Any ideas out there? I must admit that this has me stumped to. I know that there are a number of Mac programmers on this list who are far more competant about the workings of the Mac FileManager than I (including Cambridge Scientific and the RasMac-UCB people). I can only suspect that the problem is caused either by the compiler's implementation of "fopen" (I use UNIX style file I/O in RasMac) or in the function "ConvertFilename" in rasmac.c that converts a FSSpec (passed from the finder) into a filename. However, from the error messages reported the filename looks fine. Could it be a Metrowerks or Symmantec C problem on a particular version of MacOS? I must admit that I'm unable to reproduce the problem on the single Mac that I have here. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: PdbAlign/PdbDist Date: Tue, 9 Apr 1996 17:31:49 +0100 (BST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear All, > I would like to link PdbAlign/PdbDist as Pedro requests (below), but first > I'd like to have a clue what they do. More importantly, I'd like to be > able to describe what they do in terms understandable to nonspecialists > for the link on the web site. Can someone please send me a simplified > description of what these programs do (avoiding technical jargon)? As I'm the unfortunate author of these programs, it is only fair that I explain to the mailing list what they do. This suite of three programs are a set of tools for visualising the sequence differences between members of a protein family. Here at Glaxo, they were originally developed for studying the "mutability" of residues in an active site as an aid for drug specificity. Unfortunately, these programs are not available on the Apple Mac. They were originally developed for UNIX and should compile fine on the IBM PC as MSDOS programs. The assumption with these programs is that you have a multiple sequence alignment of your selected set of proteins, for example of neuraminidase sequences from different viral strains. It is also assumed that you have the PDB file for one of the sequences in the PDB file. The program "pdbalign" allows you to annotate the PDB file with information from the multiple sequence alignment. Essentially, the program works out the "variability" of each residue, and writes out a PDB file containing the variability in the b-factor field. This can then be read into RasMol and coloured by temperature to highlight mutational hotspots, or how conserved different parts of the protein are. [Different complicated measures of variability are selectable by command line options]. For example, most enzymes should display the active site in blue (almost completely conserved), with most mutations on the surface and in the loops of the protein. The program "distalign" allows the multiple sequence alignment to be annotated with information from the protein structure. This reads in the multiple sequence alignment and PDB file and outputs a multiple sequence alignment with an added sequence containing the b-factor value from the PDB file. Additional programs can be used to place interesting values in the b-factor field, for example "pdbdist" available from the above site, sets the b-factor field to be the distance from a specified distance of that residue from a specified ligand or residue. Hence, using "pdbdist" and "distalign", you can produce a multiple sequence alignment with an extra row containing a digit representing how far that residue is from the active site. For drug design, variable residue near the active site are useful for specificity and drug resistance studies. I hope some of you find this helpfull. 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 tmason@biochem.umass.edu, patw@bio.umass.edu (Pat Wadsworth), hepler@bio.umass.edu (Peter Hepler), rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Lipid bilayers, 10,000 visitors, 130 subscribers. Date: Thu, 11 Apr 1996 19:35:44 -0500 (EST) To: gierasch@chem.umass.edu, jacobson@titan.oit.umass.edu (Bruce Jacobson), I've just added my newest script to the RasMol web site. It explores the structures of model lipid bilayers obtained from molecular dynamics simulations (Heller, Schaefer, Schulten), and has great views of a model of gramicidin in a lipid bilayer complete with water molecules running through the channel (Crouzy, Roux et al.). The script runs about 10 minutes and is over 3,000 RasMol commands long -- no wonder it took me a long time to write! At the end of March, the number of distinct visitors to the RasMol web site exceeded 10,000. For the last several weeks, the site was visited by over 1,300 different people per week, 80% new each week. The subscribership to the RasMol email list stands a bit over 130. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: molinaro@lcbvax.cchem.berkeley.edu (Marco Molinaro) Subject: Re: RasMol on Mac PPC 7500 Date: Thu, 11 Apr 1996 17:24:27 -0800 To: rasmol@noc1.oit.umass.edu >Hi RasMolarians- > >I have toyed around at work with RasMol v 2.5, 2.6, and the Berkeley >2.6/1.0 on a Mac Quadra for a couple of days. I now want to run RasMol >at home on my Mac PPC 7500/100. I have downloaded any tried each of the >three aforementioned versions on my machine, and I am having a seriously >frustrating problem with all of them. > >The program launches allright, but when I try to open a PDB file that >opens fine at work, the command line interface tells me "Error: File >'Hard Drive:Applications:RasMol:1srl.pdb not found!'" Now, the path is >correct, and I get this message even after I double-click on the PDB >file and that launches RasMol. Further, the file works on the machines >at work, the RasMol GetInfo window correctly identified the machine as a >PP601, and the command line interface tells me the RasMol version is PPC >native, 8-bit. I'm usually not a computer idiot, but this has me >stumped. Any ideas out there? > Hello there, I think I may need more information as to what system version you are running, etc. I am running on a 7500 and I can run all of the versions you mentioned though I do not usually open files from the command line but instead use the pulldown menu. It sounds like you may be having a disk problem or may need to rebuild your desktop. Good luck, 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 http://www.cchem.berkeley.edu:8080/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: DNA3 fixed; new pics of MHC Date: Fri, 12 Apr 1996 23:09:44 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've released (on the web site) a revision of the DNA3 script which fixes a bug two of you reported (cytosine being rotated 180 degrees from the normal position) and another bug reported by one of you (dATP being at one point ATP). Thanks to Dmitry Bochkariov and Jose Miguel Fernandez Fernandez. (They're not where you might think: Dmitry is at U Cal Davis, Jose is in Granada, Spain!) I've also put up GIFS comparing in the same image peptides from two different viruses in the same MHC, colored simply (hydrophobic, polar, charged; 3 colors) to make the difference the T cells see really clear. (Gallery under MHC). Finally, I pointed out in the 'exclusive molecules' page that lipid bilayer and gramicidin membrane channel PDB's are included with the new lipid bilayer script (which I announced here yesterday). Thanks again to Helmut Heller, Klaus Schulten, Zhou Feng, Serge Crouzy, and Benoit Roux for providing these PDBs. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Envelope-To: rasmol@lists.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Michael.Vork@FYS.RULIMBURG.NL Subject: "Super" script for lipids Date: Sat, 13 Apr 1996 10:29:07 +0000 (EZT) To: rasmol@noc1.oit.umass.edu Did anyone try the novel script for viewing and studying lipid bilayers. If you did not, you MUST download it. It really terrific. Eric did a marvelous job on this subject !!!! ++++------+------+------+------+------+------+------+------+------+------+ From: Adam Drury Subject: RasMol v2.6 Date: Thu, 18 Apr 1996 14:12:46 +0100 To: rasmol@noc1.oit.umass.edu Hello All, I am new to this list, and have a few questions about the new version of RasMol. 1) What is the latest version of Rasmol - is it still a v2.6 Beta dated September ? When is a full version likely to come out ? 2) There appers to be a bug in v2.6 which does not allow it to run on PCs under Windows which do not have a maths co-processor - has anyone else experienced this problem ? 3) Is the source code for v2.6 Beta available anywhere by FTP ? Adam Drury ------------------------------------------------------------------------ Adam Drury Chemistry Courseware Consortium C/O CTI Chemistry Department of Chemistry University of Liverpool P.O. Box 147 Liverpool L69 3BX ENGLAND Tel : +44 (0) 151 794 3523 Fax : +44 (0) 151 794 3586 E-mail : tadrury@liverpool.ac.uk Consortium URL : http://www.liv.ac.uk/ctichem/c3intro.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RasMol v2.6 Date: Thu, 18 Apr 1996 11:50:26 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear RasMol subscribers: I have answered Adam Drury's questions directly. I have also reinstated moderation of the list. This will mean a day or so delay in messages being posted on the list, but will avoid the same old questions over and over going to all 130+ of us from people who question whether the web page is up to date (not an unreasonable point of view, generally speaking!) or who haven't tried searching the history of this list for answers to their questions. I'm sure a FAQ would help but I don't feel I can spare the time to edit it and keep it up to date (any volunteers?) -- actually the list history serves that purpose to a large degree if people will just search it. I'm sure all of us on this list are looking forward with great anticipation to 2.6 full release. I remind you that the quality of Roger Sayle's programming is of the highest level. How many bugs are there in even the beta release of 2.6? Very few, and none I'm aware of with serious consequences. If it weren't for Roger having taken the risk of releasing 2.6-beta last November, there would be no way to run scripts for the 500+ people who have downloaded them since then. Programming of RasMol-quality takes TIME and LOTS OF IT (I've done enough programming to know). It has been said that the full implementation of stereo should be easy. What may not be obvious is that the hard part is not rotating one image slightly -- the hard part is making stereo interact properly with all the other complex aspects of the program, and making the human interface work smoothly. In my experience, it is these latter issues which take over 90% of the programming effort. It is because Roger has done such a good job on these issues in the past that RasMol is so popular. Many of us have deluged Roger with suggestions for 2.6 (Yes, I'm guilty here). Please be patient! Respect the generosity of Roger and Glaxo in continuing to make RasMol available to all of us free of charge. And of course, for those who can't wait, the source code has always been available (search the history of this list for 'source' for details). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol v2.6beta2 Date: Thu, 18 Apr 1996 21:26:34 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: Eric Martz Dear Rasmolians, > I'm sure all of us on this list are looking forward with great > anticipation to 2.6 full release. I'd like to thank Eric for his many compliments, but as some of you will know the real reason that v2.6 hasn't appeared yet is that I'm incredibly easily distracted and I spend too little time fixing RasMol and too much reading e-mail and prototyping the next generation RasMol (please, no e-mails). Anyway to prove the political sway this mailing list has I've decided to release a rushed RasMol version 2.6beta2. This fixes many of the bugs and problems that people have encountered, adds some more functionality and increases performance. A complete list of changes is given below, but to summarise an acceptable side-by-side stereo is now working and the documentation still hasn't been updated. I'm still not happy with stereo and so this will probably change before v2.6final. The complete source code, RasMol26.tar.gz and a 32bit Windows executable "raswin32.exe" have been placed on the anonymous FTP site in Edinburgh (ftp://ftp.dcs.ed.ac.uk/pub/rasmol/v2.6beta) and I'll try to update the 16bit Windows and Macintosh versions before the end of next week. However, users with compilers should be able to compile from source before then. Changes between RasMol v2.6beta and RasMol v2.6beta2 o RasMol now allows a numeric parameter to the "trace" command that allows the specification of the width of the "backbone" worm. This both fixes a bug in machine generated scripts containing cartoons, but also allows functionality such as the new "trace temperature" command which displays the backbone as a wider cylinder at high temperature factors and thinner at lower. This representation should be useful to x-ray crystallographers and NMR spectroscopists. o Side-by-side stereo is now implemented as well as the "set stereo" command to control the separation between the left and right images. Note that stereo support is not implemented through out RasMol, for example, Vector PostScript probably shouldn't be generated whilst stereo is on, the RasMol "write script" command probably doesn't save the stereo state of the current image, turning stereo on and off doesn't reposition the center of the molecule and finally the performance isn't as good as it could be. o Significantly increased the performance of ribbons and cartoons on all platforms, but especially on Macintoshes and PCs without hardware accelleration. All floating point calculations have been removed from the RasMol polygon rendering code which is now integer only. o RasMol scripts can now be interrupted during a "pause" command by using either control-Z or control-D. Under VAX VMS, Control-Z can no longer be used to terminate RasMol whilst running a script, use Control-C (as before) instead. o Fixed compatability problems for UNIX interprocess communication between Tcl/Tk v3.x and Tcl/Tk 4.x. Both Tcl versions may now communicate with any of the running RasMols. o Inorder to allow RasMol to compile on IBM RS/6000 workstations running AIX, all references to the variables "hx", "hy" and "hz" have been renamed, as "hz" clashes with an AIX predefined macro. o The RasMol "write gif " command has been modified to allow generation of transparent GIFs. This may be controlled by the "set transparent on" and "set transparent off" commands. o RasMol will now display double and triple bonds automatically for any file containing bond order information, rather than require the user type "set bonds true". o Strands, ribbons and cartoons can now be drawn through protein residues that are not standard amino acids (i.e. UNK) provided that the residues contain the appropriate N-CA-C-O atom backbone. o Vector PostScript output now also contains RasMol distance monitors. o The RasMol "write mdl " command to write out an MDL Mol file now only writes out the currently selected atoms. o RasMol can now perform shading to an arbitrary background colour, rather than just black. This is controlled by the commands "set backfade on" and "set backfade off". For example, this may be used to generate depth-cued wireframe images that fade to white, rather than black. o The RasMol PDB file parser has been modified to correctly handle the new "MOL_ID:" molecule names. o The RasMol "quit" and "exit" commands now behave differently when using Inter-process communication. The "exit" command closes the link between programs, but the "quit" command terminates RasMol. o The hardware dials box handling routines in RasMol have now been modified to correctly reset the state of Evans and Sutherland ESV dials when the program exits. And probably have a dozen other things that I've forgotten. Alas I've become very lazy at keeping the RasMol "ChangeLog" upto date. My apologies for all those features that were requested but didn't quite make it into this interim release. For example, I've just remembered that I've forgotten to integrate the patches mailed to this list that allow the initial window size to be specified on the UNIX command line! > I'm sure a FAQ would help but I don't feel I can spare the time to edit > it and keep it up to date (any volunteers?) -- actually the list > history serves that purpose to a large degree if people will just > search it. I must admit that I am at fault here and should have produced a RasMol FAQ many years ago. However in my defense I cite the RasMol user manual as proof positive that I'm incapable of writing clearly and concisely. A volunteer would have my life-long appreciation. I hope this'll keep a few people happy over the next few days. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: "Adrian Kornhauser Eisenberg (comp)" Subject: Can't get into ftp://ftp.dcs.ed.ac.uk Date: Fri, 19 Apr 1996 07:57:21 -0600 (CST) To: RasMol List Hi! I'm really looking forward to try out RasMol v2.6beta2, but it seems the ftp (ftp://ftp.dcs.ed.ac.uk/pub/rasmol/v2.6beta) is not working properly... well not from here anyway... Is there something wrong with it? ****************************************************************************** Adrian KORNHAUSER EISENBERG Facultad de Medicina U.N.A.M Mail: adriank@servidor.unam.mx DEPARTAMENTO DE BIOQUIMICA Lab. 3 Tel: 623-21-75 Coordinador de RED y COMPUTO Fax: 616-24-19 ****************************************************************************** X-Confirm-Reading-To: "Andrew Coulson" X-Pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Coulson" Subject: Re: Can't get into ftp://ftp.dcs.ed.ac.uk Date: Mon, 22 Apr 1996 09:06:45 +0000 To: rasmol@noc1.oit.umass.edu Sorry you've been having trouble; I just checked the ftp site in the Department of Computer Science here, and can't see anything wrong with it. My experience with the site has been using ftp 'directly', rather than via a WWW browser, but I don't see that this will make any difference. I have occasionally had problems with the site, and the explanation was one of the following three: a) The system managers have sometimes excluded access by 'anonymous' when the system was exceptionally loaded or (on one occasion) after a security breach b) The password you use has to be recognised by the system as a plausible e-mail address c) There was a temporary hiccup when Roger Sayle completed his Ph.D. in the Department...... So the following process works for me; by all means get in touch again if it doesn't work for you!: 1) Open ftp with the site ftp.dcs.ed.ac.uk [this is resolved as colonsay.dcs.ed.ac.uk@129.215.160.5] with user anonymous, and password 2) Rasmol is to be found in /home/ftp/pub/rasmol 3) v2.6beta is a subdirectory; here are the files it contains: . .. raswin.exe raswin32.exe release.txt release.doc INSTALL rasmac26.sit.hqx rasmol.hlp RasMol26.tar.gz raswin.hlp README release.ps I hope everything is now ok.... Andrew Coulson > Date: Fri, 19 Apr 1996 07:57:21 -0600 (CST) > Reply-to: rasmol@lists.umass.edu > From: "Adrian Kornhauser Eisenberg (comp)" > To: RasMol List > Subject: Can't get into ftp://ftp.dcs.ed.ac.uk > > Hi! I'm really looking forward to try out RasMol v2.6beta2, but it seems > the ftp (ftp://ftp.dcs.ed.ac.uk/pub/rasmol/v2.6beta) is not working > properly... well not from here anyway... Is there something wrong with it? > > ****************************************************************************** > Adrian KORNHAUSER EISENBERG > Facultad de Medicina U.N.A.M Mail: adriank@servidor.unam.mx > DEPARTAMENTO DE BIOQUIMICA Lab. 3 Tel: 623-21-75 > Coordinador de RED y COMPUTO Fax: 616-24-19 > ****************************************************************************** > > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Adrian Kornhauser Eisenberg (comp)" Subject: If we find bugs in 2.6 Date: Mon, 22 Apr 1996 10:01:44 -0600 (CST) To: RasMol List If we find bugs or have problems running certain thing in RasMol 2.6b, should we report it? Or should we wait until de release version? Another question, is RasMenu suposed to work with the 2.6b version? It works but not quite as it should. thank's ****************************************************************************** Adrian KORNHAUSER EISENBERG Facultad de Medicina U.N.A.M Mail: adriank@servidor.unam.mx DEPARTAMENTO DE BIOQUIMICA Lab. 3 Tel: 623-21-75 Coordinador de RED y COMPUTO Fax: 616-24-19 ****************************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: If we find bugs in 2.6 Date: Mon, 22 Apr 1996 18:16:31 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Mon, 22 Apr 1996 10:01:44 -0600 (CST), "Adrian Kornhauser Eisenberg comp" writes: > If we find bugs or have problems running certain thing in RasMol 2.6b, > should we report it? Or should we wait until de release version? I think it would be useful to report bugs to this list so we can all know (and Roger Sayle reads this list so he'll know). It would be best if you first find out whether the bug is new or is also present in 2.6a or 2.5 when possible. Also, if people find any good tricks or enhancements that Roger forgot to list please tell the rest of us about them! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Zooming center, Win95 Date: Thu, 25 Apr 1996 14:39:53 -0500 (EST) To: pmsimoes@mail.telepac.pt Cc: rasmol@noc1.oit.umass.edu In message Sun, 21 Apr 1996 10:19:17 +0200, Paulo Simoes writes: > I'm a student, and I'm starting in X-ray crystallography. Is it > possible to center the molecule in a particular atom in order to zoom a > particular region of the protein? I don't know of any way to do this for ZOOMing. The 'center selected' and 'set picking center' commands affect only rotation as far as I know. Since the center of rotation can be anywhere you want on the screen, it seems that to keep a selected atom in the middle of the screen during zooming would require a different 'zoom-center' to be created within RasMol. I also sometimes wish for this. I'm copying this message to the RasMol email list, in case anyone else has better information. > I love RasMol 2.6, but I would like to see a Windows 95 version out. Not being a user of Win95 myself, I don't know why RasWin32 is not completely satisfactory under Win95. > I'm an undergraduate student of Biotechnology in Universidade Nova > de Lisboa (Faculdade de Ciencias e Tecnologia) in Lisbon, Portugal. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Question about RASMOL Date: Wed, 24 Apr 1996 17:40:28 +0100 (BST) To: Michael Craig Meldrum Cc: rasmol@noc1.oit.umass.edu Dear Michael, > 1. Is there a way of setting an absolute scale for a figure? I am > trying to print different molecules on the same scale for comparison > purposes. I have tried the ZOOM command but that doesn't seem to work. Thanks very much for your email. For a long time, I didn't think that this was possible but have recently found a bizarre solution. The solution is based upon the fact that the maximum "zoom" allowed by RasMol is dependent upon the size of a molecule. It transpires that for any molecule the maximum zoom provides an image where 1 Angstrom is equal to about 128 pixels. Hence you load in two molecules, for example "crambin" and "aspirin" into two different RasMol's. You then determine from the RasMol command line the maximum allowed zoom parameter. For example, if "zoom 500" reports "Parameter value too large!", then 500 is too high, otherwise if the (zoom command is successful) the value is probably too low. On my local machine the maximum zoom for "crambin" is 362, and the maximum scale for "aspirin" is 118. This means that the two images have the same scale when the ratio of the two zooms is 362:118. For example, to display "aspirin" on the same scale as the default "crambin", you should type "zoom 32" into the aspirin window (and "zoom 100" into the crambin window). > 2. I have a PDB file which, when displayed represents the > different atoms with the same radius. RASMOL does recognizes the different > atoms in the file because you can select the different atoms. I have a > small booklet on writing PDB files but I didn't see anything about > designating specific atom radii. Does this have to due with RASMOL and > do you have any other ideas? All the spacefill radii in RasMol are user definable by specifying a parameter to the spacefill command. For example, a sequence of commands such as: select atomno=1 spacefill 1.67 select atomno=2 spacefill 1.34 select atomno=3 spacefill 0.876 Allows you to set the radii of the first three atoms to the radii that are explicitly specified in the above commands. Another alternatice is to specify the atomic radii that you want in the beta-factor columns (field) of the Brookhaven PDB file, and use the "spacefill temperature" command to set the spacefill radii of all selected atoms to the value in their temperature/beta-factor value. I hope this answers your questions. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: "Adrian Kornhauser Eisenberg (comp)" Subject: Atmos selected? Date: Thu, 25 Apr 1996 15:06:04 -0600 (CST) To: RasMol List Hi! Does any one knows if there is a way for rasmol to outpout which aminoacids it has selected. I need this because sometimes y select parts of a protein by using select combined with "and" and "or". I can see the results on the screen but I also need to know what these results are in terms of a.a. number.... ****************************************************************************** Adrian KORNHAUSER EISENBERG Facultad de Medicina U.N.A.M Mail: adriank@servidor.unam.mx DEPARTAMENTO DE BIOQUIMICA Lab. 3 Tel: 623-21-75 Coordinador de RED y COMPUTO Fax: 616-24-19 ****************************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: "Matthew Templeton" Subject: Importation of Alchemy files into Rasmol Date: Fri, 26 Apr 1996 11:27:06 GMT+1200 To: rasmol@noc1.oit.umass.edu Hi everyone I'd had some problems importing Alchemy files into Rasmol 2.6-ucb. I'm trying to import the structure of an active-site inhibitor of an enzyme. The inhibitor was successfully draw in ChemPrint and imported into Alchemy. The alchemy file is the correct structure but when I import it into Rasmol it is corrupted. In particular extra bonds are generated with the alchemy molecule. Does anyone have any suggestion as to what the problem might be? Have any fellow Rasmolites encountered a similar problem? Any comments would be appreciated. Thanks Matt ___________________________________________________________ Matthew D. Templeton Email: Matt.Templeton@marc.cri.nz Molecular Genetics Group The Horticulture and Food Research Institute of New Zealand Mt. Albert Research Centre Private Bag 92-169 Auckland New Zealand Telephone: 64-9-815-4231 Facsimile: 64-9-815-4201 ____________________________________________________________ X-Confirm-Reading-To: "Andrew Coulson" X-Pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Coulson" Subject: Re: Atmos selected? Date: Fri, 26 Apr 1996 13:42:32 +0000 To: rasmol@noc1.oit.umass.edu > Hi! Does any one knows if there is a way for rasmol to outpout which > aminoacids it has selected. Two suggestions are: -- turn labels on (perhaps after doing select selected and *.CA to simplify things a bit!) -- save temp.pdb and extract the information from the text file Andrew C. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fw: Re: Zooming center, Win95 Date: Fri, 26 Apr 1996 10:28:39 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've forwarded this from Andrew with my comments interspersed. -Eric ------------------------------ Fri, 26 Apr 1996 14:22:31 +0000 From: Andrew Coulson Subject: Re: Zooming center, Win95 To: emartz@microbio.umass.edu > > possible to center the molecule in a particular atom in order to zoom a > > particular region of the protein? Andrew writes: It's easy enough to do manually; put the tip of the cursor on the atom concerned, hold down the right mouse button and move the cursor in one bold sweep to the middle of the screen. When rasmol catches up, the molecule will be in very nearly the right place .... Eric adds: True, but when you do very large zooms and only a small subset of the structure is displayed, sometimes you lose the structure off the screen completely, and you have to zoom back down to find it again. This gets a bit cumbersome, and this is when I wish for a zoom-center capability. > > I love RasMol 2.6, but I would like to see a Windows 95 version out. > Not being a user of Win95 myself, I don't know why RasWin32 is not > completely satisfactory under Win95. Andrew writes: I use Win95, and 32-bit extensions to Windows 3.1, and RasWin32 seems to be perfectly fine under both of them (apart from a problem with trace/cartoons which Roger has fixed; and the fact that RasWin32 doesn't work with DDE -- which is very sad for (I believe) a very small number of us!) Eric adds: Two others have also written to tell me that RASWIN32.EXE works fine with Win95 (Jose Miguel Fernandez Fernandez and John Ragle). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Scripts hang w/ UCB-RasMol Date: Fri, 26 Apr 1996 10:35:25 -0500 (EST) To: jmfernan@goliat.ugr.es Cc: rasmol@noc1.oit.umass.edu In message Fri, 26 Apr 1996 10:00:00 +0100, jmfernan@goliat.ugr.es (Jose Miguel Fernandez Fernandez) writes: > Hi Eric, > I have read your answer to "a undergraduate student in Lisbon" (without > email adresse). I use WIN95 and raswin32 run o.k. I have no find any > problem. Only the Berkeley enhanced version hang out when I try to run > your scripts. > Pr. Dr. Jose Miguel Fernandez-Fernandez > Departamento de Bioquimica y Biologia molecular > Facultad de Medicina. Universidad de Granada > Granada Spain E-18071 There is a bug in UCB-RasWin which causes it to hang when a 'zap' command occurs in a script (but not when issued manually in the command window). This prevents UCB-RasWin from running my scripts. I have informed Marco Molinaro at UCB about this bug some time ago. I don't know whether the same bug is present in UCB-RasMac. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: RasMol for Acorn RISC OS released Date: Fri, 26 Apr 1996 11:01:30 -0500 (EST) To: rasmol@noc1.oit.umass.edu This is from Martin Wuerthner (see signature at end): Hi. The Acorn RISC OS port of RasMol 2.6beta1 has been released recently and can be found on the following ftp servers: 1) HENSA (difficult to reach for users from outside the UK): micros.hensa.ac.uk (in /micros/arch/riscos/e/e089/rasmol.arc) 2) the University of Kaiserlautern (Germany): ftp.uni-kl.de (in /pub/acorn/long/science/chemistry/rasmol.arc) 3) the University of Stuttgart (Germany): ftp.uni-stuttgart.de (in /pub/systems/acorn/riscos/etc/rasmol110.spk) The first RISC OS release (1.10) of RasMol has the following features in addition to those of the X version: * runs on all Acorn 32-bit RISC computers under RISC OS 3.1 or higher, supports all display depths up to 24 bpp, just about runs on a 2MB machine * fully supports RISC OS cooperative multitasking even while rendering the image * Floyd-Steinberg colour dithering for 16 and 256 colour modes * support of both the RasMol mouse mode and a more RISC OS-like way using a tool bar with rotation/translation/slabbing etc. tools * extended menu structure (e.g. sub-menus to enter parameters for display options) * exports native RISC OS bitmap format, RISC OS drag-and-drop support For those who do not know Acorn: Acorn is a Cambridge-based British company producing computers mainly for educational and private use. The Acorn Archimedes and Acorn RiscPC ranges are 32-bit RISC computers based on the ARM 32-bit RISC processor designed by Acorn. The ARM processor has recently gained a large market share as an embedded control processor for mobile phones and laser printers due to its unique performance/power consumption ratio. It is also used as main processor in the Apple Newton PDA. All Acorn Computers run Acorn's native operating system RISC OS which is a modular, ROM-based operating system including a graphical user interface (RISC OS is more similar to MS Windows and MacOS than to Unix). I hope this announcement was of interest to someone... Martin -- -------------------------------------------------------------------------- Martin Wuerthner wuerthne@trick.informatik.uni-stuttgart.de Jahnstrasse 18 Phone: +49-7034-928986 71116 Gaertringen, Germany Fax: +49-7034-928988 -------------------------------------------------------------------------- [Forwarded by E Martz due to technical difficulties] /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Stereo Specs Date: Fri, 26 Apr 1996 11:39:24 -0500 (EST) To: rasmol@noc1.oit.umass.edu Forwarded by Eric M. from E. J. Milner-White, Glasgow: Now that the new rasmol2.6beta has stereo that works I'd like to buy a number of specs for viewing stereo pairs. The ones I have presently are fron Nu-3-D Vu at 71 E.28th Ave, Eugene OR, USA, FAX (503) 485-3810 and cost around 160USdollars each. They work fine and I find are essential for stereo pairs but as far as I know are just a few mirrors in a box attached to a knob you can adjust. Does anyone know a cheaper supplier? James Milner-White 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: E.J.Milner-White@bio.gla.ac.uk FAX: +44(0)141-330-4620 Tel.: +44(0)141-330-5283 /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Web site: manual, history, source code Date: Fri, 26 Apr 1996 11:42:45 -0500 (EST) To: rasmol@noc1.oit.umass.edu A few improvements on the web site (http://www.umass.edu/microbio/rasmol): Thanks to Adam Drury for pointing out that the 'all' file in the RasMol email list history on the web site did not include the 'current' messages. I believe I've fixed that. Both the 'all' and the shorter 'current' files should be updated every day at 2:17 AM local time. The hypertext form of the (version 2.5) RasMol manual at the web site is now working again, and this copy has the entire manual in a single file. That means you can easily use Netscape's Find capability (or equivalent in other browsers) to search the entire manual for key terms. I've made information about the source code of RasMol more complete and accessible, thanks to a suggestion from Adam Drury. BTW, the number of different visitors to the web site exceeded 1,500 last week. 600-some of these had visited the site previously (up from 20% a few weeks ago to 40%). This list now has 139 subscribers. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Stereo Specs Date: Mon, 29 Apr 1996 10:01:36 -0500 (EST) To: rasmol@noc1.oit.umass.edu Fri, 26 Apr 1996 12:49:52 -0400 From: rlevine@nih.gov (Rod Levine) Subject: Re: Stereo Specs To: emartz@microbio.umass.edu E. J. Milner-White asks: > >Now that the new rasmol2.6beta has stereo that works I'd like to buy a >number of specs for viewing stereo pairs. >The ones I have presently are fron Nu-3-D Vu at 71 E.28th Ave, Eugene OR, USA, >FAX (503) 485-3810 and cost around 160USdollars each. >They work fine and I find are essential for stereo pairs but as far as I >know are just a few mirrors in a box attached to a knob you can adjust. >Does anyone know a cheaper supplier? >James Milner-White I've been using the "Reflecting stereoscope" made by VCH. I got them from Aldrich. The catalog number is Z15,675-2. The US price is $42.90, and it's shown on page T114 of the 1994-95 catalog. Rod Levine NIH Bldg 3, Room 106 MSC 0320 Bethesda, MD 20892-0320 email: rlevine@nih.gov voice: 1 (301) 496-2310 fax: 1 (301) 496-0599 [Forwarded to the rasmol list by /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Soos Pal Subject: RE: If we find bugs in 2.6 Date: Sat, 27 Apr 1996 21:13:44 +0000 To: rasmol@noc1.oit.umass.edu > Also, if people find any good tricks or enhancements that > Roger forgot to list please tell the rest of us about them! I needed dipeptides, like Pro-Ala but they are still not done. I thought maybe I can select them but I only can select the two molecules and I can't do a selection which selects me Pro-Ala (in this order, bonded and only them). Do you have any suggestion how can I do such a process? I thing it would be great if I could select a part of a bigger peptide, I mean a complete amino acid chain. (I don't know, but it could be difficoult to make it and that's why it's still not in the program) Pal ++++------+------+------+------+------+------+------+------+------+------+ From: ppowers@stem.com Subject: RasMol Question Date: Mon, 29 Apr 96 08:56:38 PST To: rasmol@noc1.oit.umass.edu Does anybody know where I can find Rasmole images of the following molecules: 1) Fluorescein 2) Biotin 3) Sulforhodamine-G Thanks! Sincerely, Rick Powers Systemix, Inc. Palo Alto, CA USA ppowers@stem.com ++++------+------+------+------+------+------+------+------+------+------+ From: biota@onramp.net (Cynthia S. Smagula) Subject: Use of RasMol Images Date: Mon, 29 Apr 1996 11:30:32 -0600 To: rasmol@noc1.oit.umass.edu I would like to use RasMol-generated images in icons for a web site and perhaps in a book. The images would be greatly reduced in size, cropped, and simplified. How may RasMol-images of PDB structures be used? Are there any limitations as to online and offline publication? Is the giving of credit (to the lab that determined the structure, to RasMol) a prerequisite? Thanks- Cynthia S. Smagula, Ph.D. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . BIOTA PUBLICATIONS Internet BioInformation publishers of BIOINFORMATION ON THE WORLD WIDE WEB WWW: http://www.biota.com/biota E-mail: biota@onramp.net FAX: 214.733.7300 PHONE : 214.733.7389 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol Question Date: Mon, 29 Apr 1996 19:42:04 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: ppowers@stem.com Dear Rick, > Does anybody know where I can find RasMol images of the following molecules > 1) Fluorescein > 2) Biotin > 3) Sulforhodamine-G I suspect that a small molecule database such as Klotho would be a better starting point, but Brookhaven PDB codes 1STP, 1AVD and 2AVI all contain biotin bound to proteins and PDB codes 4FAB and 1FLR contain fluorescein bound to immunoglobulins. For biotin, load any of the above files and type "restrict btn" to limit the display to just the bound conformation of biotin. The command "save pdb " can be used to create a file containing just the molecule of interest. For fluorescein, type "restrict fds". I hope this helps. Roger -- "RasMol Question" (Apr 29, 8:56am) References: <9603298307.AA830793827@internet.stem.com> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: RasMol Question Date: Mon, 29 Apr 1996 13:01:33 -0400 To: rasmol@noc1.oit.umass.edu >On Apr 29, 8:56am, ppowers@stem.com wrote: > Subject: RasMol Question > Does anybody know where I can find Rasmole images of the following > molecules: > > 1) Fluorescein > 2) Biotin > 3) Sulforhodamine-G > > Thanks! > > Sincerely, > > Rick Powers > Systemix, Inc. > Palo Alto, CA USA > ppowers@stem.com >-- End of excerpt from ppowers@stem.com A good source for PDB files of small molecules is Toni Kazic's KLOTHO http://ibc.wustl.edu/klotho Unfortunately, I didn 't find these structures there. However KLOTHO is a reliable source of PDB files (models) with proper CONECT records for many small biologically relevant molecules. Somtimes such things may be found as heterogens in full structures. So if you can find them in a structure query engine (e.g. http://www.ncbi.nlm.nih.gov/Structure) you can download the PDB file and chop out the heterogen portion with a text file editor, as I have done here. Note that sometimes this method may provide a structure with missing atoms, (i.e. there are no hydrogens in these structures). I did not find a PDB structure of Sulforhodamine-G - Perhaps someone else can help? Chris Hogue Visiting Scientist, NCBI. HEADER Immunoglobulin 19-Jan-95 1FLR 1FLR COMPND Mol_id: 1; Molecule: 4-4-20 (IgG2akappa) Fab Fragment; 1FLR COMPND 2 Chain: L, H; Heterogen: Fluorescein 1FLR SOURCE Mol_id: 1; Organism_scientific: Mus Musculus; 1FLR SOURCE 2 Organism_common: Mouse; Strain: BalbC; Variant: BalbCV; 1FLR SOURCE 3 Cell_line: 4-4-20 Murine-Murine Hybridoma; Organ: Spleen; 1FLR SOURCE 4 Cell: Lymphocyte-Plasma Cell 1FLR AUTHOR M.Whitlow 1FLR REMARK 19 NOTE! NCBI-MMDB PDB-Format File derived from ASN.1 1FLR REMARK 19 Refer to original ASN.1 File For Citations. 1FLR HETATM 3384 C1 FLU 1 600 28.852 22.311 42.336 1.00 11.85 1FLR HETATM 3385 O1 FLU 1 600 29.932 21.976 42.826 1.00 25.94 1FLR HETATM 3386 C2 FLU 1 600 28.101 21.255 41.765 1.00 17.15 1FLR HETATM 3387 C3 FLU 1 600 26.893 21.692 41.215 1.00 19.74 1FLR HETATM 3388 O2 FLU 1 600 26.141 20.574 40.574 1.00 19.69 1FLR HETATM 3389 C4 FLU 1 600 25.101 21.027 40.118 1.00 4.54 1FLR HETATM 3390 C5 FLU 1 600 24.428 19.924 39.557 1.00 14.84 1FLR HETATM 3391 C6 FLU 1 600 23.225 20.272 38.949 1.00 19.29 1FLR HETATM 3392 O3 FLU 1 600 22.571 19.366 38.432 1.00 29.97 1FLR HETATM 3393 C7 FLU 1 600 22.723 21.543 38.937 1.00 9.68 1FLR HETATM 3394 C8 FLU 1 600 23.432 22.616 39.533 1.00 21.81 1FLR HETATM 3395 C9 FLU 1 600 24.642 22.274 40.132 1.00 9.53 1FLR HETATM 3396 C10 FLU 1 600 25.287 23.429 40.756 1.00 9.29 1FLR HETATM 3397 C11 FLU 1 600 26.421 22.938 41.259 1.00 19.13 1FLR HETATM 3398 C12 FLU 1 600 27.154 23.982 41.902 1.00 13.87 1FLR HETATM 3399 C13 FLU 1 600 28.402 23.565 42.405 1.00 2.00 1FLR HETATM 3400 C14 FLU 1 600 24.786 24.653 40.745 1.00 19.48 1FLR HETATM 3401 C15 FLU 1 600 24.617 25.425 39.605 1.00 18.09 1FLR HETATM 3402 C16 FLU 1 600 24.009 26.664 39.534 1.00 17.02 1FLR HETATM 3403 C17 FLU 1 600 23.524 27.254 40.749 1.00 18.13 1FLR HETATM 3404 C18 FLU 1 600 23.745 26.440 41.867 1.00 6.02 1FLR HETATM 3405 C19 FLU 1 600 24.302 25.191 41.969 1.00 23.07 1FLR HETATM 3406 C20 FLU 1 600 24.334 24.672 43.283 1.00 16.57 1FLR HETATM 3407 O4 FLU 1 600 23.764 23.410 43.277 1.00 21.78 1FLR HETATM 3408 O5 FLU 1 600 24.854 25.151 44.423 1.00 30.65 1FLR CONECT 3384 3385 CONECT 3384 3386 CONECT 3384 3399 CONECT 3386 3387 CONECT 3387 3388 CONECT 3387 3397 CONECT 3388 3389 CONECT 3389 3390 CONECT 3389 3395 CONECT 3390 3391 CONECT 3391 3392 CONECT 3391 3393 CONECT 3393 3394 CONECT 3394 3395 CONECT 3395 3396 CONECT 3396 3397 CONECT 3396 3400 CONECT 3397 3398 CONECT 3398 3399 CONECT 3400 3401 CONECT 3400 3405 CONECT 3401 3402 CONECT 3402 3403 CONECT 3403 3404 CONECT 3404 3405 CONECT 3405 3406 CONECT 3406 3407 CONECT 3406 3408 END HEADER Biotin Binding Protein 23-Apr-93 2AVI 2AVI COMPND Avidin Complex With Biotin 2AVI SOURCE Hen Egg-White 2AVI AUTHOR O.Livnah, J.Sussman 2AVI REMARK 19 NOTE! NCBI-MMDB PDB-Format File derived from ASN.1 2AVI REMARK 19 Refer to original ASN.1 File For Citations. 2AVI HETATM 243 C1 BTN 1 150 -4.698 31.241 28.703 0.00 10.56 2AVI HETATM 244 C10 BTN 1 150 -4.993 30.078 27.791 0.00 10.89 2AVI HETATM 245 C9 BTN 1 150 -3.706 29.348 27.363 0.00 10.94 2AVI HETATM 246 C8 BTN 1 150 -3.581 29.217 25.866 0.00 8.38 2AVI HETATM 247 C7 BTN 1 150 -2.195 28.823 25.509 0.00 5.71 2AVI HETATM 248 C2 BTN 1 150 -1.643 29.584 24.301 0.00 7.94 2AVI HETATM 249 C6 BTN 1 150 -1.392 29.832 21.666 0.00 7.19 2AVI HETATM 250 C4 BTN 1 150 -0.324 28.953 23.805 0.00 10.52 2AVI HETATM 251 C5 BTN 1 150 -0.057 29.369 22.354 0.00 10.66 2AVI HETATM 252 C3 BTN 1 150 0.121 27.065 22.534 0.00 13.18 2AVI HETATM 253 O1 BTN 1 150 -5.599 32.069 28.926 0.00 10.38 2AVI HETATM 254 O2 BTN 1 150 -3.532 31.372 29.132 0.00 9.40 2AVI HETATM 255 O3 BTN 1 150 0.156 25.866 22.202 0.00 12.38 2AVI HETATM 256 N1 BTN 1 150 0.453 28.107 21.811 0.00 11.83 2AVI HETATM 257 N2 BTN 1 150 -0.329 27.518 23.725 0.00 11.83 2AVI HETATM 258 S1 BTN 1 150 -2.754 29.801 22.861 0.00 3.65 2AVI CONECT 243 244 CONECT 243 253 CONECT 243 254 CONECT 244 245 CONECT 245 246 CONECT 246 247 CONECT 247 248 CONECT 248 250 CONECT 248 258 CONECT 249 251 CONECT 249 258 CONECT 250 251 CONECT 250 257 CONECT 251 256 CONECT 252 255 CONECT 252 256 CONECT 252 257 END ++++------+------+------+------+------+------+------+------+------+------+ From: Walter Stafford Subject: setting stereo rotation angle Date: Fri, 26 Apr 1996 13:36:05 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Cc: STAFFORD@bbri.harvard.edu How do i change the stereo rotation angle - i'd like more depth. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Selecting AA sequences Date: Tue, 30 Apr 1996 20:20:50 -0500 (EST) To: rasmol@noc1.oit.umass.edu From: George Helmkamp One trick you may consider for dipeptides is to find a protein PDB file with that structure and edit it to restrict the file to just those atoms in which you are interested. You may have to do a bit of "editing" to get the final structure you want, for example, the N of the 3' amino acid in the polypeptide can be changed to O to create a "carboxylate" function. Note added by Eric Martz: I think the original inquiry meant: is it possible to select a particular AA sequence in RasMol? I don't know of any way to do this. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Adam Drury Subject: RasMol for Windows / Maths Co-processor Date: Tue, 30 Apr 1996 09:24:01 +0100 To: rasmol@noc1.oit.umass.edu Hello All, I recently tried using the original version of RasMol 2.6 beta for Windows on a PC without a maths co-processor (a 486 SX Toshiba portable), and found that it would not run (giving a Stack Underflow error). I tried it on two other PCs (386s) without co-processors, which gave different errors, but still did not work. I was wondering whether anyone else had experienced this kind of problem with the Windows version. This problem does not occur with RasMol 2.5. On a related issue, I am interested to know about how other people are using RasMol in teaching, and not research (particularly in teaching chemistry, and not biochemistry/biology). The reason the above problem is annoying is that for TEACHING, there is still widespread use of machines without co-processors in this country, and I would assume this would be true for universities in other countries as well. This currently means that I cannot use RasMol 2.6 for teaching on all PCs in this department. I understand that for larger molecules, a maths co-processor is essential, but could the source code not be compiled so that it makes use of it if present, and is just slow without it, which would mean it would run on all 386s and above. I look forward to hearing your comments on this issue. Adam Drury ------------------------------------------------------------------------ Adam Drury Chemistry Courseware Consortium C/O CTI Chemistry Department of Chemistry University of Liverpool P.O. Box 147 Liverpool L69 3BX ENGLAND Tel : +44 (0) 151 794 3523 Fax : +44 (0) 151 794 3586 E-mail : tadrury@liverpool.ac.uk Consortium URL : http://www.liv.ac.uk/ctichem/c3intro.html rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol news brief in Nature Date: Tue, 30 Apr 1996 20:08:51 -0500 (EST) To: m.francisco@natureny.com Cc: marcey@kenyon.edu, ras32425@ggr.co.uk (Roger Sayle/RasMol), Re: Planned news brief on RasMol To: Mr. Michael Francisco, Nature Biotechnology Dear Mr. Francisco: You are welcome to use any images which I have made* in your forthcoming news brief on RasMol. In the gallery at the RasMol web site, you will find that some images are available in higher resolution which might look better in print. If you will indicate what specifically appeals to you, I can make a high resolution (1,200 x 1,000) GIF version of it for you if not already available. Or if you wish, I can nominate a few for your consideration. One possibility would be an image of the entire IgG antibody molecule (data provided by Eduardo Padlan). It would of course be best to cite the paper in which the atomic coordinates were determined for any image you publish. This information can be extracted from the PDB data file from which the image was made, but is explicitly stated on my web site for most gallery images. I imagine that Roger Sayle (the author of RasMol) would also be happy to have you use any of his images (also on my web site in the gallery). You can verify this from him at ras32425@ggr.co.uk. Version 2.6-beta-2 of RasMol was just made available, and it can make stereo pairs. I can make a stereo pair version of any image already in the web gallery if you wish. *The images of lipid bilayers are particularly impressive, in my opinion, although most RasMol use is on proteins or nucleic acids. If you wish to use a lipid bilayer image, you should ask for permission from the authors of the model data files, since these are not in the Brookhaven database. I can give you the email address(es) if interested. I would be happy to read a draft of the brief you intend to publish and comment on it within 24 hours of receipt by email. Please be sure to mention the RasMol home page (URL below; it has been visited by over 10,000 different people and is currently visited by 1,500 different people per week). It would also be good to mention the educational potential of RasMol scripts (all of the few presently available to my knowledge are on my web site). And it would be good to mention Chemscape Chime, free for academic and personal use, which is 'RasMol on a web page'. It has great educational potential as illustrated by David Marcey's tutorial on DNA polymerase. You might enjoy taking a look at Roger Sayle's personal history of RasMol (under 'introduction' at the web site). I am copying this message to the RasMol email list (about 140 subscribers) in case anyone there wishes to add something to what I have said. > Dear Mr. Martz > > I writing on behalf of the journal Nature Biotechnology. In our > next issue, we are running a news brief on the RasMol program. We > would like a picture/image to accompany the piece. I discovered > the RasMol Home Page on the internet and was wondering if we might > be able to use a graphic/molecular model to be printed in our > publication. If you could let us know of any copyright regulations > etc. as soon as possible it would be greatly appreciated. > > Please send any return correspondence to: > > Michael Francisco > m.francisco@natureny.com > phone: 212-726-9288 > > Thank you for your assistance. > > Sincerely, > Tara Marathe > intern /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Confirm-Reading-To: "Andrew Coulson" X-Pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Coulson" Subject: Re: setting stereo rotation angle Date: Tue, 30 Apr 1996 09:55:53 +0000 To: rasmol@noc1.oit.umass.edu > How do i change the stereo rotation angle - i'd like more depth. set stereo or set stereo - (oddly enough, rasmol doesn't seem to like +5 instead of 5, but it is happy with -5!) The default, set by stereo on appears to be +5 degrees, correct for cross-eyed viewing. A stereoscope or relaxed-eye view seems to need about -5. I'm not absolutely certain about these signs, because my eyes seem to compensate for many kinds of errors in stereo diagrams -- but +5 for cross-eyes, and -5 for relaxed produces the expected sense of rotations about the y-axis. Andrew Coulson > ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: setting stereo rotation angle Date: Tue, 30 Apr 1996 11:37:22 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: STAFFORD@bbri.harvard.edu On Fri, 26 Apr 1996, Walter Stafford wrote: > How do i change the stereo rotation angle - i'd like more depth. The stereo depth for side-by-side stereo in RasMol can be increased using the "set stereo" command. The integer parameter states the angle in degrees between the left and right images. I believe that positive values result in cross-eyed stereo and negative values in relaxed stereo. May I also recommend that stereo values, much like mouse bindings, are good examples of user preferences that may be stored in the ".rasmolrc" file under UNIX, and the "RASMOL.INI" file under Microsoft Windows. The commands in these files typically contain per-user defaults, and are read by RasMol each time the program is started. A typical file conatins commands such as echo In the event of an emergency, contact system support echo on extension 2525 or send e-mail to rasmol@ggr.co.uk echo set mouse quanta set stereo -10 I hope this helps. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: MDL's Chemscape Chime Date: Tue, 30 Apr 1996 21:13:15 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: marcey@kenyon.edu (David/Chime) Now that I've finally spent some time with Chime, I'm mightily impressed. This is just to encourge the rest of you who haven't downloaded it yet to do so -- it will be worth it! David Marcey's Chime tutorial on DNA polymerase, and Nixon, Leach and Rzepa's Chime tutorial on the photosynthetic reaction center show the power of this approach for educational use. Chime is a derivative of RasMol which acts like RasMol but sits directly in a web page (not a separate helper window). It lacks a mechanism to input typed commands, but will run the full RasMol command set from scripts. I've today put lots more links to Chime things on my RasMol web site (see "what's new" there). I suggest that this email list is an appropriate place for detailed discussions of Chime as well as RasMol and other RasMol derivatives. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Braden N. McDaniel" Subject: RasWin32/Visual C++ 4.0 Date: Tue, 30 Apr 1996 21:25:15 -0400 To: "'RasMol Mailing List'" Okay...is it standard protocol to introduce oneself in a first message = to the list? Anyway, I'm a student at the University of Miami majoring = in marine science, biology, and computer science. I'm a relatively inexperienced C programmer...and I'm trying to gain = some by toying with this program. My initial goal is to add some = enhancements to the interface of RasWin32. Well, actually I think my = *initial* goal is to fix that annoying bug where RasWin32 enters the = wrong information about its location in WIN.INI. But the first step in this little endeavor is getting the thing to = compile--and so far I haven't been able to do that. So, has anyone = compiled version 2.6b2 successfully with Visual C++ 4.0? Braden ++++------+------+------+------+------+------+------+------+------+------+ From: David Vaughan Subject: Re: RasWin32/Visual C++ 4.0 Date: Tue, 30 Apr 1996 21:28:50 -0500 To: rasmol@noc1.oit.umass.edu At 09:25 PM 4/30/96 -0400, you wrote: >Okay...is it standard protocol to introduce oneself in a first message to the list? Anyway, I'm a student at the University of Miami majoring in marine science, biology, and computer science. > >I'm a relatively inexperienced C programmer...and I'm trying to gain some by toying with this program. My initial goal is to add some enhancements to the interface of RasWin32. Well, actually I think my *initial* goal is to fix that annoying bug where RasWin32 enters the wrong information about its location in WIN.INI. > >But the first step in this little endeavor is getting the thing to compile--and so far I haven't been able to do that. So, has anyone compiled version 2.6b2 successfully with Visual C++ 4.0? > >Braden > > > i just did that tonight! what you need to do is create a project with the rasmol files in it. edit rasmol.h & find the line that #defines IBMPC (it is currently commented out). take off the comments from that. make sure you don't have irrelevant files in the project (such as mac or xwindow related files). the makefile_nt shows what files are important. that's about it. the only file i actually modified was rasmol.h -- the other errors were all related to files i shouldn't have included in the 1st place. if you have any further questions, let me know & i'll be glad to help. ++++------+------+------+------+------+------+------+------+------+------+ From: David Vaughan Subject: 3D viewing Date: Tue, 30 Apr 1996 21:41:24 -0500 To: rasmol@noc1.oit.umass.edu is anybody working on interfacing rasmol with LCD shutter glasses? LCD shutter glasses have clear lenses that can be made opaque via an LCD shutter. they provide a 3D view by making the left lens opaque while the right image is shown, and then making the right lens opaque while the left image is shown. they are synchronized to the video output so this can happen very quickly (generally 30 times per second). the image can be high resolution and does not have the color distortion problems of color-filter 3d glasses. since rasmol now supports stereo, it seems like it would be really nice to be able to get a good 3d picture (without crossing your eyes ;)) if anybody knows of any other molecular visualization programs that support shutter glasses or any work currently under way on rasmol to support them, i'd appreciate the info. thanks! ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime buttons Date: Wed, 01 May 1996 13:29:54 -0500 (EST) To: rasmol@noc1.oit.umass.edu I'm forwarding this with a comment below. -Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: mjhsieh@life.nthu.edu.tw (Meng-Juei Hsieh) Subject: Re: MDL's Chemscape Chime Date: Thu, 2 May 1996 01:06:11 +0800 To: rasmol@noc1.oit.umass.edu Chemscape Chime is also very fast in my dx4-100 pc :) I'm impressed by the script function by pushing the button embed in the HTML, I had done some try, found it is easy. I didn't see the user juide for some script button in the FAQ list. Hope I can read it next time. -- Francis M.J. Hsieh | email addr: mjhsieh@life.nthu.edu.tw UnderGrad student at Dept. | u801629@oz.nthu.edu.tw of Life Science,NTHU, | HOMEPAGE: Taiwan Republic | http://life.nthu.edu.tw/~mjhsieh/ - - - - - You can find the button syntax and other Chime operation details by using Netscape's View Source to view the HTML of the Chime pages on the web. For details on how to set up Netscape frames (as used in the Chime tutorials), select Help from the top menu line of Netscape, then How to Create Web Services, where you will find a document entitled "Frames, an Introduction". A new version of Chime will be available very soon on the MDLI server if it is not already (the old one expired yesterday). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: 4,000 new visitors in April Date: Wed, 01 May 1996 17:49:12 -0500 (EST) To: rasmol@noc1.oit.umass.edu 5,159 different people (Internet addresses) visited the RasMol Home Page during April, requesting >80,000 file-fetches. 4,210 (82%) of these had not visited previously, while 949 (18%) had been there before. The visiting rate in April was essentially equal to that in March. In this little histogram, each * represents approximately 1,000 visitors. December * January ** February **** March ***** April ***** Total visitors to date is >14,000. 47% of April's visitors were from within the US, and the remainder were from 54 other countries, in this order: >100 visitors de/jp/ca/uk >50 visitors fr/ml/se/au/dk >25 visitors it/es/no 51 April visitors visited every week; 107 in 3 of 4 weeks; 575 visited in 2 of 4 weeks; and the remaining 4,426 visited in only 1 of the 4 weeks. Our RasMol email list currently has 144 subscribers. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Braden N. McDaniel" Subject: RE: RasWin32/Visual C++ 4.0 Date: Wed, 1 May 1996 17:03:16 -0400 To: "'rasmol@lists.umass.edu'" Thanks, that helped...but I ain't there yet. It compiled fine (save one = warning when compiling command.c), but I got a schlew of (62) linker = errors of the form "unresolved external symbol". BTW, I created the project by importing the existing raswin32.mak = file--it was apparently created with Visual C++ 2.0. Braden PS: I tried e-mailing you directly about this, but I couldn't get your = e-mail address to work. ---------- Sent: Tuesday, April 30, 1996 10:28 PM From: David Vaughan[SMTP:dvaughan@holli.com] Subject: Re: RasWin32/Visual C++ 4.0 To: rasmol@noc1.oit.umass.edu i just did that tonight! what you need to do is create a project with = the rasmol files in it. edit rasmol.h & find the line that #defines IBMPC=20 (it is currently commented out). take off the comments from that. make sure you don't have irrelevant files in the project (such as mac or = xwindow related files). the makefile_nt shows what files are important. that's about it. the only file i actually modified was rasmol.h -- the other=20 errors were all related to files i shouldn't have included in the 1st = place. if you have any further questions, let me know & i'll be glad to help. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PRC kills Netscape? Date: Wed, 01 May 1996 20:13:40 -0500 (EST) To: tim@mdli.com, rasmol@noc1.oit.umass.edu I've downloaded (for Windows 3.1) the Chime version 0.9a2 released today at the MDLI site. The good news is (Tim will be glad to hear) it works! In particular, I could display Marcey's tutorial as usual. However, I have the same problem with 0.9a2 which I had with 0.8b, namely, whenever I try to view the Nixon/Rzepa PRC tutorial (either from the UK or from MDLI's server) it kills my Netscape with a general protection fault after the text appears in the left frame but before the graphics window appears in the right frame. This has occurred repeatably on two different computers, one with 8 megs and one with 16 megs of memory (latter tested only with 0.8b so far). Has anyone else had a similar experience? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: PRC kills Netscape? Date: Thu, 02 May 1996 07:03:00 -0700 To: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu At 08:13 PM 5/1/96 -0500, Eric Martz wrote: >I've downloaded (for Windows 3.1) the Chime version 0.9a2 released >today at the MDLI site. The good news is (Tim will be glad to hear) >it works! In particular, I could display Marcey's tutorial as usual. >However, I have the same problem with 0.9a2 which I had with 0.8b, >namely, whenever I try to view the Nixon/Rzepa PRC tutorial (either >from the UK or from MDLI's server) it kills my Netscape with a >general protection fault after the text appears in the left frame but >before the graphics window appears in the right frame. This has occurred >repeatably on two different computers, one with 8 megs and one with 16 >megs of memory (latter tested only with 0.8b so far). Has anyone >else had a similar experience? I just tried out 1prc again to make sure it works for me. I tried on a Windows 95 machine and on a Windows 3.1 machine. Using Navigator 2.01 or Navigator Atlas PR2 it works fine (MDL's new server is even fairly fast at downloading it). The only thing I can think of is that my machines both have 20 megs of ram, but that does not seem like it could be it, because I know that others can view the 1prc example with much less. I have 'local' versions of some of the example files (including 1prc). I can e-mail you a self extracting archive that you can extract onto you hard disk. These examples have 8.3 filenames, so they work fine on a Windows 3.1 machine. You just File->Open the HTML (*.HTM) files to view them. Eric, I will e-mail the file directly to your account after this message, and you can give it a try. I would like to get to the bottom of this mystery... Perhaps these machines are running some program in common that could be causing 'interference' ? Are these Windows 3.1 machines ? Let me know if I can be of any further help tracking this down, -tim > >/*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Author of the RasMol web site: http://www.umass.edu/microbio/rasmol >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: Highlighting one A.A. type Date: Thu, 02 May 1996 17:56:53 -0500 (EST) To: ppowers@stem.com Cc: rasmol@noc1.oit.umass.edu In message Thu, 02 May 96 08:24:33 PST, ppowers@stem.com writes: > Dear helpful Rasmol group, > > Can anyone tell me how to highlight just one type of amino acid in a > display image? For example, to show a spacefilling whole IgG, shown > in grey, with all the Lysines in yellow? > > Your help is greatly appreciated! > > Sincerely, > > Rick Powers > Systemix, Inc. > Palo Alto, CA USA > ppowers@stem.com This will do what you want (type these commands in the command line window, or save them in a plain text file named e.g. mycolors and then type into the command line window 'script mycolors'): select all wireframe off spacefill color [180,180,180] select lys color yellow To color a single lysine, click on it (to report its residue number, for example 123) then 'select 123', 'color yellow'. The reason for the [180,180,180] is that 'gray' is not a predefined color in RasMol. The 180's are the RGB (red, green, blue) intensities on a scale of 0-255. Also, search the email history for 'user color' where there is a more complicated example. One of my favorites is: select hydrophobic color [180,180,180] select polar color greenblue select charged color green Something like this is used in my hemoglobin script to show how most of the center of the molecule is hydrophobic, and most of the polar or charged residues are on the surface. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: PRC kills Netscape? Date: Fri, 03 May 1996 15:02:38 -0500 (EST) To: rasmol@noc1.oit.umass.edu From: William McClure At 08:13 PM 5/1/96 -0500, Eric Martz wrote: >namely, whenever I try to view the Nixon/Rzepa PRC tutorial (either >from the UK or from MDLI's server) it kills my Netscape with a >general protection fault after the text appears in the left frame but On the Mac, I've had "Netscape error 11" crashes while trying to set up new pages (or new features) on my machine and occasionally on the WWW. If it happens twice, I clear the Netscape cache. For local trouble shooting, this lets me remove the suspected problem and reload without getting the old (cache) version. My explanation may be faulty, but restarting Netscape with a cleared cache definitely helps some repeated crashes. -Will McClure Eric Martz adds: Will, by 'clearing the cache' I assume you mean manually deleting all files in \netscape\cache. If not, please specify. I'll let you know if this reduces our crash frequency. Thanks for the suggestion. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: PRC kills Netscape? Date: Fri, 03 May 1996 15:13:15 -0500 (EST) To: rasmol@noc1.oit.umass.edu This is an update or correction to what I said two days ago. Using Chime 0.9a2 for Windows 3.1, at 800 x 600 resolution on a computer with 16 megabytes of memory (martz3), I was able to load the Nixon, Leach & Rzepa 1PRC tutoral repeatedly (via Trumpet Winsock modem/PPP). In this series of tests, Netscape did crash once with a General Protection Fault (in KRNL386.EXE), but this was not repeatable. Since I can no longer run Chime 0.8b, I can't verify whether the 'repeatable' crashes I observed on martz3 prior to 4/30 still repeat. 1PRC does crash repeatably on another computer (martz2, 8 megabytes of memory, Windows for Workgroups 3.11, either 800 x 600 or 640 x 480, 256 colors, direct ethernet connection), but I discount this because Netscape (either 1.22 or 2.01) crashes at random intervals (several times per day) on this computer with non-Chime documents for reasons unknown to us. I would like to know whether anyone else (other than Tim Maffett) has viewed the 1PRC Chime tutorial in a Windows 3.1 system, and whether they experienced any General Protection Fault crashes. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: PRC kills Netscape? Date: Fri, 03 May 1996 17:30:47 -0500 (EST) To: rasmol@noc1.oit.umass.edu I cleared the Netscape 2.01 cache (by deleting all files in c:\netscape\cache) and so far, so good! I've been able to load the Nixon/Rzepa 1PRC Chime tutorial several times without incident. I could not do this at all yesterday. I've now made my AUTOEXEC.BAT clear the cache on every boot. Thanks, Will McClure! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: PRC kills Netscape? Date: Fri, 03 May 1996 18:16:20 -0500 (EST) To: rasmol@noc1.oit.umass.edu From: William McClure Eric, I meant choosing "Network Preferences..." under the "options" menu; selecting "Cache" and clicking on the "Clear cache now" button. This is sort of "manual", but I didn't mean trashing the cache from the system folder, although that could be done instead, I guess. -Will PS The most virulent crashes lately have been while setting up Chime-containing windows. I've learned a lot about what Netscape 2.0 doesn't like, but I don't think I could write simple sentences about it! Eric adds: I wondered if there was a menu option somewhere to clear the cache -- thanks. I'm working strictly on DOS/Windows, BTW (no 'folders', rather 'directories'). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Chemscape Chime circumvents Rasmol Helper Date: Fri, 03 May 1996 20:30:33 -0500 (EST) To: rasmol@noc1.oit.umass.edu Forwarded for those on the list who may be interested. -Eric ------------------------------ Fri, 03 May 1996 06:50:51 -0700 From: Tim Maffett Subject: Re: Chemscape Chime circumvents Rasmol Helper To: tstainba@vax7.curtin.edu.au, chime-feedback@mdli.com Cc: emartz@microbio.umass.edu At 02:32 PM 5/3/96 +0800, Eleanor Stainback wrote: >Hello, > >I have downloaded and installed Chemscape Chime, looked through >some tutorials and even constructed my own page. I must say >that it looks great and will prove very useful for some of >the web tutorials I am creating for our Biochemistry units. Thank you for the compliment. (If you don't mind I would love to see your tutorials when you are done.) >However, there were a couple of problems : >1) I am running Netscape Navigator 2.01 on a PowerPC - whenever >I attempt to resize the page after viewing a page with the >Chime plugin a fatal error occurs and I have to restart the >system (probably a problem for Netscape to solve) > Unfortunately this IS a Netscape Navigator 2.01 bug. We spent several days trying to figure out how we could 'detect' that Navigator had made an error and somehow fix it, but it was to no avail. Netscape has acknowledged this bug and they have promised to fix it. (and I must say that with the Atlas PreRelease 2 of Navigator I have NOT seen the problem, but I have not specifically tested for it) >2) I have designed several tutorials which allow students >to click on an icon or filename in the Web page and have a pdb >file displayed in Rasmol (running as a helper application). These >tutorials are designed in part to teach the students to use Rasmol >by entering commands into the separate command window. Having >installed the Chime plugin, when I click on an icon which is linked >to a pdb file using an anchor link (), the >chime plugin captures the file and displays the image within >the netscape browser - Rasmol doesn't start up as the helper app. > Is there anyway to circumvent this? In some instances I want to have >an inline display of the molecule, but other times I want the separate >Rasmol Application (complete with command line window) to appear. For >my web pages which use chime I used the markup, >but apparently the markup works as well. In 2.01 of Navigator Netscape did not provide any way to the plugin, OR the user, to override this behavior. Netscape is bringing up the plugin in what they call 'full screen' mode, and that is that the plugin takes over the entire window. We have talked with them about this since January, and I can report that they HAVE done something about it. If you download the Atlas PreRelease 2 (3.0 beta 3) of Netscape Navigator you will have an 'enhanced' 'Helpers' tag on the Options->General Preferences menu item dialog. In this new helpers tab you can specify if you want the Chime plugin or RasMac to be used for entire files of a given type (for tags). [I will add here that I have been using Atlas PreRelease 2 for a couple weeks, and it has been very stable. For me it has worked better than 2.01 did, because they have fixed some of the other plugin bugs as well. (I can't promise anything about Netscape software however! ;) ] One other note, Netscape has NOT yet put this new helper settings dialog into the Windows version of Navigator Atlas PR2. They have promised it on all platforms by PR3. > >If you could help me with this second problem I would be greatly >appreciative. Right now I am circumventing the problem by >removing the plugin from the Netscape plugins folder before >starting the browser app. Give Atlas PR2 a try and tell me how it works for you. I suppose another option would be for Chime to support a command window. Chime does support the entire Rasmol scripting language. I made the decision that the command window was a bit of an 'expert' mode item, and it would not be used much by most people. It interests me that you have tutorials to teach your students how to use it. I would be interested un your thought on this. [snip] -tim >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- >Eleanor (Nell) Stainback | nell@ppe.curtin.edu.au >School of Biomedical Sciences | tstainba@cc.curtin.edu.au >Curtin University of Technology | Phone: (61)(09) 351 7516 >GPO Box U1987, Perth, | Fax: (61)(09) 351 2342 >Western Australia 6001 | > > _--_|\ > / \ > >>>-------> \_.--._/ > ^ >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: <73834.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William McClure Subject: Re: Chemscape Chime circumvents Rasmol Helper Date: Sat, 4 May 1996 10:43:06 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Excerpts from mail: 3-May-96 Chemscape Chime circumvents.. by Tim Maffett > I suppose > another option would be for Chime to support a command window. > Chime does support the entire Rasmol scripting language. I made > the decision that the command window was a bit of an 'expert' mode > item, and it would not be used much by most people. It interests > me that you have tutorials to teach your students how to use it. > I would be interested un your thought on this. Consider this my strong vote/endorsement for the RasMol command window in Chime. Here's why: 1) Students (sophomore and higher biochemistry classes) become 'experts' very quickly and Instructors here expect them to write scripts that display selected features from PDB files, that they view at PDB, Molecules R Us, and other sites. 2) Our University will install Netscape 2.0 in the student computer clusters this summer for the Fall term '96. Researchers can use any alpha or beta versions of software they want to, but the student clusters stick to cannonical final release versions. The Atlas PR2 version certainly won't be in the student machines until well into1997. 3) Until then, we will have to choose between having Rasmol available for students to view PDB files on the WWW or having Chime installed to view local files only. Yanking Chime from the plug-in folder ('directory'?) between uses doesn't seem like a suitable option. I hate to make choices between two mutually exclusive and terrific teaching resources. Unless some wizard comes up with fix to this, we may have to have designated "Chime machines" and "RasMol-only" machines. In fact that's the current set up for my lab computers. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: RasMol citation Date: Sun, 5 May 1996 15:55:40 -0400 To: rasmol@noc1.oit.umass.edu Cc: oeder@pdb.pdb.bnl.gov What is the definitive citation that we should give for RasMol? I want to be sure that we have it correct in our documentation, and I could not find it just now on the Rasmol page on the WWW. Thank you. Nancy -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank oeder@bnl.gov Brookhaven National Laboratory (516) 344-5744 phone Biology Department, Bldg. 463 (516) 344-5751 FAX P.O. Box 5000 Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime command window? Date: Mon, 06 May 1996 10:20:18 -0500 (EST) To: rasmol@noc1.oit.umass.edu I forward this message with my thoughts added at the end. -Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: "Braden N. McDaniel" Date: Sun, 5 May 1996 19:39:10 -0400 > Consider this my strong vote/endorsement for the RasMol command window >in Chime. Here's why: > 1) Students (sophomore and higher biochemistry classes) become >'experts' very quickly and Instructors here expect them to write scripts >that display selected features from PDB files, that they view at PDB, >Molecules R Us, and other sites. How do you propose a command window would be implemented in a situation where there will likely be multiple molecules showing on a page? One needs a way of explicity relating a command window to its associated molecule window. Sure, you give the windows a corresponding label like a number, but this is confusing an not at all intuitive. Seems to me that a better option would be to simply add a "Run Script..." option to the context menu. What do you think of that? Braden ----- Eric replies: Take a look at UCB-Rasmol to see how they have implemented multiple molecules. Seems quite intuitive -- you simply select which molecule you want to operate on from a menu, or you can operate on the whole set. Chime already runs scripts, and you can invoke a script with a button in an html document. However, what several of us want is the ability to type commands interactively as we do in RasMol. For example, to select a chain or subset of atoms of interest, color them arbitrarily, spacefill them, etc. (without having to write a script). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Chemscape Chime circumvents Rasmol Helper Date: Mon, 06 May 1996 10:43:53 -0500 (EST) To: rasmol@noc1.oit.umass.edu I forward this from Tim to circumvent temporary technical difficulties getting the list to accept it. -Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Date: Sun, 05 May 1996 20:59:31 -0700 To: rasmol@noc1.oit.umass.edu At 10:43 AM 5/4/96 -0400, you wrote: >Excerpts from mail: 3-May-96 Chemscape Chime circumvents.. by Tim Maffett > >> I suppose >> another option would be for Chime to support a command window. >> Chime does support the entire Rasmol scripting language. I made >> the decision that the command window was a bit of an 'expert' mode >> item, and it would not be used much by most people. It interests >> me that you have tutorials to teach your students how to use it. >> I would be interested on your thoughts on this. > > Consider this my strong vote/endorsement for the RasMol command window >in Chime. Here's why: > 1) Students (sophomore and higher biochemistry classes) become >'experts' very quickly and Instructors here expect them to write scripts >that display selected features from PDB files, that they view at PDB, >Molecules R Us, and other sites. I do see the need for a command line mode, and will put it on a list for future possible enhancements. I see Chime as complimenting RasMol, not replacing it, so I had not put the command line mode high on the list in the past. I am beginning to see that perhaps it is a 'basic' piece of functionality that we may need to implement though... > 2) Our University will install Netscape 2.0 in the student computer >clusters this summer for the Fall term '96. Researchers can use any >alpha or beta versions of software they want to, but the student >clusters stick to cannonical final release versions. The Atlas PR2 >version certainly won't be in the student machines until well into1997. I think that Altas (Navigator 3.0) will be FINAL by the end of summer, if not before. (I think that the 4.0 version is slated for christmas or jan/feb 1997). It would be unfortunate if the students were not able to run the released 3.0 version because it will have so many enhancements (aside from fixing this Chime/RasMol thing). I do think the Atlas setting to allow RasMol (RasMac/RasWin) to be started for PDB file links (and having Chime for embedded structures) is a nice solution though, in general, because it gives the user the freedom to choose. (and I do understand that it takes different parts of organizations longer to 'adopt' new technology. I just hope your student computing cluster staff finds the time to install Navigator 3.0 before fall (provided it is ready by then;) ) > 3) Until then, we will have to choose between having Rasmol available >for students to view PDB files on the WWW or having Chime installed to >view local files only. Yanking Chime from the plug-in folder >('directory'?) between uses doesn't seem like a suitable option. > I hate to make choices between two mutually exclusive and terrific >teaching resources. Unless some wizard comes up with fix to this, we >may have to have designated "Chime machines" and "RasMol-only" machines. >In fact that's the current set up for my lab computers. This is certainly not the 'ideal' situation, and I will try to find some solution. > >-Will McClure > -tim Architect - Internet Technologies MDL Information Systems, Inc /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: jmfernan@goliat.ugr.es (Jose Miguel Fernandez Fernandez) Subject: MACIMBAD Date: Mon, 6 May 1996 18:55:49 +0100 To: rasmol@noc1.oit.umass.edu Does anybody knows a modellization program call MACIMDAD? Its commercial, where can I get it? Its freeware, where is in the web? I have try to search it but I have fracased. There is a MSDOS WINDOWS o UNIX version? Thank you Pr. Dr. Jose Miguel Fernandez-Fernandez Departamento de Bioquimica y Biologia molecular Facultad de Medicina. Universidad de Granada Granada Spain E-18071 email jmfernan@goliat.ugr.es ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: User colors Date: Mon, 06 May 1996 18:20:24 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've forwarded this with my comment at the end. -Eric Martz From: William McClure I would like to specify some nonstandard colors for several PDB files and select them in Rasmol with the 'User' option. The Rasmol help window says this is done by inserting "COLO" records in the PDB data file, following a convention used in the Raster3D pgm. My question is, what exactly is put into a line of text to make a "COLO" record? If someone has done this and could post a few lines taken from such a modified PDB file, I would appreciate it. -Will McClure -------- Eric adds: Will, have you seen the short sample script I posted here earlier? The advantage is that if you can color the way you want with a script, you can apply that script to any PDB file, rather than hard-coding into a single PDB file. If you want to consider that method, use Netscape to search for 'user color' in the 'all' history file for the RasMol email list. However several people have asked how to put user colors into the PDB file and I, too, am curious what the syntax should be. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Closure of SWISS-PROT Date: Mon, 13 May 1996 11:18:56 -0500 (EST) To: rasmol@noc1.oit.umass.edu SWISS-PROT SHOULD HAVE BEEN 10 YEARS OLD IN JULY 1996, BUT IT MAY DISAPPEAR ON JUNE 30, 1996. Due to funding problems, SWISS-PROT as well as PROSITE, and the ENZYME nomenclature databases will disappear on June 30, 1996 if no solution is found before that date. The ExPASy WWW server and all services associated with it will also shut down. The distribution of the SWISS- 2DPAGE database will also be discontinued. Other external databases, WWW services and software packages that depend on SWISS-PROT, PROSITE and ENZYME as well as on the links provided between biomolecular databases will also be severely affected by this problem. Users of services and databases such as ENTREZ, BLOCKS, SRS, Owl, etc. should also be aware that most annotations at the protein level available through these services originate from SWISS-PROT or PROSITE. While the databases listed above as well as the ExPASy server are used in almost every laboratory doing molecular biology in the world, the funding for these projects has always been very modest (to say the least) and is now, due to procedural problems, going to disappear. [If you are not interested in the details of these problems and you want to send us a email or letter (fax) of support explaining why you think that these resources should stay available to the biological user community, you can skip the following section and jump to the end of this message] SUMMARY OF THE CURRENT SITUATION AND WHAT SHOULD HAVE HAPPENED Currently SWISS-PROT is developed as a collaboration between two sites: - The Medical Biochemistry Department of the University of Geneva, where in addition to the principal investigator of the project (Amos Bairoch), five annotators and a programmer are working on SWISS-PROT and related projects. Three of the five annotators are paid by a Swiss National Fund (FNRS) grant that ends on June 30. One additional annotator position, which is paid for by a special EMBL grant which also ends at the same time. The last position is on a Glaxo academic grant which will end in December. - The EMBL outstation, the European Bioinformatics Institute (EBI) in Hinxton, where six persons are working on SWISS-PROT: a coordinator (Rolf Apweiler), four annotators and a programmer. The EBI has recently embarked on major work to complement SWISS-PROT with a computer annotated supplement called TrEMBL which together with SWISS-PROT produces the first really non-redundant annotated protein sequence database. The completion of this work will require expanded resources at the EBI. About two years ago, a decision was reached in Switzerland that due to the international nature of the SWISS-PROT database, it ought not be funded by money reserved for national projects, but rather from funds intended for projects at the European or International level and to which Switzerland participates. Therefore we were asked to write a grant proposal at the European level. As such a proposal requires participants from at least two or more EU states (which Switzerland is not), an application was submitted in December 1995 which requests: - Five positions in Geneva for the annotators whose contracts will otherwise end in June 1996. - Four positions at EBI, to allow the development of TrEMBL and to cope with the increasing flow of data from genomic projects. - One position in Ireland, with Prof. Keith Tipton, to maintain and update the enzyme nomenclature (EC number) of the International Union of Biology and Molecular Biology (IUBMB). This nomenclature is the backbone of the ENZYME database. - One position at the Weizmann Institute in Israel and a partial position at the company Compugen to develop, in collaboration, the Bioccelerator sequence search hardware engine in ways that will help the maintenance of TrEMBL. - One position at INRIA in France, to develop software in collaboration with Compugen. We have been advised that this proposal was evaluated favorably by the scientific experts of the EU (equivalent of an US Study Section), but was not accepted at a higher level. The main (and apparently only) reason seems to be that those judging the proposal were under the impression that it requested funds solely for new developments. They were unaware that the CURRENT ACTIVITIES could not be maintained without this funding. They also seem to have failed to take note of the fact that the money for the Swiss operation was not coming out of the EU budget, but directly from Swiss government funds, provided that the EU approved the project. They therefore rejected this project while accepting other projects which themselves depend on the existence of SWISS-PROT (for example, a project in which Geneva is also involved, to establish a G-protein linked receptor database which will extend SWISS-PROT to provide information specific to this field of research). Having learned the extent of the problem, the EU seems genuinely concerned but does not seem to have the means of reversing such a decision. They are asking us to resubmit the proposal. But such a process will take almost a year and we only have two months left of salaries.... In Switzerland, money for SWISS-PROT is available, but can not be assigned to such a purpose before the EU accepts the grant. So we are in a catch 22 situation where everyone agrees that there is a problem, that it should be solved, but that they are unable to do anything for procedural reasons ! WHAT CAN WE AND YOU DO ? In the absence of public funding two scenarios seem possible. SWISS-PROT and PROSITE could pass into private hands as proprietary databases, or some non-profit association could be established which would recoup the ENTIRE costs of the operation through subscriptions. Two pharmaceutical companies have already expressed interest in the former solution, and existing examples of the latter are CAS (Chemical abstracts) and CCDC (Cambridge Crystallographic Data Centre). However we see enormous benefits to the user community from the public availability of the data. The first of these solutions would be incompatible with the mission of our partners at the EBI, but if it comes between a complete disappearance and such a solution, there does not seem to be a choice. At the time when there is growing concern about the privatisation of genomic data, we are facing a situation that could lead to the disappearance of what we think are the most widely used information resources on protein sequences because of our reliance on soft public money. We would much prefer to continue to offer and extend services to all the biological user community free of charge. To do so we need your help to convince the various funding agencies that you need these services for your research. We are therefore asking our user community to send emails of support stating why you think that these resources should continue to be available. You can send these messages to: help.sprot@hon.ch Do not forget to include in such an email, your full name, title and organization to which you belong. If you wish to write a letter of support, you can fax it to the following number: + 41-22-346 87 58 Or send it by post to: Amos Bairoch Dept. Medical Biochemistry 1, rue Michel Servet 1211 Geneva 4 Switzerland Many thanks to all of you. Amos Bairoch PS1: Feel free to forward this message to colleagues. PS2: Apologies to all those of you who have (will) receive multiple copies of this message. PS3: This text is also available on WWW at: http://expasy.hcuge.ch/sprot/help-sprot.html -End of message- /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Using Chime and Rasmol scripts? Date: Mon, 13 May 1996 14:28:22 -0500 (EST) To: rasmol@noc1.oit.umass.edu I've forwarded this with some long replies added at the end. -Eric Martz ------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty) Date: Mon, 13 May 1996 Can anyone point me to good info on: 1.The HTML needed to embed pdb images in WWW pages using the Chime plug-in. 2.How to get Chime to run Chime, or Rasmol scripts, on an embeded pdb. Looking at source HTML of pages on the Web hasn't helped me much. TIA ------------------------------------------------------------------------ Fergus Doherty, PhD. Department of Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH. U.K. Internet: Fergus.Doherty@nottingham.ac.uk Tel: (0)115 970 9366 FAX: (0)115 942 2225 URL http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html Dear Fergus: I, too, have been trying to do this and have had quite a few frustrating hours because of the current lack of documentation. Tim Maffett (the main author of Chime) has been very helpful, though. Here are some things I've learned which should help you. I'm assuming you've found the Netscape help on frames (use the help menu at the top of Netscape). There is a separate document on frame syntax. Some specific answers to your questions are #4,5,6 below. However #1,2,3 may influence the environment you choose to work in, or whether you want to develop Chime documents now or wait a bit longer. 1. ATLAS VS. NETSCAPE. Tim recommends using Atlas P2 (from Netscape) instead of Netscape 2.01, as the plug-in support is supposed to be better. I haven't tried it yet. All my tests have been with 2.01 in local mode. BEGIN QUOTE FROM TIM MAFFETT: In Netscape Atlas PreRelease 2 and up there is also a 'type=' tag which you can use to get netscape to load a plugin WITHOUT a source document. This will be very useful for a variety of reasons, but one example is (of a rasmol script button): The above will allow you to have a chime [X] button WITHOUT having to have a rasmol script file on the server, and without have to have Navigator go get that file (which is slow). Everything is 'inline'. With Atlas PR3 it will be possible to use 'regular' links to communicate with Chime. What Netscape calls LiveConnect will working, which will allow Java and JavaScript to talk to Plugins. ... what it will mean is that the chime 'button' will not really be needed anymore (if you don't want to use it), and much fancier possibilities will be present with the programmability of Javascript, including buttons, etc. ... Netscape supports a url protocol called 'javascript:', which just is a sequence of commands to execute in javascript for the current page. For example: "javascript:document.history.back(0)" would send you back one page. (this kind of thing has worked since 2.0) With LiveConnect the following will be possible: (for example) If you have a Chime plugin on a page, and you named it 'Dna1', then you now have an plugin 'object' which can be addressed as 'Dna1'. This plugin object will have properties and methods (variables and functions) which can be performed on it. (again, for example) plugin.Dna1.ExecuteRasmolScript("dock1.spt"); would execute the script 'dock1.spt' script on the Chime plugin object named 'Dna1'. So you could have a href tag in your HTML like this: Dock It Now when someone clicks this tag then the dock1 script will execute, and the link will change colors, because the user has 'followed' that link. END QUOTE FROM TIM MAFFETT 2. RESIZING BUG. Eleanor Stainback has reported and Tim has confirmed that Netscape 2.01 has a bug: when you resize a Chime window, you may get a fatal error. This bug may not be present in Atlas P2. 3. RASMAC vs. CHIME AT SAME INSTALLATION. Eleanor Stainback said: >I have designed several tutorials which allow students >to click on an icon or filename in the Web page and have a pdb >file displayed in Rasmol (running as a helper application). These >tutorials are designed in part to teach the students to use Rasmol >by entering commands into the separate command window. Having >installed the Chime plugin, when I click on an icon which is linked >to a pdb file using an anchor link (), the >chime plugin captures the file and displays the image within >the netscape browser - Rasmol doesn't start up as the helper app. > Is there anyway to circumvent this? In some instances I want to have >an inline display of the molecule, but other times I want the separate >Rasmol Application (complete with command line window) to appear. For >my web pages which use chime I used the markup, >but apparently the markup works as well. Tim Maffett replied: "In 2.01 of Navigator Netscape did not provide any way to the plugin, OR the user, to override this behavior. Netscape is bringing up the plugin in what they call 'full screen' mode, and that is that the plugin takes over the entire window. We have talked with them about this since January, and I can report that they HAVE done something about it. If you download the Atlas PreRelease 2 (3.0 beta 3) of Netscape Navigator you will have an 'enhanced' 'Helpers' tag on the Options->General Preferences menu item dialog. In this new helpers tab you can specify if you want the Chime plugin or RasMac to be used for entire files of a given type (for tags). One other note, Netscape has NOT yet put this new helper settings dialog into the Windows version of Navigator Atlas PR2. They have promised it on all platforms by PR3." 4. SRC 1ST IN . This took me over an hour to discover. If other parameters are first, you may get nothing displayed. 5. CAN'T LOAD PDB VIA SCRIPT. As I understand it, for Netscape 2.01 with Chime, you can't first load a PDB into a frame by -ing a script which contains a load command. Scripts must be applied to a PDB previously loaded with a previous referencing the PDB. Scripts can only be applied via the button mechanism. For example (from Tim): When the button is pushed the hitme.spt script file will get run against PDB in the chime plugin with the name 'hitme'. I haven't tried to see if the script file (which must have a name ending in .spt) can include a zap and a load for a different PDB. 6. INITIAL APPEARANCE VIA IN-LINE SCRIPT. You can control the initial appearance of the PDB with an "in-line" script, using this syntax: As indicated above, you can continue the script on multiple lines if each line ends on a semicolon, and the end quote is at the end of the last line. 7. FRAME VS EMBED NAMES. Also from Tim: "One other thing, make sure that the 'target=' and 'name=' names you give chime plugins are NOT the same as any frame names. The reason for this is that in Atlas PR2 Netscape has made 'target=' in an tag a argument that Netscape is now using to decide where to place a plugin! In future versions of Chime I will probably add the ability to say 'scripttarget=' or somesuch to avoid this confusion." /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Fw: Rasmol 2.6b2; minor bugs Date: Tue, 21 May 1996 15:43:26 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: ras32425@ggr.co.uk (Roger Sayle/RasMol) ------------------------------ Tue, 21 May 1996 11:27:18 -0700 From: John Lawton Subject: Rasmol 2.6b2; minor bugs To: emartz@microbio.umass.edu Hi Eric, I wanted to bring up some minor "bugs" that a colleague and myself have encountered while using rasmol2.6b2. 1. When the first Molecule is loaded in, it appears rotated 180 degrees about the x axis. 2. Stereo seperation values have the wrong sign. i.e. the command: 'set stereo -5' should put it in crosseyed. Right now -5 sets the view as wall-eyed. JL /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Weekly digest available Date: Wed, 22 May 1996 16:07:43 -0500 (EST) To: rasmol@noc1.oit.umass.edu During a recent burst of messages to this list, Andrew Sparks suggested that some subscribers might prefer receiving a periodic summary of messages rather than each message separately. I've configured the RasMol email list so that those who wish can have all messages for each week delivered concatenated into a single 'digest' message. If you prefer to receive the digest, send to listproc@lists.umass.edu this message: set rasmol mail digest To restore delivery to the per-message basis: set rasmol mail ack ('ack' stands for 'acknowledge' which means that when you send a message to the list, you will receive your own message back as confirmation that the message was broadcast. Don't ask why this is the inverse of digest -- it doesn't make any sense to me either, but it works.) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: wfreeman@uic.edu (Wade Freeman) Subject: Does the In-Line Option Work for You? Date: Thu, 23 May 1996 11:07:33 -0800 To: rasmol@noc1.oit.umass.edu I've created a number of pdb files meant to show relationships in crystal structures and created scripts using RasMac2.6. In using these scripts I've noticed two problems: a) Changes in the background color are not picked up when a script is loaded. I work around this by editing the script file (I use BareBonesEditor) to move the background command so that is comes AFTER the zap command instead of preceding it. b) Attempts to use the in-line option always crash the system. Thus: I edit a script to include the command load pdb inline instead of load pdb myfilename and copy in the pdb file to follow an exit that I've inserted at the end of all other Rasmol commands. When I double-click on the icon for the revised Rasmac V2.6 document, I get a system error and end up re-starting with CNTL-APPLE-POWER. Always. Has anyone else had anything like either of these difficulties? Is there a way to use the inline option (which looks useful) successfully? I 'm running a Macintosh 7200/75 under System 7.5.3. Wade Freeman References: ++++------+------+------+------+------+------+------+------+------+------+ From: William McClure Subject: Re: Does the In-Line Option Work for You? Date: Fri, 24 May 1996 08:31:25 -0400 (EDT) To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu Excerpts from mail: 23-May-96 Does the In-Line Option Wor.. by Wade Freeman@uic.edu > b) Attempts to use the in-line option always crash the system. Thus: I > edit a script to include the command > load pdb inline > instead of > load pdb myfilename > and copy in the pdb file to follow an exit that I've inserted at the end > of all other Rasmol commands. The following is a script (without the coordinate portion of the file) that was written by David hackney in our department. It displays lysozyme and a bound inhibitor. For editing, we keep such scripts as plain text files. They must be called from within RasMac 2.6 on a local machine. They can also be called from a WWW page link with a properly configured server (filename.spt mime type and RSML file type, etc.). If they are saved from the WWW page they are converted to the RSML file type; opening such a file on the local machine launches RasMac and runs the script. This approach works well for simple scripts without too many pauses, i.e. for setting up a few choice views for student use. -Will McClure zap load pdb inline zoom 130 wireframe off select hetero and not water spacefill select protein ribbon color structure echo echo Lysozyme - trisaccharide in sites A-C as spacefill echo exit HEADER HYDROLASE (O-GLYCOSYL) 01-FEB-75 6LYZ 6LYZ 3 COMPND LYSOZYME (E.C.3.2.1.17) 6LYZB 1 SOURCE HEN (GALLUS $GALLUS) EGG WHITE *****cut****** Remainder of HEADER and coordinates follow (deleted here). ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: French Ministry of Education Plan Date: Fri, 24 May 1996 20:30:32 -0500 (EST) To: ras32425@ggr.co.uk (Roger Sayle/RasMol) Cc: rasmol@noc1.oit.umass.edu Did the plan of the French Ministry of Education to distribute RasMol plus PDB files to all secondary schools and colleges in France ever happen? Does anyone know a contact in the FM of Education? Are there any other cases of organized, largescale distribution of RasMol for educational purposes? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Neil Millar Subject: rasmol for schools Date: Sun, 26 May 1996 13:47:03 +0100 To: RasMol mailing list Dear Eric and the Rasmollers, Firstly many thanks to Roger for such a brilliant program and to Eric for producing such a useful web site. I first came across rasmol a few years ago when I was doing research into muscle contraction, but my research money ran out, so I had to get a proper job. So now I teach biology and physics at a secondary school in the north of England. And I can tell you it's a lot tougher than research! I have been using rasmol to teach sixth-formers (16-18 year olds) about proteins, lipids, DNA and other groovy stuff, and it has been a great success. In order to publicise it in UK schools I wrote an article about rasmol for the "School Science Review", a journal for secondary school science teachers. It should appear in the June issue (I think). Since few UK schools or teachers are on the internet yet I have offered a disk copying service to distribute rasmol. After the artucle is published I'll find out if that was wise, and how much interest there will be from UK schools. Many UK schools use the Acorn Archimedes computer, a technically lovely computer but now rapidly being sidelined by the ubiquitous windows PCs. I was therefore delighted to see that there is now an "Arch" version of rasmol. I have tried it and it works beautifully. Martin Wuerthner has done a great job of porting rasmol, and has even added a few touches of his own. It seems to run faster than my windows version and will run exactly the same scripts. I have a question about rasmol on windows 95. The text in the command window is always tiny, regardless of the size of the window. Does anyone know of a way to change this? This is presumably a windows 95 question rather than a rasmol question. I would also be interested to hear more about the French experiment with rasmol in schools. If it takes off here in the UK I'll let you know. Best Wishes, Neil Millar Conyers School, Green Lane, Yarm, Teeside TS15 9ET, UK ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: rasmol for schools Date: Tue, 28 May 1996 09:55:51 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Dear Neil Millar: Thanks for your report. Send me the ref. to your School Sci Rev article and we can post it on the RasMol bibliography page. And if you have the text in machine readable form, we could put full text as well on the web site. Perhaps there are other articles directed at teachers of high school (in the US, age 15-18) students, but I haven't seen them. I know that a RasMol workshop for HS teachers was held recently in central New York State (by Joe Calvo at Cornell). [If others on the RasMol email list know of workshops, publications, talks etc. on RasMol for education, please share so we can all have an awareness of what is happening.] /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Workshop for College Faculty Date: Tue, 28 May 1996 10:27:16 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear Rasmolites: A dozen faculty from my University have registered to attend a one-day RasMol workshop which I'm planning to hold in August. These are primarily faculty teaching college freshmen and sophomores (typically ages 19-20) in larger classes (50-200 students) from all four undergraduate campuses of the U of Massachusetts. The goal is for the participants to leave feeling inspired and ready to use RasMol in their classes, either in lecture projections, or in student assignments. Another hope is that some of the participants will want to give similar workshops at other campuses. I'm curious -- How many other workshops with similar goals exist or are being planned? Also, since this will be my first, any advice from the experienced is welcome. I'm envisioning this as a 10 AM to 4 PM affair, with an hour off for lunch. It will be held in a new computer lab with 20 Mac 7100/80's all with direct network connections to the Internet. It will assume basic familiarity with Windows or Macintosh and a mouse but not necessarily any web browsing experience nor any RasMol experience. I envision introducing each topic for 5-10 minutes with screen projection, then having 20 minutes or so for students to try it out. A paper handout with all procedures would be provided to facilitate post-workshop carry through. Topics I envision: 1. Use of a web browser; exploration of the RasMol web site. 2. Downloading and installing RasMol. 3. Using RasMol pull-down menus to explore the structure of a protein-DNA complex (Brookhaven 1D66): reporting residue ID with a mouse click, representations, coloring schemes, rotation and zoom, slabbing, shadowing, and specular effects. 4. Introduction to the RasMol command-line interface: selection and restriction, predefined residue groups, labeling, showing disulfide and hydrogen bonds. 5. Finding a molecule of your choice at Brookhaven, downloading and exploring it with RasMol. 6. Downloading, installing, and running RasMol scripts for use in lectures. 7. Brief introductions to Chime (RasMol as a Netscape plug-in), and UCB-RasMol. 8. A brief introduction to writing scripts for RasMol. This workshop is restricted to UMass Faculty since UMass is providing support, but I'd like to offer similar workshops at other locations if I can get the funds to do so, or if the host campus can fund the workshop. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Fw: Stereo viewer for RasMol Date: Wed, 29 May 1996 08:23:07 -0500 (EST) To: rasmol@noc1.oit.umass.edu ------------------------------ Wed, 29 May 1996 12:54:26 +0000 From: "Andrew Coulson" Subject: Stereo viewer for RasMol To: emartz@microbio.umass.edu Dear Eric, UK readers may be interested to know that the VCH Reflecting Stereoscope, Order Number 1010097, can be ordered directly by sending a sterling cheque for 22.75 pounds by post to VCH fao Gaby Diller Boschstrasse 12 Postfach 11 12 61 D 69541 Weinheim Germany The phone number of their office in Cambridge, UK, is 0223 321111 The stereoscope is light enough to be held in one hand, and is very suitable for use with RasMol. It works very well, but I'm afraid is still too expensive to be easily provided to a whole class. Andrew /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: RasMol for OS/2? Date: Tue, 04 Jun 1996 14:23:27 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: bbraun@ucla.edu Is there a native OS/2 version of RasMol? Here is one enthusiast who would like to use it. -E. Martz ------------------------------ Mon, 03 Jun 96 22:52:59 From: "Benjamin Braun" Subject: RE: RasMol for OS/2 To: "emartz@microbio.umass.edu" Dr. Martz, I'd like to thank everyone involved for RasMol. It really has fulfilled its promise to bring appreciation of 3D structures to biologists at large. Secondly, I wanted to request a native OS/2 executable. OS/2 does run Win 3.1 programs. In fact, it can run each program in a separate memory space, in contrast to Windows 95, which has a single memory space that all 16-bit programs share. Nonetheless, most people who use OS/2 prefer native OS/2 programs. This is because it is frustrating to use multiple interface styles at once, and because OS/2 offers an object-oriented interface that is often superior to Windows 3.1. In the case of RasMol, the latter point may not be as important, although I could imagine its uses. For example, viewing preferences for a given file could be saved with the file "settings," and therefore persist from session to session. The consistency of interface is significant. I don't think I would expect PowerMac users to run a Windows version even if SoftWindows was as fast as native code. This may not be the same situation, but my point is that interface consistency is important to computer users. Several cross-platform tools exist for OS/2, among them gnu, emx, and a toolkit from IBM called "Developer API Extentsions" (DAPIE) that eases porting Win32 source code to OS/2. Regrettably I lack the expertise to recompile for OS/2 myself. Thank you very much for your time. Please let me know of any developments. Sincerely, Benjamin Braun bbraun@ucla.edu /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Free molecular visualization: http://www.umass.edu/microbio/rasmol Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: rhodes@usm.maine.edu (Gale Rhodes) Subject: RasMac with Stereo Date: Tue, 4 Jun 1996 09:12:55 -0400 To: rasmol@noc1.oit.umass.edu While a version of RasMol 2.6b with working stereo is now available on the PC side, RasMac with stereo has still not appeared. Do you know of anyone who has obtained the source code and compiled RasMac 2.6b with working stereo? If so, would you please let me know. I would greatly appreciate being able to use it until Roger Sayle compiles the Mac version of 2.6b with stereo, or until version 2.6 appears. Cheers! ***************************** Gale Rhodes rhodes@usm.maine.edu Professor of Chemistry Chemistry Department University of Southern Maine 96 Falmouth Street Portland, Maine 04103 Phone: (207)780-4734 Fax: (207)780-4933 ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul L. Moses" Subject: Re: RasMol for OS/2? /Mac Date: Tue, 4 Jun 1996 14:54:32 -0400 To: rasmol@noc1.oit.umass.edu Cc: bbraun@ucla.edu Following up on this thread, I think that RasMac needs to use non-modal windows. The current version of RasMac seems to violate Apple interface standards because you cannot click outside the RasMac windows and run other applications. On the plus side, I have discovered that if you find and download the Motorola math library, it speeds up execution SUBSTANTIALLY. Paul --------------------------------- "Information is entropy." - Jean Baudrillard "RasMol for OS/2?" (Jun 4, 2:23pm) References: <51814.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: RasMol for OS/2? ; Cn3D beta testers? Date: Tue, 4 Jun 1996 16:56:10 -0400 To: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu Cc: bbraun@ucla.edu Hi Benjamin, I will look into what is involved in the RasMol recompile under OS/2 with the OS/2 developer API . What the developer API extentions are is a new set of 800 or so C functions that have the exact same syntax as the most-used Win32 API functions (those that do windowing, menuing, graphics, etc). One nagging problem with making an OS/2 port has been that the drawing space (y-axis) in OS/2 is upside-down compared to that in Windows - but this has also been addressed in the API extentions. However some of the object-oriented features of OS/2 do not map through to the Win32 compatible functions - so the real gains are probably in execution speed and interface consistency. I have tried in vain to get OS/2's native internet browser to launch Win16 RasMol 2.6 as a Mime-type application - but it does all work very nicely from Netscape 2.0 (Win16) run within the Win-OS/2 interface. If anyone wishes to try out a Win32 or SGI version of my new structure viewer Cn3D, please contact me, as I am looking for a few beta testers. You should already be familiar with Network Entrez, or have installed it (see the URL below - the Network Entrez Now! button) before you volunteer. Beta-test versions for Mac and Solaris, and Linux will be forthcoming. Cn3D is a standalone public-domain viewer that fetches MMDB data (ASN.1) directly over the internet, and will soon be integrated into the Network Entrez system. It does not read PDB files, but the MMDB database contains the entire Brookhaven database (up to the latest release). Cn3D contains no RasMol code, but its source code, like that of RasMol and Network Entrez, is also in the public domain. Christopher Hogue NCBI. hogue@ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/Structure >On Jun 4, 2:23pm, Eric Martz wrote: > Subject: RasMol for OS/2? > Is there a native OS/2 version of RasMol? Here is one enthusiast > who would like to use it. -E. Martz > ------------------------------ > From: "Benjamin Braun" > Mon, 03 Jun 96 22:52:59 > To: "emartz@microbio.umass.edu" > Subject: RE: RasMol for OS/2 > > Dr. Martz, > > I'd like to thank everyone involved for RasMol. It really has fulfilled > its promise to bring appreciation of 3D structures to biologists at large. > > Secondly, I wanted to request a native OS/2 executable. OS/2 does run Win > 3.1 programs. In fact, it can run each program in a separate memory space, > in contrast to Windows 95, which has a single memory space that all 16-bit > programs share. Nonetheless, most people who use OS/2 prefer native OS/2 > programs. This is because it is frustrating to use multiple interface > styles at once, and because OS/2 offers an object-oriented interface that > is often superior to Windows 3.1. In the case of RasMol, the latter point > may not be as important, although I could imagine its uses. For example, > viewing preferences for a given file could be saved with the file > "settings," and therefore persist from session to session. The consistency > of interface is significant. I don't think I would expect PowerMac users > to run a Windows version even if SoftWindows was as fast as native code. > This may not be the same situation, but my point is that interface > consistency is important to computer users. > > Several cross-platform tools exist for OS/2, among them gnu, emx, and a > toolkit from IBM called "Developer API Extentsions" (DAPIE) that eases > porting Win32 source code to OS/2. Regrettably I lack the expertise to > recompile for OS/2 myself. > > Thank you very much for your time. Please let me know of any developments. > > Sincerely, > > Benjamin Braun > bbraun@ucla.edu > > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor of Immunology emartz@microbio.umass.edu > Free molecular visualization: http://www.umass.edu/microbio/rasmol > Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html > Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 > Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >-- End of excerpt from Eric Martz References: ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: RasMol for OS/2? /Mac Date: Wed, 5 Jun 1996 07:53:45 -0400 (EDT) To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu Cc: bbraun@ucla.edu Excerpts from mail: 4-Jun-96 Re: RasMol for OS/2? /Mac by "Paul L. Moses"@dgs.dgsy > Following up on this thread, I think that RasMac needs to use non-modal > windows. The current version of RasMac seems to violate Apple interface > standards because you cannot click outside the RasMac windows and run other > applications. Some sort of malfunction at your Mac, Paul. I run GIFConverter, MS Word, Netscape+CHIME, et al. all the time with the RasMac windows open. I couldn't edit scripts or make WWW graphics otherwise. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMac with Stereo Date: Thu, 6 Jun 1996 11:45:43 +0100 (BST) To: rhodes@usm.maine.edu Cc: rasmol@noc1.oit.umass.edu Dear Gale (& Eric) > While a version of RasMol 2.6b with working stereo is now available on the > PC side, RasMac with stereo has still not appeared. Do you know of anyone > who has obtained the source code and compiled RasMac 2.6b with working > stereo? If so, would you please let me know. I would greatly appreciate > being able to use it until Roger Sayle compiles the Mac version of 2.6b > with stereo, or until version 2.6 appears. I apologise for taking so long to get around to compile RasMac 2.6beta2. However, you'll be pleased to hear that I've now FTPed the appropriate files backwards and forwards between my Mac and UNIX boxes, and placed the file "rasmac.sit.hqx" in /pub/rasmol/v2.6beta on ftp.dcs.ed.ac.uk. The PDB site at Brookhaven should mirror this file automatically tonight. Anybody on this list who maintains a RasMol mirror might want to update this file. Please remember to transfer the file in "binary" mode. Once again, I'm sorry for the delay. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol for OS/2? /Mac Date: Thu, 6 Jun 1996 12:36:30 +0100 (BST) To: "Paul L. Moses" Cc: rasmol@noc1.oit.umass.edu Dear Paul, > Following up on this thread, I think that RasMac needs to use non-modal > windows. The current version of RasMac seems to violate Apple interface > standards because you cannot click outside the RasMac windows and run > other applications. Thanks very much for your e-mail. Can any other RasMac users confirm this behaviour. My Mac seems quite happy to run several applications simultaneously with RasMac, indeed making a copy of the executable you can display two RasMac windows side-by-side (poor man's stereo!). The only exception might be when RasMac is performing a CPU intensive task during which time RasMac doesn't share the CPU with other processes for a few seconds. The only modal windows in RasMac are the dialog boxes, principally, the About, FileOpen, FileSave and Print menu options. Roger [Thanks for the tip about the Motorola Maths Library. I'll try it out!] -- 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol for OS/2? ; Cn3D beta testers? Date: Thu, 6 Jun 1996 12:56:44 +0100 (BST) To: hogue@ncbi.nlm.nih.gov Cc: bbraun@ucla.edu, rasmol@noc1.oit.umass.edu On Tue, 4 Jun 1996, Christopher Hogue wrote: Hi Christopher, > I will look into what is involved in the RasMol recompile under OS/2 with > the OS/2 developer API . > One nagging problem with making an OS/2 port has been that the drawing > space (y-axis) in OS/2 is upside-down compared to that in Windows. One feature of RasMol that you can use to assist in the port is that it is able to generate internal bitmaps top-to-bottom or bottom-to-top. This is normally controlled by the C preprocessor macro "INVERT" that is defined in the souce file "rasmol.h" when the macro "IBMPC" is defined. By modifying the logic at this one point in the program, the image can be inverted. But remember to check for chirality problems if the macro is not compatible with the display! I hope this helps. When I was working over at the NCBI on adding mmdb (ASN.1) to RasMol, the format was changing almost daily. Can I assume from the impending release of Cn3D that this standard has now stable? 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol in Bio Classes? Date: Thu, 06 Jun 1996 16:49:17 -0500 (EST) To: rasmol@noc1.oit.umass.edu I would like to get in touch with anyone who is using RasMol (or Chime) in undergraduate college (student ages 18-22) BIOLOGICAL science (including BIOchemistry) classes, or plans to do so in the coming academic year. If you are not doing so yourself, but know someone else who is, please put me in touch with them. I am aware that the following people are doing so, so they do not need to contact me except to bring me up to date on their activities, if they wish. Joseph Calvo, Cornell NY US Jose-Miguel Fernandez-Fernandez, Granada ES Frank Fitch, U Chicago IL US Judith Kelley, U Conn, Storrs CT US David Marcey, Kenyon Coll OH US William McClure, Carnegie-Mellon U PA US Jens Nyborg, U Aarhus DK Gale Rhodes, U Southern Maine US Duane Sears, UCSB CA US Tom Terry, U Conn, Storrs CT US Thanks, -Eric /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul L. Moses" Subject: Re: Motorola Maths Library for Macs? Date: Thu, 6 Jun 1996 11:06:39 -0400 To: mbxfd@unix.ccc.nottingham.ac.uk (Fergus Doherty), At 15:55 +0000 6/6/96, Fergus Doherty and an infinite number of monkeys typed: +Paul, + +In a post to the RasMol list you mentioned the 'Motorola Maths Library'. I +take it this is an extension that replaces the 'Math Lib'. Is it freely +available, and if so, where can I get it? + +Thanks + +Fergus + +------------------------------------------------------------------------ +Fergus Doherty, PhD. + +URL http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html +http://www.ccc.nottingham.ac.uk/~mbzmail/students/student.html Hi Fergus (and Roger, and everyone), The page where I obtained the Motorola Math extension is at http://www.cs.miami.edu/~belsley/mac/mac_sw.html There are a lot of other software links there too. The direct link is: http://www.cs.miami.edu/%7Ebelsley/mac/files/MathLibMot1.0.1.hqx MathLibMoto 1.0.1: Replaces Apple's Trig Math Library, with Motorola's, which is upto 10 times faster. It is a mere 81k download, well worth the bother. It goes into the Extensions folder, and you do not even have to reboot for it to work. Check out the Readme for more details. I noticed a substantial speed boost as I ran the model scripts from umass. Btw, apologies to Roger, he is correct: I noticed the "unable to click outside the window" problem while stuck in the middle of a long script. Of course, that's when you most want to run something, anything else... :) Cheers, Paul Training-Nutrition listowner and webmaster For info send a request to trnutreq@dgs.dgsys.com Homepage URL http://www2.dgsys.com/~trnutr/index.html "Re: RasMol for OS/2? ; Cn3D beta testers?" (Jun 6, 12:56pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: MMDB and Cn3D Date: Thu, 6 Jun 1996 17:58:32 -0400 To: rasmol@noc1.oit.umass.edu Cc: hogue@glowworm.nlm.nih.gov, ras32425@ggr.co.uk Hi Roger, Yes MMDB ASN.1 specification has been stable now since October 1995, when we turned on the MMDB services of Network and WWW-Entrez. For those on the RasMol list who want to read more about the MMDB project, Network or WWW-Entrez, visit, http://www.ncbi.nlm.nih.gov/Structure Chris Hogue NCBI >On Jun 6, 12:56pm, Sayle Dr R A wrote: > Subject: Re: RasMol for OS/2? ; Cn3D beta testers? > > Hi Christopher, > [snip] > I hope this helps. When I was working over at the NCBI on adding mmdb > (ASN.1) to RasMol, the format was changing almost daily. Can I assume > from the impending release of Cn3D that this standard has now stable? > > 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 >-- End of excerpt from Sayle Dr R A ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Guide to 'Movie' Script Creation Date: Mon, 10 Jun 1996 15:50:32 -0500 (EST) To: rasmol@noc1.oit.umass.edu Emartz says: Well, inspired by the discussion led by John Walshaw at the BioMOO last week with the Principles of Protein Science course students, I've spent an intense 3 days and have now put on the web the first draft of (fanfare heard clearly on real brass horns [not tinny computer beeps]) ... "Guide to 'Movie' Script Creation for RasMol and Chime" (see link under 'what's new' at www.umass.edu/microbio/rasmol) Emartz sighs "whew" Johnr jumps! RogerS [somewhere else] feels a wave of goosebumps. Andrew Coulson gets back to work with renewed vigor. Cathy says "Uh oh". TRex beams, noting quietly that it didn't take Emartz all summer after all. JohnW applauds [I hope]. PeterMR . o O Emartz stands and the circulation is restored to his bottom (temporarily) The housekeeper arrives to cart Henryb off to bed. Emartz adds: Admittedly an ambitious title and there is almost nothing in it (yet) about Chime. I'll be especially interested in hearing about the inevitible misconceptions, blunders and oversights. Pay attention Roger Sayle, Tim Maffett, Marco Molinaro, and Andrew Coulson and all soon-to-be script writers. Suggestions are invited from all quarters. Get to work Cathy O'Malley (who kindly volunteered to test drive it). JohnW adds: be brutally honest! If you're wondering where my wires got crossed, A transcript of the discussion meeting on RasMol & movie-making held in the BioMOO on Wednesday can be found at: http://www.cryst.bbk.ac.uk/PPS2/technology/RasMol/mooras2.html http://www.dl.ac.uk/PPS/technology/RasMol/mooras2.html http://www.pdb.bnl.gov/PPS2/technology/RasMol/mooras2.html http://www.man.poznan.pl/PPS/technology/RasMol/mooras2.html /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: where is the color table? Date: Wed, 12 Jun 1996 18:57:42 -0500 To: rasmol@noc1.oit.umass.edu Dear Rasmoleans, Where do the standard color tables for RasMol live? For some reason my chlorines are routinely coming out gray instead of CPK colors or lime green (not an official color name), and I am supposing this is the problem. I cannot discover the default color data to save my life. Thanks, Toni ++++------+------+------+------+------+------+------+------+------+------+ From: "Adrian Kornhauser Eisenberg (comp)" Subject: Re: where is the color table? Date: Thu, 13 Jun 1996 15:45:45 -0600 (CST) To: rasmol@noc1.oit.umass.edu Well maybe this will not be usefull... But why don't you change their color to what ever you want... It's just two command to change ALL of them. One "select " and one "color ". But may be that is not the problem. I'm not a very experienced used, so accept my apologies if I goofed and did not understood the problem. :D ****************************************************************************** Adrian KORNHAUSER EISENBERG Facultad de Medicina U.N.A.M Mail: adriank@servidor.unam.mx DEPARTAMENTO DE BIOQUIMICA Lab. 3 Tel: 623-21-75 Coordinador de RED y COMPUTO Fax: 616-24-19 ****************************************************************************** "where is the color table?" (Jun 12, 6:57pm) References: <199606122357.SAA19959@athe.wustl.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: where is the color table? Date: Thu, 13 Jun 1996 19:28:05 -0400 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu Hi Toni, > > Where do the standard color tables for RasMol live? For some reason my > chlorines are routinely coming out gray instead of CPK colors or lime green > (not an official color name), and I am supposing this is the problem. I > cannot discover the default color data to save my life. > > Thanks, > > Toni >-- End of excerpt from Toni Kazic These appear to live inside the RasMol source code in the file abstree.h (see the end of this message). Implementation of the actual RGB values that map to the colour indices is platform dependent, but I do get green on two platforms: If I load the PDB file 5HVP, and issue the commands >select cl >spacefill it colors the 2 chloride ions green on SGI and Win32 RasMol 2.6. BUT sometimes other color settings can disrupt this, e.g. >select all >colour shapely Warning: Unable to allocate shade! ... When you see this warning, RasMol (as I understand it) has run out of colors, and you may find the wrong colours being used, in this case the Cl ions turn purple. In the case of a 3D viewer like RasMol, it is important to remember that when you ask for an RGB color - say 255 0 0 (red); the program has to make several shades of red as a gradient from light to dark in the real color palette that it uses to paint the screen with. These shades are combined for depth-cueing. So for a system color palette with only 256 slots there are not really that many 3D colors you can ask for. Chris Hogue. NCBI. excerpt from abstree.h ------------------ /* CPK Colour Indices * 0 Light Grey 1 Sky Blue 2 Red 3 Yellow * 4 White 5 Pink 6 Golden Rod 7 Blue * 8 Orange 9 Dark Grey 10 Brown 11 Purple * 12 Deep Pink 13 Green 14 Fire Brick 15 Mid Green */ #define MAXELEMNO 104 typedef struct { char symbol[2]; int covalrad; int vdwrad; int cpkcol; char *name; } ElemStruct; /* Structures with Implicit Hydrogens */ #define VDWCarbon 468 #define VDWNitrogen 375 #define VDWOxygen 350 #define VDWSulphur 462 #ifdef ABSTREE ElemStruct Element[MAXELEMNO] = { { { ' ', ' ' }, 170, 360, 12, "" }, /* 0 */ { { 'H', ' ' }, 80, 275, 4, "HYDROGEN" }, /* 1 */ { { 'H', 'e' }, 400, 550, 5, "HELIUM" }, /* 2 */ { { 'L', 'i' }, 170, 305, 14, "LITHIUM" }, /* 3 */ { { 'B', 'e' }, 88, 157, 12, "BERYLLIUM" }, /* 4 */ { { 'B', ' ' }, 208, 387, 13, "BORON" }, /* 5 */ { { 'C', ' ' }, 180, 387, 0, "CARBON" }, /* 6 */ { { 'N', ' ' }, 170, 350, 1, "NITROGEN" }, /* 7 */ { { 'O', ' ' }, 170, 337, 2, "OXYGEN" }, /* 8 */ { { 'F', ' ' }, 160, 325, 6, "FLUORINE" }, /* 9 */ { { 'N', 'e' }, 280, 505, 12, "NEON" }, /* 10 */ { { 'N', 'a' }, 243, 550, 7, "SODIUM" }, /* 11 */ { { 'M', 'g' }, 275, 375, 15, "MAGNESIUM" }, /* 12 */ { { 'A', 'l' }, 338, 375, 9, "ALUMINIUM" }, /* 13 */ { { 'S', 'i' }, 300, 550, 6, "SILICON" }, /* 14 */ { { 'P', ' ' }, 259, 470, 8, "PHOSPHORUS" }, /* 15 */ /* 262? */ { { 'S', ' ' }, 255, 452, 3, "SULPHUR" }, /* 16 */ { { 'C', 'l' }, 250, 437, 13, "CHLORINE" }, /* 17 */ { { 'A', 'r' }, 392, 692, 12, "ARGON" }, /* 18 */ { { 'K', ' ' }, 332, 597, 12, "POTASSIUM" }, /* 19 */ { { 'C', 'a' }, 248, 487, 9, "CALCIUM" }, /* 20 */ { { 'S', 'c' }, 360, 330, 12, "SCANDIUM" }, /* 21 */ { { 'T', 'i' }, 368, 487, 9, "TITANIUM" }, /* 22 */ { { 'V', ' ' }, 332, 265, 12, "VANADIUM" }, /* 23 */ { { 'C', 'r' }, 338, 282, 9, "CHROMIUM" }, /* 24 */ { { 'M', 'n' }, 338, 297, 9, "MANGANESE" }, /* 25 */ { { 'F', 'e' }, 335, 487, 8, "IRON" }, /* 26 */ { { 'C', 'o' }, 332, 282, 12, "COBALT" }, /* 27 */ { { 'N', 'i' }, 405, 310, 10, "NICKEL" }, /* 28 */ /* >375! */ { { 'C', 'u' }, 380, 287, 10, "COPPER" }, /* 29 */ { { 'Z', 'n' }, 362, 287, 10, "ZINC" }, /* 30 */ { { 'G', 'a' }, 305, 387, 12, "GALLIUM" }, /* 31 */ { { 'G', 'e' }, 292, 999, 12, "GERMANIUM" }, /* 32 */ /* 1225? */ { { 'A', 's' }, 302, 207, 12, "ARSENIC" }, /* 33 */ { { 'S', 'e' }, 305, 225, 12, "SELENIUM" }, /* 34 */ { { 'B', 'r' }, 302, 437, 10, "BROMINE" }, /* 35 */ { { 'K', 'r' }, 400, 475, 12, "KRYPTON" }, /* 36 */ { { 'R', 'b' }, 368, 662, 12, "RUBIDIUM" }, /* 37 */ { { 'S', 'r' }, 280, 505, 12, "STRONTIUM" }, /* 38 */ { { 'Y', ' ' }, 445, 402, 12, "YTTRIUM" }, /* 39 */ { { 'Z', 'r' }, 390, 355, 12, "ZIRCONIUM" }, /* 40 */ { { 'N', 'b' }, 370, 332, 12, "NIOBIUM" }, /* 41 */ { { 'M', 'o' }, 368, 437, 12, "MOLYBDENUM" }, /* 42 */ { { 'T', 'c' }, 338, 450, 12, "TECHNETIUM" }, /* 43 */ { { 'R', 'u' }, 350, 300, 12, "RUTHENIUM" }, /* 44 */ { { 'R', 'h' }, 362, 305, 12, "RHODIUM" }, /* 45 */ { { 'P', 'd' }, 375, 360, 12, "PALLADIUM" }, /* 46 */ { { 'A', 'g' }, 398, 387, 9, "SILVER" }, /* 47 */ { { 'C', 'd' }, 422, 437, 12, "CADMIUM" }, /* 48 */ { { 'I', 'n' }, 408, 362, 12, "INDIUM" }, /* 49 */ { { 'S', 'n' }, 365, 417, 12, "TIN", }, /* 50 */ { { 'S', 'b' }, 365, 280, 12, "ANTIMONY" }, /* 51 */ { { 'T', 'e' }, 368, 315, 12, "TELLURIUM" }, /* 52 */ { { 'I', ' ' }, 350, 437, 11, "IODINE" }, /* 53 */ { { 'X', 'e' }, 425, 525, 12, "XENON" }, /* 54 */ { { 'C', 's' }, 418, 752, 12, "CAESIUM" }, /* 55 */ { { 'B', 'a' }, 335, 602, 8, "BARIUM" }, /* 56 */ { { 'L', 'a' }, 468, 457, 12, "LANTHANUM" }, /* 57 */ { { 'C', 'e' }, 458, 465, 12, "CERIUM" }, /* 58 */ { { 'P', 'r' }, 455, 405, 12, "PRASEODYMIUM" }, /* 59 */ { { 'N', 'd' }, 452, 447, 12, "NEODYMIUM" }, /* 60 */ { { 'P', 'm' }, 450, 440, 12, "PROMETHIUM" }, /* 61 */ { { 'S', 'm' }, 450, 435, 12, "SAMARIUM" }, /* 62 */ { { 'E', 'u' }, 498, 490, 12, "EUROPIUM" }, /* 63 */ { { 'G', 'd' }, 448, 422, 12, "GADOLINIUM" }, /* 64 */ { { 'T', 'b' }, 440, 415, 12, "TERBIUM" }, /* 65 */ { { 'D', 'y' }, 438, 407, 12, "DYSPROSIUM" }, /* 66 */ { { 'H', 'o' }, 435, 402, 12, "HOLMIUM" }, /* 67 */ { { 'E', 'r' }, 432, 397, 12, "ERBIUM" }, /* 68 */ { { 'T', 'm' }, 430, 392, 12, "THULIUM" }, /* 69 */ { { 'Y', 'b' }, 485, 385, 12, "YTTERBIUM" }, /* 70 */ { { 'L', 'u' }, 430, 382, 12, "LUTETIUM" }, /* 71 */ { { 'H', 'f' }, 392, 350, 12, "HAFNIUM" }, /* 72 */ { { 'T', 'a' }, 358, 305, 12, "TANTALUM" }, /* 73 */ { { 'W', ' ' }, 342, 315, 12, "TUNGSTEN" }, /* 74 */ { { 'R', 'e' }, 338, 325, 12, "RHENIUM" }, /* 75 */ { { 'O', 's' }, 342, 395, 12, "OSMIUM" }, /* 76 */ { { 'I', 'r' }, 330, 305, 12, "IRIDIUM" }, /* 77 */ { { 'P', 't' }, 375, 387, 12, "PLATINUM" }, /* 78 */ { { 'A', 'u' }, 375, 362, 6, "GOLD" }, /* 79 */ { { 'H', 'g' }, 425, 495, 12, "MERCURY" }, /* 80 */ { { 'T', 'l' }, 388, 427, 12, "THALLIUM" }, /* 81 */ { { 'P', 'b' }, 385, 540, 12, "LEAD" }, /* 82 */ { { 'B', 'i' }, 385, 432, 12, "BISMUTH" }, /* 83 */ { { 'P', 'o' }, 420, 302, 12, "POLONIUM" }, /* 84 */ { { 'A', 't' }, 302, 280, 12, "ASTATINE" }, /* 85 */ { { 'R', 'n' }, 475, 575, 12, "RADON" }, /* 86 */ { { 'F', 'r' }, 450, 810, 12, "FRANCIUM" }, /* 87 */ { { 'R', 'a' }, 358, 642, 12, "RADIUM" }, /* 88 */ { { 'A', 'c' }, 295, 530, 12, "ACTINIUM" }, /* 89 */ { { 'T', 'h' }, 255, 460, 12, "THORIUM" }, /* 90 */ { { 'P', 'a' }, 222, 400, 12, "PROTACTINIUM" }, /* 91 */ { { 'U', ' ' }, 242, 437, 12, "URANIUM" }, /* 92 */ { { 'N', 'p' }, 238, 427, 12, "NEPTUNIUM" }, /* 93 */ { { 'P', 'u' }, 232, 417, 12, "PLUTONIUM" }, /* 94 */ { { 'A', 'm' }, 230, 415, 12, "AMERICIUM" }, /* 95 */ { { 'C', 'm' }, 228, 412, 12, "CURIUM" }, /* 96 */ { { 'B', 'k' }, 225, 410, 12, "BERKELIUM" }, /* 97 */ { { 'C', 'f' }, 222, 407, 12, "CALIFORNIUM" }, /* 98 */ { { 'E', 's' }, 220, 405, 12, "EINSTEINIUM" }, /* 99 */ { { 'F', 'm' }, 218, 402, 12, "FERMIUM" }, /* 100 */ { { 'M', 'd' }, 215, 400, 12, "MENDELEVIUM" }, /* 101 */ { { 'N', 'o' }, 212, 397, 12, "NOBELIUM" }, /* 102 */ { { 'L', 'r' }, 210, 395, 12, "LAWRENCIUM" } /* 103 */ /* Lw? */ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: where is the color table? Date: Fri, 14 Jun 1996 11:35:20 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: Toni Kazic Dear Toni, > Where do the standard color tables for RasMol live? For some reason my > chlorines are routinely coming out gray instead of CPK colors or lime green > (not an official color name), and I am supposing this is the problem. I > cannot discover the default color data to save my life. For those interested the CPK colour tables are maintained as two data structures in different RasMol source files. The first data structure in "transfor.c" maintains the RGB values for 16 different CPK colours. This means that CPK colours are refered to by a single index 0-15. /* CPK Colour Indices * 0 Light Grey 1 Sky Blue 2 Red 3 Yellow * 4 White 5 Pink 6 Golden Rod 7 Blue * 8 Orange 9 Dark Grey 10 Brown 11 Purple * 12 Deep Pink 13 Green 14 Fire Brick 15 Mid Green */ The exact datastructure is defined as "static ShadeRef CPKShade[]" where a ShadeRef contains the Red, Green and Blue components; "r", "g" and "b". The second data structure in RasMol for CPK colouring is the periodic table, Element, in the source code file "abstree.h". This array maintains the atomic symbol, name, Van der Waals radius, covalent (bonding) radius and the CPK colour index of the first 104 elements. In the problem described above, Element[17].cpkcol has the value 13 indicating that Chlorine (Atomic number 17) should be displayed in 'green'. Checking CPKShade[13] reveals that green has the RGB values 0,255,0 respecitively. Hence, CPK colouring should be equivalent to: select chlorine colour [0,255,0] I suspect from your description of the problem that the true cause is that the "Cl" is being placed in the wrong columns of the PDB file, resulting in the atoms being interpreted as carbon atoms, hence the light grey colour. If the RasMol "select chlorine" command replies "0 atoms selected" then my suspicions are confirmed. I hope this helps and describes some of the mysterious workings of RasMol. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Re: where is the color table? T)) To: ras32425@ggr.co.uk Cc: rasmol@noc1.oit.umass.edu Hi Roger, Well, no doubt you are right but I am still puzzled. I am running 2.5.1 on a Sun under Solaris 2.something. The command select chlorine replies "No atoms selected!", while select *.cl replies "1 atom selected!" for 2-chloroethanol (after which I apply Adrian's suggestion). However I am surprised by the comment about columns in the pdb file. Here it is for 2-chloroethanol: COMPNDStr1 REMARK [C@2H2]([C@2H2][Cl])[OH] ATOM 1 C 1 -0.201 0.292 0.494 ATOM 2 C 1 0.643 -0.356 -0.603 ATOM 3 Cl 1 2.360 -0.138 -0.233 ATOM 4 O 1 -1.588 0.115 0.195 ATOM 5 H 1 0.027 -0.176 1.450 ATOM 6 H 1 0.027 1.354 0.547 ATOM 7 H 1 0.415 0.111 -1.559 ATOM 8 H 1 0.415 -1.419 -0.656 ATOM 9 H 1 -2.145 0.519 0.879 TER CONECT 1 2 4 5 6 CONECT 2 1 3 7 8 CONECT 3 2 0 0 0 CONECT 4 1 9 0 0 Does RasMol only read column 14???? Surely not as there are more elements than alphanumeric characters. Where would transfor.c and abstree.h normally live? Still baffled, Toni "Re: where is the color table?" (Jun 14, 11:05am) References: <199606141605.LAA22519@athe.wustl.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: where is the color table? Date: Fri, 14 Jun 1996 15:23:22 -0400 To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Hi Toni, Yes Roger was right try: > ATOM 1 C 1 -0.201 0.292 0.494 > ATOM 2 C 1 0.643 -0.356 -0.603 > ATOM 3 CL 1 2.360 -0.138 -0.233 > ATOM 4 O 1 -1.588 0.115 0.195 Also, lowercase has not traditionally been allowed in the PDB format (but to RasMol it is ok). Chris Hogue NCBI >On Jun 14, 11:05am, Toni Kazic wrote: > Subject: Re: where is the color table? > Hi Roger, > > Well, no doubt you are right but I am still puzzled. I am running 2.5.1 on > a Sun under Solaris 2.something. The command > > select chlorine > > replies "No atoms selected!", while > > select *.cl > > replies "1 atom selected!" for 2-chloroethanol (after which I apply > Adrian's suggestion). However I am surprised by the comment about columns > in the pdb file. Here it is for 2-chloroethanol: > > > COMPNDStr1 > REMARK [C@2H2]([C@2H2][Cl])[OH] > ATOM 1 C 1 -0.201 0.292 0.494 > ATOM 2 C 1 0.643 -0.356 -0.603 > ATOM 3 Cl 1 2.360 -0.138 -0.233 > ATOM 4 O 1 -1.588 0.115 0.195 > ATOM 5 H 1 0.027 -0.176 1.450 > ATOM 6 H 1 0.027 1.354 0.547 > ATOM 7 H 1 0.415 0.111 -1.559 > ATOM 8 H 1 0.415 -1.419 -0.656 > ATOM 9 H 1 -2.145 0.519 0.879 > TER > CONECT 1 2 4 5 6 > CONECT 2 1 3 7 8 > CONECT 3 2 0 0 0 > CONECT 4 1 9 0 0 > > > Does RasMol only read column 14???? Surely not as there are more elements > than alphanumeric characters. > > Where would transfor.c and abstree.h normally live? > > > Still baffled, > > > Toni > > >-- End of excerpt from Toni Kazic ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Chlorines re-greened Date: Fri, 14 Jun 1996 21:44:40 -0500 To: rasmol@noc1.oit.umass.edu Thanks Chris, you are absolutely right, the Cl was in the wrong column (and for the sake of propriety I have written it as CL). Now I have to figure out why the new version of CONCORD is writing the pdb file out differently from the old . . . Thanks again, Toni ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul L. Moses" Subject: Finally up and running! Date: Sat, 15 Jun 1996 12:00:26 -0400 To: rasmol@noc1.oit.umass.edu Hi Rasmol folks, THought you might like to see my site now that I have finally got the ftp links fixed. The main page is http://www2.dgsys.com/~trnutr/index.html >From there you can check the RasMol configuration page, or move straight on to the FAQs. The Macronutrient, Micronutrient, Nonnutrient, and More Complex Biochemistry documents are the ones with related pdb files. (The Biochem one has the most.) Let me know what you think or if you encouter any errors. Paul --------------------------------- "Information is entropy." - Jean Baudrillard ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Command line parameters, auto-starting scripts w/ rasmol.ini Date: Mon, 17 Jun 1996 12:42:23 -0400 To: rasmol@noc1.oit.umass.edu I'm forwarding this message from Henry Brzeski with my comments interspersed. My comments are marked **. -Eric Martz >Date: Mon, 17 Jun 1996 12:53:54 +0100 >To: rasmol@noc1.oit.umass.edu >From: Henry Brzeski >Subject: command line arguments in RasMol scripts > >This is a reply I wrote to another list concerning the problem of running >rasmol scripts with rasmol 2.6 beta 2. You might like to try it and if you >can get it to work then you can share it with the world > >>Is it possible to pass arguments from the RasMol command line to this RasMol >>script? So that you can type e.g.: >>script myscript Tyr112 >>and it selects Tyr112 and does with it what it is supposed to do. > >rasmol 2.5 accepted script commands on the command line ie 'rasmol -script >myscript' but I do not know what it would do with Tyr112. You will have to >try this **As far as I know, RasMol cannot substitute such arguments into a script. **Perhaps Roger can comment. >rasmol 2.6 beta 2 has more problems with such a start because sometimes it >stalls (I think it is after the first 'zap' or 'pause'). **RasWin 2.6 beta-1 and beta-2 erroneously exit the script at a 'pause' **(not necessarily the first pause, but an early one). **I don't know whether the same is true for RasMac. **(It is UCB-RasWin which dies at the first 'zap'. Again, I don't know **about UCB-RasMac.) >If you want to run >a script from rasmol2.6 beta 2 then you should do the following >1 put all your scripts and files in a directory >2 set the properties (for win95 - I can't remember what win 3.1 calls it) so **Win 3.1x calls it the 'working directory' in the Properties dialog. >that the program starts in this directory >3 add to this directory a file called rasmol.ini which includes the line >'script myscript' >4 sit back and enjoy **Thank you Henry! You're absolutely right, this method of auto-starting **the script avoids the 'exit on pause' bug. The script runs as intended. **I was not aware of this, but I just confirmed it with RasWin 2.6 beta2. >good luck > >h > >Henry Brzeski >Dept of Bioscience and Biotechnology >The Todd Centre >University of Strathclyde >31 Taylor Street >GLASGOW >G4 0NR 041- 552 4400 extn 3727 > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: RasMol in Schools Date: Mon, 17 Jun 1996 13:35:46 +0100 To: rasmol@noc1.oit.umass.edu Last night I spoke with secondary school teachers about using rasmol in school classrooms and demonstrated some of the things you could do with it. They were very impressed and thought that rasmol allowed you to get a feel for the 3D structure of proteins and DNA in a way that is impossible to achieve by other means. I see this as being immensely useful in schools (as long as the scripts and molecules are chosen with care). Do you see this as being an area for development? I would happily make any acripts I and my teachers devise available to other school teachers. The teachers want to use it for school children in the age range 14-16. Is anybody doing this already? h Henry Brzeski Dept of Bioscience and Biotechnology The Todd Centre University of Strathclyde 31 Taylor Street GLASGOW G4 0NR 0141-552 4400 extn 3727 "Re: where is the color table?" (Jun 13, 3:45pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: ong@bcl7.biochem.uga.edu Subject: stereo Date: Mon, 17 Jun 1996 14:51:14 -0700 To: rasmol@noc1.oit.umass.edu Dear rasmol user, Recently, I figure out the stereo mode is working for cross-eye user, not for parellel-eye user. Ping-lin ong uga athens, ga 30602 -- - Ping-lin Ong - Department of Biochemistry and Molecullar biology - University of Georgia - Athens, Georgia 30602 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: changing the font size in the command window Date: Tue, 18 Jun 1996 20:23:33 -0500 (EST) To: chu@GBF-Braunschweig.DE Cc: rasmol@noc1.oit.umass.edu In message Tue, 18 Jun 1996 19:13:14 +0200, chu@GBF-Braunschweig.DE (Claus Hultschig) writes: > Dear Professor Martz, > Today I want to ask you for a further advise on RasMol. Is the a way to > change the size of the font in the command line window. I did not find a > way ether by "playing around" or by checking the manual. > Thanks for your help > Sincerely > Claus Hultschig There is no way that I know of. Sometimes I would like to make it larger when I use the command line window to describe the graphics in a "movie" script. I am copying this to the RasMol email list in case anyone there has a comment (anyone responding please note that Claus is not a subscriber so cc your message to him directly as well as to the list). > Claus Hultschig > National Research Center for Biotechnology (GBF) > GNA/MERK > Mascheroder Weg 1 > D-38124 Braunschweig > Germany > Tel.:(++49)-531-6181-223, -228 or -269 > Fax.:(+49)-531-6181-292 > e-mail:chu@gbf-braunschweig.de > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Jing Zhou Subject: export resolution from Rasmac Date: Tue, 18 Jun 1996 15:29:58 -0700 To: rasmol@noc1.oit.umass.edu I try to use Rasmac to make colorful transparency printed from an HP inkjet. I use the export-gif function. Everything is fine except the resolution. It's always 72dpi, which looks not good when printed out. Is there any method to increase the export resolution besides making a large picture and using a graphic application to reduce its size while increasing its resolution? Thanks. -Jing ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Cross eyes Date: Tue, 18 Jun 1996 20:35:04 -0500 (EST) To: braden@shadow.net Cc: rasmol@noc1.oit.umass.edu > From: "Braden N. McDaniel" > To: "'rasmol@lists.umass.edu'" > Subject: RE: stereo > Date: Mon, 17 Jun 1996 22:00:18 -0400 > This is not unusual. It works on the same principle as that employed in > random dot stereograms. I believe it has more to do with the focus of > one's eyes than with their direction. Comment added by Eric Martz: In order to perceive side-by-side stereo images (unlike, I believe, random dot stereograms) in 3D, the eyes must line up or register the two images. Depending on the direction in which the two side-by-side images have been rotated relative to each other, this requires either crossing the eyes or focussing the eyes close to parallel, also called "wall-eyed". Alternatively a viewer can be used which has been mentioned previously on this list. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Confirm-Reading-To: "Andrew Coulson" X-Pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Coulson" Subject: Re: Cross eyes Date: Wed, 19 Jun 1996 11:16:19 +0000 To: emartz@microbio.umass.edu Cc: rasmol@noc1.oit.umass.edu Stereo viewing: Basically you have to override a very robust and reliable servo mechanism in your brain and eyes. To see stereo, your brain superimposes two images, and it uses information from your eye focussing and swivelling machinery to tell it what alignment to use; it also feeds back information from the merged image to keep your eyes pointed and focussed in the right place. The problem is that with side-by-side images on a piece of paper or a computer screen, you have to focus on them at ten inches away, but view them as though they were the images presented to your left and right eyes by an object 'at infinity'. There are two ways you can do this. One is usually described as 'letting your gaze relax'; eyes focussed close to, but gaze parallel as for seeing something in the distance. I learnt to do this as a small boy lying in bed gazing at a wallpaper design with a simple repetitive pattern of daisies. The image of one floats over on top of its neighbour, and then the pattern seems to be magnified and as though you were seeing it with exceptional clarity. It's a pleasant sensation, and I'm sure that's why one does it; mildly addictive! The trouble with this method is that there is a limit to how far one can make the images 'float', so if the picture is too big or the images too separated you can't merge them. The alternative way, which doesn't suffer quite so much from this limit, is the opposite; you make your eyes converge _more_ than they should be doing for the focus position. The effect is that the image on the right is used by your left eye, and vice versa. This in turn means that any stereo-pair of images is meant to be viewed either directly (left-eye-view on the left, right-eye-view on the right), or cross-eyed (the inverse). If you have a pair designed to be viewed one way, and you want to use the other, you have to interchange the individual images. In RasMol, the two different views are generated by rotating the left hand picture a little about the y-axis. Specifying a positive or negative value for this rotation corresponds to making the images suitable either for 'direct' or for 'cross-eyed' viewing. RasMol (latest Windows version) is set up so that the default ('set stereo on') is a rotation of the left image by +5 degrees. The result is suitable for viewing by cross-eyed stereo. If you want to produce images for direct viewing, do 'set stereo -5', instead. It is interesting to experiment with rotations larger and smaller than 5 degrees. It is sometimes difficult to tell what is going on when you are viewing or trying to view stereo images, because your brain is very good at resolving contradictions and almost letting you see in stereo when actually the wrong image is being presented to each eye. One way to tell is if rotations appear to be in the correct sense. If you rotate with the mouse, the front of the molecule should go to the right and down as the cursor goes to the right and down. Another way is to see how the images are merging. If they merge to the side of your dominant eye (left in my case), you are seeing them directly; if to the side of the non-dominant eye, your eyes are crossed. Finally, viewing in cross-eyes is more of a strain than viewing directly (that's why the latter is preferred, even though it only works for small images not widely separated). Mirror- or lens- (or mirror+lens-) viewers are intended for viewing 'directly'; they allow bigger and more separated images to be viewed successfully, and may also magnify them, or at least compensate for the extra path length in using the viewer. Salvador Dali became interested in stereo images -- I think as a result of seeing some molecular graphics stereo, since he includes DNA molecules, etc, in some of his stereo paintings. There is a wonderful collection of these in the Salvador Dali museum in Figueras, near Barcelona. It is astonishing that he could paint left- and right-eye images with such precision. The paintings are of two types. Some are quite small, and set up for direct viewing with a pair of mirrors at 90 degrees. You put your nose on the glass case on the line where the mirrors meet. The big pictures are side-by-side and meant to be viewed (without optical aid) from across the room. You can see people standing for hours quietly letting the images drift together.......... A few years ago the Computer Centre here got a colour printer which will print A0 posters (16xA4), and I used RasMol to produce a stereo pair of cro bound to DNA. This work ('Homage to SD, 1992') was hung in one of the Biocomputing Research Unit rooms for viewing in cross-eyed mode from about 25 feet away. We moved offices in January, and now they're just rolled up on top of the filing cabinet.......... Andrew Coulson ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Autostart script on Macintosh? Date: Wed, 19 Jun 1996 15:38:35 -0500 (EST) To: rasmol@noc1.oit.umass.edu Thanks to Henry Brzeski, I've realized that the RASMOL.INI file can autostart a script under RasWin when RasWin's icon is double-clicked (assuming that the File, Properties, Working directory points to the one containing the RASMOL.INI and the script which it starts). The command line argument method (raswin.exe -script scriptname) suffers from a bug which kills the script at an early pause, but as far as my testing has gone, the RASMOL.INI method avoids this. The RasMol 2.5 manual says that under unix, a file named .rasmolrc can autostart a script. But what about the Macintosh? I know that if the script file's signature (creator and type) are set correctly, double-clicking on the script will invoke RasMac and run the script (I haven't yet explored the software available to change the signature -- I'll post a message about this shortly). I realize that this is adequate, but I wonder -- is there a RASMOL.INI or command-line equivalent method for the Mac? (Again, assuming that RasMac and the script files are all in the same folder). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol 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: Mac Signature Utilities Date: Wed, 19 Jun 1996 15:42:52 -0500 (EST) To: rasmol@noc1.oit.umass.edu This message, from the flow cytometry list, seems highly germaine to RasMac scripts. I haven't explored File Buddy yet myself but intend to do so soon, and will document what I find in my guide to script creation (www.umass.edu/microbio/rasmol/makescrp.htm). -Eric Martz ------------------------------ Tue, 14 May 1996 16:47:27 -0400 From: vanburen%flovax.dnet.wayne.edu@rocdec.roc.wayne.edu Subject: RE: cellquest/powermacs/facsconvert To: Cytometry Mailing List Marcia Woda wrote: >I believe I am not the only person confused about the above topic. Cellquest >will not even read Cellquest generated files if they have taken a brief >excursion off the hard drive ie. to your file server . You need to restore the file signature (more on this later). >Facsconvert was >explained to me, and the users's guide also states, that this program >converts FCS 1.0 files to FCS 2.0. Yes, it does. >How then it also restores the infamous >Mac data resource fork is a mystery to me. No, it does not. It is true that Mac files have two parts: a data fork and a resource fork. However, FCS files do not have a resource fork, and therefore this fork cannot be restored. What does need to be restored are the Type and Creator attributes (together known as the 'signature'). The Creator usually refers to the application that created the file; for example, MSWD is the Creator code for a file created by Microsoft Word. If you save a file in MacWrite II format from Microsoft Word, the Creator code changes to MWII. This change occurs because the Creator code is used to find the application to launch when you open (double-click) a document file (a MSWD file would launch Microsoft Word, while a MWII file would launch MacWrite II). The Type usually refers to the kind of file; for example, TEXT is the Type code for a Microsoft Word file saved as 'Text only'. If you were to save the same file as a 'Normal' document, the Type would change to WDBN. The trick is to get a program that can change the signature back to BDLY (Creator) and BDLM (Type). (If you forget the signature, most programs will let you choose a file as an example of the signature you want to use). I found about 22 different shareware/freeware programs on Info-Mac, a popular repository for Macintosh programs. In fact, it is so popular that you must use a mirror site to download from. I found a list of shareware archives on the Apple WWW server at , and a list of Info-Mac mirrors at . One of these programs is called File Buddy, and will let you create a drag- and-drop applet to change the signature. Just select the FCS files in the Finder and drop them on the applet; it took 4 seconds to do 30 files on a Quadra 800. /\/\/\_ Eric Van Buren, vanburen%flovax.dnet@rocdec.roc.wayne.edu \ \ \ Analytical Cytometry, Karmanos Cancer Institute and \_^_/ Immunology & Microbiology, Wayne State University, Detroit, MI /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Author of the RasMol web site: http://www.umass.edu/microbio/rasmol Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Vms-To: SMTP%"rasmol@lists.umass.edu" ++++------+------+------+------+------+------+------+------+------+------+ From: moreaut@univ-tours.fr Subject: ANNOUNCEMENT: PROLYSIS Web server Date: Wed, 19 Jun 1996 21:21:23 +0200 To: rasmol@noc1.oit.umass.edu PROLYSIS is a Web server intended as a Web resource for proteases and protease inhibitors. This server contains informations of general interest and images, as well as useful links to other Internet resources related to proteases and their inhibitors. Suggestions and/or comments as well as material that can be added in PROLYSIS are welcomed. Please point your browser at: http://prolysis.phys.univ-tours.fr/Prolysis *------------------------------------------------------------------* | Dr. Thierry MOREAU | | Laboratoire d'Enzymologie et Chimie des Proteines | | 2bis, Bd Tonnelle Phone: (33) 47 36 62 06 | | 37032 TOURS cedex Fax: (33) 47 36 60 46 | | FRANCE Email: moreaut@univ-tours.fr | *------------------------------------------------------------------* ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: RasMol in Schools Date: Fri, 21 Jun 1996 20:18:03 -0500 (EST) To: rasmol@noc1.oit.umass.edu Henry, I find it interesting (and a little sad) that there was no response on the list to your message of this topic. Did you get any private replies? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html >Immunology: http://www.bio.umass.edu/immunology/immunology.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: biota@onramp.net (Cynthia S. Smagula) Subject: Rasmol-related information Date: Sat, 22 Jun 1996 09:39:36 -0600 To: rasmol@noc1.oit.umass.edu Rasmol people- I wrote this partially in response to the posting about Rasmol in schools. This is a topic that I am interested in- I have not introduced myself to the list because I have a somewhat commercial interest in molecular-level web bioinformation, and don't want to appear to be advertising for myself. On the other hand, I would like to tell you about an information resource that I am compiling, because I feel that it may be a useful resource, extending the utility of Rasmol by linking it to the many related protein structural analytic tools, some of which are very easy to use (Molecules R US comes to mind). I spent several years with the structural biology group at HHMI in Dallas and keenly felt that structural information should be more widely available. So I was delighted to find Rasmol (and MAGE). I have spent the last year putting together a book entitled "BioInformation on the World Wide Web: An Annotated Directory for Molecular Biologists (http://www.biota.com/biota). The book is accompanied by URLinks software for direct linking to sites from within Netscape. One of the longest chapters is devoted to setting up interactive graphics viewers and to applications that use interactive display. Links to updated information (i.e., on enhanced versions and authoring) is available at an online companion site. I'm putting together the second edition now, and expect it will include about 1000 annotated sites of interest. This is not an AtoZ directory, but is hopefully a webtool itself. The goal is to make the web's vast repository of molecular analytic tools directly accessible to anyone with an online browser. If someone on this list is interested in obtaining a copy for review purposes, please let me know. I am interested in reaching students and educators at all levels, researchers, and libraries. Cynthia S. Smagula, Ph.D. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . BIOTA PUBLICATIONS Internet BioInformation publishers of BIOINFORMATION ON THE WORLD WIDE WEB http://www.biota.com/biota biota@onramp.net 214.733.7389 phone 214.857.8923 FAX ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Autostart script on Macintosh? Date: Mon, 24 Jun 1996 19:29:35 +0100 (BST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear Mac Users, > The RasMol 2.5 manual says that under unix, a file named .rasmolrc > can autostart a script. > But what about the Macintosh? I know that if the script file's signature > (creator and type) are set correctly, double-clicking on the script > will invoke RasMac and run the script. Alas there isn't yet a way to start an initialisation script from RasMac, other than by double clicking on the script to be run in the Finder. Note that the script file can be double clicked on whilst RasMac is running, i.e. after a file has already been loaded manually. This should apply the contents of the script to the current molecule. Is there a standard for storing personal or per-folder preferences on the Macintosh? I shall probably add support for running a "rasmol.ini" script file if one is found in the Mac's "preferences" folder. i.e. a per-machine initialisation script. I've also managed to track down and fix the bug that is causing scripts to stop after the first pause command in scripts that are specified when the program is started (for example, on the UNIX and MSDOS command lines). It appears I was closing the specified file at the end of the start-up code in RasMol, even when the script had paused and would need to be read later. > I haven't yet explored the software available to change the signature. I use the "Get File Info" option on the "File" menu of Apple's RezEdit. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Rasmol (and Internet) in Schools Date: Thu, 27 Jun 1996 12:34:59 -0500 (EST) To: rasmol@noc1.oit.umass.edu Clare sent this privately to Henry Brzeski in response to his posting, and kindly CC'd it to me. I thought it would be of some general interest to the list subscribership, so with Clare's permission I am forwarding it. (Following this, I'll post my views concerning 'commercials' on this list.) ------------------------------ From: Clare Sansom In response, mostly, to Henry Brzeski's post on "Rasmol in Schools"... I am a specialist in molecular graphics amd modelling, and have been a consultant on the Internet course "Principles of Protein Structure" (http://www.cryst.bbk.ac.uk/PPS2/) since last year. After rather more years than I care to mention as a postdoc (on both sides of the Atlantic) I am now negotiating a part time position at Birkbeck College (London), starting in September, developing teaching material in biochemistry and biophysics to be distributed over the Internet. For the rest of the time I will be working as a freelance consultant. I hope to specialise in the interface between the 'net and education/training, especially in the biological sciences and the pharmaceutical industry. I will be offering:- * HTML mark-up and web site construction * Training (in bioinformatics, the Internet and/or PC techniques) * Advice on hardware and software purchase * Technical writing & scientific journalism * Book illustration (especially molecular graphics) * Help with online conferences, and computer presentations at "real-life" conferences * The production of distance learning resources I have recently returned from a short sabbatical in Poznan, Poland, and I am interested in pursuing my links with Poland and central Europe in general; in fact, I hope to be able to go back to Poznan for a semester as a visiting lecturer. One of my developing interests is in the possibility of extending the techniques developed for the Principles of Protein Structure course to material for use in GCSE / "A" level (US high school) chemistry and biology. I would be very interested in knowing more about experiences with Rasmol in schools and colleges, and am even wondering whether it would be possible (or desirable) to apply for a grant to develop such material. [Of course, in an ideal world, my consultancy would be free to educational establishments - *particularly* schools - but this isn't an ideal world, and I still have a mortgage to pay...] If anyone would like to discuss these ideas further, I (ClareS) and Henry (HenryB) would be very happy to meet in BioMOO (http://bioinfo.weizmann.ac.il). And, if anyone *does* know of any openings for freelance computer consultants in the areas mentioned above, please feel free to email me directly. Thank you very much, Best regards, Dr Clare Sansom Department of Biochemistry and Molecular Biology University of Leeds ces@bmb.leeds.ac.uk (until end Aug '96) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html >Immunology: http://www.bio.umass.edu/immunology/immunology.html 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: Commericals? Date: Thu, 27 Jun 1996 12:51:20 -0500 (EST) To: rasmol@noc1.oit.umass.edu Do commercials belong on the RasMol email list? Certainly not if they are blatantly commercial, repetitive, or annoying to the subscribers. In general, I have no objection to truly informative messages which have commercial content. I think the policy which the NSF published a few years ago, when they owned the US Internet backbone before it was commercialized, is still a good guideline for lists such as this. Unfortunately I can't find a copy, and they've taken it off the net. However, here is a condensed paraphrase of that policy I made for another email list which I manage: In accord with the 'Acceptable Use Policy' of the US National Science Foundation's NSFNET, the purpose of the list is to support research and education. For-profit use of the list, such as for advertising, is prohibited, except for occasional brief announcements of new products or services relevant to the topic of the list. Subscribers with commercial affiliations are welcome, as is their participation in educational/research discussions, including such discussions which may concern their commercial products. Other subscribers to this list should feel free to voice their opinions on this issue. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html >Immunology: http://www.bio.umass.edu/immunology/immunology.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Christoph Weber" Subject: Re: Commericals? Date: Thu, 27 Jun 1996 16:38:56 -0700 To: rasmol@noc1.oit.umass.edu I have no problem with commercial postings that conform to the guidelines which Eric posted. Preferably a commercial post would be an answer to a question or a follow-up in a thread, or would have some other very obvious connection to Rasmol and its function/use/problems/whatever. Christoph -- | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-554-7283 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: export resolution from Rasmac Date: Tue, 2 Jul 1996 16:12:55 +0100 (BST) To: Jing Zhou cc: rasmol@noc1.oit.umass.edu Dear Jing, > I try to use Rasmac to make colorful transparency printed from an HP > inkjet. I use the export-gif function. Everything is fine except the > resolution. It's always 72dpi, which looks not good when printed out. > Is there any method to increase the export resolution besides making a > large picture and using a graphic application to reduce its size while > increasing its resolution? Thanks very much for your e-mail. Unfortunately, raster images generated by RasMol are currently limited by the screen resolution. Hence your proposal to expand the screen, and then reduce the image in a graphics application is currently the only option. The exception to the above rule is images produced in Vector Postscript "vectps" format. These output files have the advanatge of being generated at the printer's resolution, but the disadvantage of not supporting all of RasMol's representations. The 72dpi problem is currenly being worked on. The principal problem is that 300 or 600dpi would require many megabytes more memory, unless the image is generated a patch at a time... 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Cross-eyed or Wall-eyed? Date: Wed, 03 Jul 1996 14:01:47 -0500 (EST) To: rasmol@noc1.oit.umass.edu I'm preparing some figures with RasMol which I hope will be published (on paper). These are stereo pairs. Should they be cross-eyed or wall-eyed? (Search for 'stereo viewing' in the 'current' history file for this list, and you'll get Andrew Coulson's excellent introduction to this topic posted June 19.) Is there a convention? Or a good reason for preferring one over the other? I find it easier to view cross-eyed than wall-eyed (where I find a mirror-viewer headset helpful), so I was planning to use the former. Then I tried to show an example to one of my students who said he is unable to cross his eyes. (How common is this?) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html >Immunology: http://www.bio.umass.edu/immunology/immunology.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Pedro M Coutinho Subject: Re: Cross-eyed or Wall-eyed? Date: Wed, 03 Jul 1996 14:38:51 CDT To: rasmol@noc1.oit.umass.edu Cc: pedro@iastate.edu Hi everybody! Eric Martz wrote: > I'm preparing some figures with RasMol which I hope will be published > (on paper). These are stereo pairs. Should they be cross-eyed or > wall-eyed? (Search for 'stereo viewing' in the 'current' history file for > this list, and you'll get Andrew Coulson's excellent introduction to this > topic posted June 19.) Is there a convention? Or a good reason for > preferring one over the other? I find it easier to view cross-eyed than > wall-eyed (where I find a mirror-viewer headset helpful), so I was planning > to use the former. Then I tried to show an example to one of my students > who said he is unable to cross his eyes. (How common is this?) Most of the articles I see are wall-eyed (or parallel-eyed). This allows the images to be seen with steroscopes (as used in the past to view aerial steroscopic images), and I think that mirror-viewers can also view this option. However, I still find some articles where the stereo images are cross-eyed, but these are more the exception than the rule (I think...). Personally, I can only see wall-eyed without a viewer, but whenever I have to look at a cross-eyed image I still can see the mirror image and so get some depth perception. The option I prefer is the sets of three images - left/right/left - as found in the journal Protein Engineering. If you are a wall-eyed person you look at the two images on the left, if you are a cross-eyed person look at the two in the right. This accommodates everybody. The images in both extremities are then the same!! I have not worked with Rasmol to produce images for publication but the rules learned with other software can be applied here. I usually produce single postscript images (vectps mode in Rasmol) with a 6-7 degrees difference on the y axis. I patch them togheter and manipulate the postscript code to reduce their size and place them side by side with the centers separated by approximately 6.5 centimeters. The results can be great!! Only some basic knowledge of postscript is needed to do this! Until recently this was the only way to produce the three-images wall-eyed/cross-eyed stero picture... Lately I tend to do this with Molscript. But, a more complete Molscript export mode in Rasmol could certainly produce Molscript scripts needing minimal manipulation to generate the desired stereo images. That's all! I hope this is useful for someone!... :-) Pedro C. --------------------------------- H2N-CH-CO-NH-CH-CO-...-NH-CH-COOH -- Pedro M. Coutinho - Graduate Student \ \ \ IOWA STATE UNIVERSITY R1 R2 Rn Department of Chemical Engineering Phone: 1-515-294-9370 2114 Sweeney Hall Fax: 1-515-294-2689 Ames, IA 50011-2230 E-mail: pedro@iastate.edu U.S.A. URL: http://www.public.iastate.edu/~pedro/ ---------------------------------------------------------------------- rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Cross-eyed or Wall-eyed? Date: Thu, 04 Jul 1996 12:24:20 -0500 (EST) To: steipe@lmb.uni-muenchen.de Cc: a.coulson@ed.ac.uk (ANDREWC@srv0.bio.ed.ac.uk Andrew Coulson/RasMol), Dear Boris: Thank you for that very good trick for wall-eyed stereo viewing (starting close to the image)! It is a big help. And thanks for your opinion on the convention for paper publication. I have not put any stereo pairs in the web gallery yet, but I plan to do so in the future (and anyone else should feel free to contribute some). Then I plan to combine your explanation with Andrew Coulson's in a document I'll make available for novices at the web gallery. It occurs to me, however, that there is one very large advantage of cross-eyed images for CRT screen viewing (as in the web gallery). In order to make the two images close enough together for wall-eyed viewing (yet still non-overlapping), the image must be made small, and therefore low resolution. Consequently, in for example a cartoon representation, turns may go to one pixel and lose clarity. Cross-eyed pairs can be made full-screen, much higher resolution, and still easily viewed in stereo for those of us who can cross our eyes. Since printed images can be much higher resolution than a screen, the reasons you gave seem compelling for using the wall-eyed convention for printed images. I also tried using overlapping red and blue images (with the molecule loaded twice in UCB-RasMol) with red and blue glasses, but (i) the inexpensive glasses I have don't adequately filter out the unwanted image, and (ii) UCB-RasMol attempts to put one image behind the other rather than turning on both colors in overlapping regions. Presumably the latter problem could in principle be solved with a user option in a future version (something for your list, Marco?). Does anyone know a source of red/blue glasses that work well with CRT screen phosphor colors? Of course, the red/blue method obviates the large advantage of being able to use colors to distinguish substructures of interest. In conclusion, FOR CRT SCEEN VIEWING, all of the above three methods have serious limitations. The cross-eyed method allows high resolution, but is fatiguing and not available to all. The wall-eyed method is less fatiguing and available to all, but suffers from low resolution. The red/blue method loses the option of coloring substructures (and can't be implemented in RasMol yet). /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu >Free molecular visualization: http://www.umass.edu/microbio/rasmol >Flow cytometry: http://www.bio.umass.edu/mcbfacs/flowhome.html >Immunology: http://www.bio.umass.edu/immunology/immunology.html Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: MDL chime Date: Fri, 05 Jul 1996 13:20:37 +0100 To: rasmol@noc1.oit.umass.edu Did you see the article about MDL and GLAXOWellcome in Nature Biotechnology [Nature Biotechnology Vol 14(6) p 690 (1996)]. From the way the article is written it sounds as if GLAXOWellcome are unhappy with MDL's use of Roger's rasmol code. It makes interesting reading. h Henry Brzeski Dept of Bioscience and Biotechnology The Todd Centre University of Strathclyde 31 Taylor Street GLASGOW G4 0NR 0141-552 4400 extn 3727 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime premature expiration fixed Date: Sun, 07 Jul 1996 15:50:47 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: tim@mdli.com I just found out that there was a bug in the Chime released in May (at least the Windows 3.1 version). It announced that it would expire July 31st, but it actually stopped working July 1st. There is a newer version availble from www.mdli.com which fixes this. Unfortunately, it has a new bug (Windows 3.1 version) which causes the top portion of the image to be corrupted. Tim Maffett of MDLI, who is in charge of Chime development, subscribes to this list, and will hopefully keep us informed. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: <57049.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: More RasMol/Chime Stuff Date: Mon, 8 Jul 1996 11:48:06 -0400 (EDT) To: rasmol@noc1.oit.umass.edu, emartz@microbio.umass.edu Cc: tim@mdli.com Two pages that display (RasMol/Chime) the intermediates in glycolysis and the TCA cycle are available. Selected features of each reaction in the pathways are highlighted in separate substrate and product frames. These two pages and some others that might be useful for teaching biochemistry are listed at: http://info.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Problem with Chime 0.9a Win3.1 fixed Date: Mon, 08 Jul 1996 23:39:08 -0700 To: rasmol@noc1.oit.umass.edu Cc: emartz@marlin.bio.umass.edu There was indeed a problem with the Windows 3.1 version of Chime released on our web site last week. This version had a bug (caused by a compiler optimization (thanks microsoft!)) which caused 'smearing' of the top part of the molecule display. We have released a new version of the Windows 3.1 Chime which fixes this problem. As a bonus the spelling errors in the menus, introduced a month or so ago, have also been fixed. This new windows 3.1 version of chime can be downloaded from our web page: http://www.mdli.com/chemscape/chime/download.html Currently only the non-installer version is available. This archive is only a little over 200k, but it does require some "user intervention" to install. Details are available on the download page listed above. We hope to have the (larger) automatic installation versions Chime available within a week. This version of Chime does not expire until 1997. We will have released the final 1.0 version of Chime long before then. The final 1.0 version of Chime will continue to have a free license for academic and personal home use. I apologize to those of you that downloaded the previous version only to discover the smearing bug! -tim Tim Maffett tim@mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. ++++------+------+------+------+------+------+------+------+------+------+ From: th@mrc-cpe.cam.ac.uk (Tim Hubbard) Subject: Re: Problem with Chime 0.9a Mac Date: Tue, 9 Jul 1996 14:51:53 +0000 To: rasmol@noc1.oit.umass.edu Dear Chime, The new plug in for macintosh (0.9) used with netscape gold 3b5 does not seem to recognise the mime type chemical/x-pdb. Is this a bug? The same pages seem to work fine with 0.8b2 under netscape 2.02 and other molecule types do load correctly with the new plug-in with 3b5. Thanks, Tim Hubbard ------------------------------------------------------------------------------ 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/ ------------------------------------------------------------------------------ available ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: The *correct* Windows 3.1 0.9c version of Chime is now Date: Tue, 09 Jul 1996 10:05:08 -0700 To: rasmol@noc1.oit.umass.edu I am *very* sorry, but due to a mistake on our webmaster's part the correct files were *NOT* available for download until early this morning. I should have verified the availability of the file before sending my message, and I errored by not doing so. The corrected, bug fixed, version of Chime 0.9c for Windows 3.1 is now available on our website: http://www.mdli.com/chemscape/chime/download.html This time I downloaded and installed this version myself to verify that it is the correct version. Again, we apologize for any inconvenience that we may have caused for many of you. -tim Tim Maffett tim@mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Problem with Chime 0.9a Mac Date: Tue, 09 Jul 1996 10:26:43 -0700 To: rasmol@noc1.oit.umass.edu At 02:51 PM 7/9/96 +0000, Tim Hubbard wrote: >Dear Chime, > >The new plug in for macintosh (0.9) used with netscape gold 3b5 does not >seem to recognise the mime type chemical/x-pdb. Is this a bug? The same >pages seem to work fine with 0.8b2 under netscape 2.02 and other molecule >types do load correctly with the new plug-in with 3b5. > >Thanks, I just downloaded Navigator 3.0 Beta 5 and verified that the 0.9a version of Chime *is* working for all of the different MIME types on my PowerMac. I suspect that the problem you are seeing may be caused by a new feature of Navigator in 3.0 which allows the user to enable/disable EACH of the different MIME types a plugin supports. This is a feature we (and others) requested to allow users to selectively choose helper apps, such as Rasmol, for some MIME types, and still use a plug for other types. (Netscape still needs to work on this in my opinion because it would be nice to be able to specify a helper app for all NON embedded MIME data. This would allow Chime to operate for pages designed for it, but still invoke Rasmol when following a link to a pdb file (for example)). If you go to the Options->General Preferences menu item you will bring up a dialog. Select the 'Helpers' tab on this dialog, and scroll down through the list of MIME types until you find the chemical/... MIME types. For each MIME type you can specify a helper application to handle it or a plugin (Chime?). There are several other options I have not explored entirely. I have found that some of the chemical MIME types are set to 'Unknown: Prompt User' after a new installation instead of 'Chemscape Chime'. If this fails to solve your problem be sure to let me know, and we will certainly work to get to the bottom of it. Please feel welcome to report any other problems you encounter, -tim Tim Maffett tim@mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. > >Tim Hubbard > >------------------------------------------------------------------------------ >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/ >------------------------------------------------------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: th@mrc-cpe.cam.ac.uk (Tim Hubbard) Subject: Re: Problem with Chime 0.9a Mac Date: Wed, 10 Jul 1996 10:07:46 +0000 To: rasmol@noc1.oit.umass.edu Dear Tim, > I just downloaded Navigator 3.0 Beta 5 and verified that the 0.9a >version of Chime *is* working for all of the different MIME types >on my PowerMac. it may not be important, but I am running this on a PB540c (68040 machine) Also I am running Netscape GOLD > I suspect that the problem you are seeing may be caused by a new feature >of Navigator in 3.0 which allows the user to enable/disable EACH of >the different MIME types a plugin supports. This is a feature we (and others) >requested to allow users to selectively choose helper apps, >such as Rasmol, for some MIME types, and still use a plug for other types. >(Netscape still needs to work on this in my opinion because it would >be nice to be able to specify a helper app for all NON embedded MIME >data. This would allow Chime to operate for pages designed for it, but >still invoke Rasmol when following a link to a pdb file (for example)). > > If you go to the Options->General Preferences menu item you will >bring up a dialog. Select the 'Helpers' tab on this dialog, and >scroll down through the list of MIME types until you find the >chemical/... MIME types. For each MIME type you can specify a helper >application to handle it or a plugin (Chime?). There are several other >options I have not explored entirely. > I have found that some of the chemical MIME types are set to 'Unknown: >Prompt User' after a new installation instead of 'Chemscape Chime'. In fact I tried to select this option (Helpers) and the machine crashed - this happened a number of times - sometimes it just refuses to select this tab. Maybe this is a netscape gold bug or something that has happened when I installed chime. In fact, the following occurs to me - since I think netscape shares its preferences file, what happens if I install chime 0.8b2 under netscape 2.02 and then later 0.9a under netscape gold 3.0b5 - does some of the mime stuff get written twice into the same netscape preference file? Sorry - haven't been able to test any of this - just letting you know in case this sounds a likely explaination for the problem best wishes, Tim p.s. what is the ETA for the SGI version? ------------------------------------------------------------------------------ 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/ ------------------------------------------------------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: French RasMol Date: Wed, 10 Jul 1996 14:55:00 -0500 (EST) To: rasmol@noc1.oit.umass.edu I forward this with the permission of Naoum Salame. In case it hasn't been mentioned, Jose Miguel Fernandez-Fernandez has plans to translate some scripts (at least) into Spanish. I've inserted a comment in []. -Eric Martz ------------------------------ Mon, 8 Jul 1996 From: Naoum Salame To: emartz@microbio.umass.edu Dear Eric, [snip] 1 - Two years ago, Roger Sayle allowed us to distribute RASMOL without charge to french schools and universities. We first translated RASMENU into French, and we worked mainly in order to design educational applications according to the French curricula at the Lycee (students 16-18 years old). [Eric adds: RASMENU is a front end for RasWin which allows many command line window commands to be initiated from menus, increases the flexibility of the existing menus, and provides a 'spin' command. RASMENU runs only under Windows with 16-bit RasWin. It is available from ftp.dcs.ed.ac.uk] 2 - Last december, we published a paper on RASMOL educational interest in a french biology teachers review (Association of Biology and Geology Teachers Bulletin). 3 - We are now about to disseminate a teacher document with the the current version of the software (this will be possible by the end of September). 4 - We are also planning for a specific server offering biology and geology freeware and public databases. For the moment, this server is under construction, but you can connect to it at the following address: www.inrp.fr and from there to the home page of bio-geo server. Presently are available different links concerning RASMOL, especially to the UMass RasMol Home Page, as well as the scripts there. We intend to provide on this server all the texts and examples we have prepared as companions of RASMOL. Sincerely Naoum Salame Institut National de Recherche Pedagogique 91, rue Gabriel Peri 92120 MONTROUGE FRANCE Tel.: (033) 1 46128712 Fax : (033) 1 46128701 email : salame@inrp.fr /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: ryan david Subject: standard atom color Date: Wed, 10 Jul 1996 14:48:13 -0400 To: rasmol@noc1.oit.umass.edu Members: I am curious as to the coloric trend of atoms. Was there ever a set standard? It seems to me, for example, that red is always Oxygen, just as yellow is Sulfur. Was this a set agreement by the scientific community, or just a popular trend? Thanks, Ryan David ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: History files repaired/working again Date: Wed, 10 Jul 1996 23:11:13 -0400 To: rasmol@noc1.oit.umass.edu The history of this email list, accessible from the RasMol Home Page web site, is now working properly again. 8 messages which were broadcast to the list were missing from the history files. These have been restored (primarily on the topics of stereo viewing and Chime). If you want to review them, look at messages in the range from June 27 (when the history mechanism broke) thru July 8 (when it was fixed). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Problem with Chime 0.9a Mac Date: Thu, 11 Jul 1996 11:07:07 -0700 To: rasmol@noc1.oit.umass.edu At 10:07 AM 7/10/96 +0000, Tim Hubbard wrote: >Dear Tim, > >> I just downloaded Navigator 3.0 Beta 5 and verified that the 0.9a >>version of Chime *is* working for all of the different MIME types >>on my PowerMac. > >it may not be important, but I am running this on a PB540c (68040 machine) > >Also I am running Netscape GOLD > >> I suspect that the problem you are seeing may be caused by a new feature >>of Navigator in 3.0 which allows the user to enable/disable EACH of >>the different MIME types a plugin supports. This is a feature we (and others) >>requested to allow users to selectively choose helper apps, >>such as Rasmol, for some MIME types, and still use a plug for other types. >>(Netscape still needs to work on this in my opinion because it would >>be nice to be able to specify a helper app for all NON embedded MIME >>data. This would allow Chime to operate for pages designed for it, but >>still invoke Rasmol when following a link to a pdb file (for example)). >> >> If you go to the Options->General Preferences menu item you will >>bring up a dialog. Select the 'Helpers' tab on this dialog, and >>scroll down through the list of MIME types until you find the >>chemical/... MIME types. For each MIME type you can specify a helper >>application to handle it or a plugin (Chime?). There are several other >>options I have not explored entirely. >> I have found that some of the chemical MIME types are set to 'Unknown: >>Prompt User' after a new installation instead of 'Chemscape Chime'. > >In fact I tried to select this option (Helpers) and the machine crashed - >this happened a number of times - sometimes it just refuses to select this >tab. Maybe this is a netscape gold bug or something that has happened when >I installed chime. The fact that selecting this tab is causing your machine to crash indicates to me that this must be some kind of Netscape Navigator 3.0Gold Beta 5 problem. This works for me, so perhaps Netscape has a 68040 specific problem. I am sure that installing Chime has nothing to do with this problem, and my removing Chime from the plugins directory you should be able to rule Chime involvement out. > >In fact, the following occurs to me - since I think netscape shares its >preferences file, what happens if I install chime 0.8b2 under netscape 2.02 >and then later 0.9a under netscape gold 3.0b5 - does some of the mime stuff >get written twice into the same netscape preference file? I am sure that having two versions of Chime installed will not cause problems. Chime does not have a settings file of it's own currently, and all of the supported MIME types are the same in the two versions you list. It is might be possible the two versions of netscape are interferring with one another, but on my powermac I have all versions since 2.0 installed and do not see problems when running the different versions. I will forward your message to our mac group and see if we have a PowerBook 540c that we can try NetNav Gold 3.0B5 out on. I will also ask them to test it with Chime if they can get it to work by itself. > >Sorry - haven't been able to test any of this - just letting you know in >case this sounds a likely explaination for the problem > >best wishes, > >Tim I am not sure that our discussion is of general benefit to the subscribers of the rasmol mailing list now that it is getting into seemingly machine specific netscape problems, etc. Feel free to email me directly at tim@mdli.com if you would like. > >p.s. what is the ETA for the SGI version? Are internal deadline is early August, but I may be sooner.. or later. We have had a number of unexpected problems on the other platforms which have delayed the SGI version. I want to assure you that we are very anxious to get it done though... > >------------------------------------------------------------------------------ >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/ >------------------------------------------------------------------------------ -tim ++++------+------+------+------+------+------+------+------+------+------+ From: Joerg Gampfer Subject: potential surface Date: Mon, 15 Jul 1996 11:52:29 +0200 (MDT) To: rasmol@noc1.oit.umass.edu hello !! my questions is concerning the creation of potential surfaces of proteins. how does the programm calculate the "color dots potential" - is that depending on the information in the original .pdb file. the "color charge" command does not always color the residues in the right way - how can i change that ?? is there a possibility to create hydrophobic or hydrophlic surfaces ?? thanks alot for help Joerg Gampfer, Biozentrum Wuerzburg, Germany ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: potential surface Date: Mon, 15 Jul 1996 15:04:44 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: Joerg Gampfer Dear Joerg, > my questions is concerning the creation of potential surfaces of proteins. > how does the programm calculate the "color dots potential" - is that > depending on the information in the original .pdb file. the "color charge" > command does not always color the residues in the right way - how can i > change that ?? Thanks very much for your e-mail. Unfortunately, the "colour dots potential" command is not very sophisticated. It assumes that the partial charge of each atom is stored in the b-factor column of the PDB file. It then uses this value in Coulomb's law with a constant dielectric to produce a potential value for each dot in a RasMol dot surface. Unfortunately, most PDB files contain true anisotropic b-factor values in the b-factor/temperature field. Hence the charges will need to be inserted from another program. If there is sufficient demand, I'll post one of my UNIX/MSDOS programs, "pdbcharge", for setting the b-factor field of a protein PDB file to either the formal, amber or charmm charge on each atom. I suspect there are much better programs available on the WWW. The alchemy format file "asprin.alc" in the RasMol distribution does include partial charges and can be used to generate a potential coloured dot surface, i.e. http://www.umass.edu/microbio/rasmol/sayle3.htm Although the Coulombic approximation is reasonable for small molecules, for electrostatics around proteins Poisson-Boltzmann calculations such as those performed by GRASP, http://tincan.bioc.columbia.edu/Lab/grasp/, are much more accurate. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: standard atom color Date: Mon, 15 Jul 1996 19:00:55 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: ryan david Dear All, > I am curious as to the coloric trend of atoms. Was there ever a set > standard? It seems to me, for example, that red is always Oxygen, just as > yellow is Sulfur. Was this a set agreement by the scientific community, > or just a popular trend? If anybody knows of an official standard, for example IUPAC or ACM recommendation, please let me know. However, my understanding is that the commonly used colour schemes are derived from the original CPK plastic models developed by Corey, Pauling and Kultun. The exception to this rule is that carbon, which is conventionally black, is changed by molecular graphics programs to avoid clashing with the ubiquitous black background (and also to allow diffuse shading, c.f. "background white", "colour black","spacefill"). This then begs the question what colour should carbon be?... MSI/Biosym make carbon "green" (which clashes with the halogens) and Tripos occasionally make carbon "white" (which clashes with hydrogen which they then make cyan). RasMol takes the popular option of making carbon grey (which probably should clash with metals). I'd be interested in hearing of some of the variations of these colour schemes in use. 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 == tripos.spt =========================================================== select carbon colour white select hydrogen colour cyan ========================================================================= "Re: standard atom color" (Jul 15, 7:00pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christoph Weber" Subject: Re: standard atom color Date: Mon, 15 Jul 1996 12:12:02 -0700 To: rasmol@noc1.oit.umass.edu Dear all, in response to Roger Sayle's posting, here are my opinions: > MSI/Biosym make carbon "green" (which clashes with the halogens) and > Tripos occasionally make carbon "white" (which clashes with hydrogen > which they then make cyan). RasMol takes the popular option of making > carbon grey (which probably should clash with metals). I do see why a commrecial software vendor may want to choose a strong color as opposed to grey for carbon. It certainly adds recocgnition value to their product. However, from a scientific point of view it is much to obtrusive, given the chemical/biological importance of functional groups. White carbon and cyan hydrogens is even worse, as it flies in the face of the de facto standard and makes life much more difficult than it should be. Grey carbon as used in Rasmol is effective and simple. Potential clashes with metals can be alleviated by adding color to the metal and/or changing the reflectance of its surface. Also, they will have different radii, which can be overemphasized for clarity. Many times, a metal will need to be drawn as CPK, while the rest of the molecule may be more schematic. My 2 cts. Christoph -- | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-554-7283 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Double bonds Date: Tue, 23 Jul 1996 23:42:08 -0400 To: rasmol@noc1.oit.umass.edu I am having difficulty getting RasWin 2.6 beta-2 to display any double (or triple) bonds. On February 7, 1996, Roger Sayle stated (see history for this list) that this version should display multiple bonds provided that CONECT records in the PDB file indicate more bonds than atoms in the molecule. I downloaded oleate from KLOTHO but have no luck, even after 'set bonds on'. However, either I don't understand the format of CONECT records (highly likely) or there are errors in the oleate PDB file. Are all atoms in a record connected to their neighbors? Or are only pairs connected (but then what is the 5th position for?)? For example, atom 1 appears to be connected to atom 5 in the last one of these records: CONECT 1 2 3 4 0 CONECT 2 1 0 0 0 CONECT 3 1 0 0 0 CONECT 4 1 5 21 22 This makes no sense since carbon 4, not carbon 5, is proximal to carbon 1. However the double bond between atoms 1 (C) and 2 (O) is indicated correctly. Also, a double bond occurs between carbons 11 and 12, but I see no indication of this in the CONECT records: CONECT 9 8 10 31 32 CONECT 10 9 11 33 34 CONECT 11 10 12 35 0 CONECT 12 11 13 36 0 CONECT 13 12 14 37 38 CONECT 14 13 15 39 40 Can someone please direct me to (or provide) a simple PDB file for which RasMol can display double bonds? (I also got some alkenes and alkynes from David Woodcock's site at Okanagan, but they lack any CONECT records.) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: Lac repressor-operator interactions Date: Wed, 24 Jul 1996 08:34:44 +0100 To: rasmol@noc1.oit.umass.edu My interest is in how gene regulatory proteins bind specificially to their DNA recognition sites. There is a large amount of data now to help understand this DNA-protein interaction and I have used some to generate a script to show how the lac repressor binds specifically to its DNA operator. Links to this script can be found in Eric's list of scripts in http://klaatu.oit.umass.edu:80/microbio/rasmol/ and it would be best to follow this route if you need any explanations on what to do. If you are an old hand at this game then you can go directly to http://klaatu.oit.umass.edu:80/microbio/rasmol/scrip_mz.htm#lacrepin. As ever, comments and suggestions welcome. h Henry Brzeski Dept of Bioscience and Biotechnology The Todd Centre University of Strathclyde 31 Taylor Street GLASGOW G4 0NR 0141-552 4400 extn 3727 References: <9607240342.AA09245@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Double bonds Date: Wed, 24 Jul 1996 07:55:09 -0400 (EDT) To: rasmol@noc1.oit.umass.edu The pdb files from Klotho (for small molecules) have CONECT lines that specify far too many bonds...as far as RasMol is concerned. I have used them as follows: I open the file with RasMac; save it as a RSML file (this deletes all of the CONECT lines); then I add the CONECT lines I want to the RSML file: and save it as TEXT (or convert it back into RSML as above. Here's an example of a RasMol-massaged Klotho file for fumarate: Header Saved as...from RasMac 2.6; CONECT edited 7/2/96. COMPND Fumarate. ATOM 1 C 1 1.608 0.736 0.700 1.00 0.00 ATOM 2 O 1 2.812 0.584 0.556 1.00 0.00 ATOM 3 O 1 1.176 1.600 1.524 1.00 0.00 ATOM 4 C 1 0.660 -0.084 -0.080 1.00 0.00 ATOM 5 C 1 -0.660 0.084 0.080 1.00 0.00 ATOM 6 C 1 -1.608 -0.736 -0.700 1.00 0.00 ATOM 7 O 1 -2.812 -0.584 -0.556 1.00 0.00 ATOM 8 O 1 -1.176 -1.600 -1.524 1.00 0.00 ATOM 9 H 1 1.028 -0.816 -0.780 1.00 0.00 ATOM 10 H 1 -1.028 0.816 0.780 1.00 0.00 TER 11 1 CONECT 1 2 3 4 0 CONECT 4 0 5 9 0 CONECT 5 4 6 10 0 CONECT 6 0 7 8 0 END The only double bond specified is between atomno=4 and atomno=5. This does not solve all problems, however; this double bond shows up on an embedded image on a Netscape page when selected from a Chime "Option" menu list, but I cannot get RasMac to show it. I've tried several variations of the "set bonds on" command described in the 2.6 Release Notes without results. BTW A second problem with some of the Klotho files for RasMol viewing is that after the spurious CONECT lines are removed (by saving as RSML), RasMol "decides" to make its own spurious bonds between some phosphorus atoms in nucleotides (maybe it thinks closely-positioned pentavalent atoms should be connected with five bonds). -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: wfreeman@uic.edu (Wade Freeman) Subject: Re: Double bonds Date: Wed, 24 Jul 1996 07:38:35 -0800 To: rasmol@noc1.oit.umass.edu I have had the same success in displaying double bonds, namely zero, and would like some help as well. I'm using the Rasmac2.6b. I *can* respond to the question of the connectivity specified by "CONECT 4 1 5 21 22" in the example cited by Eric Martz. This record means that atom 4 is bonded to Atoms 1, 5, 21, and 22. I base this on a reading of the appended extract from a Brookhaven publication. Wade Freeman ***Taken from description of PDB records**** CONECT Overview The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues (see Appendix 4 for the list of standard residues). These records are generated by the PDB. Record Format COLUMNS DATA TYPE FIELD DEFINITION ---------------------------------------------------------------------------- ----- 1 - 6 Record name "CONECT" 7 - 11 Integer serial Atom serial number 12 - 16 Integer serial Serial number of bonded atom 17 - 21 Integer serial Serial number of bonded atom 22 - 26 Integer serial Serial number of bonded atom 27 - 31 Integer serial Serial number of bonded atom 32 - 36 Integer serial Serial number of hydrogen bonded atom 37 - 41 Integer serial Serial number of hydrogen bonded atom 42 - 46 Integer serial Serial number of salt bridged atom 47 - 51 Integer serial Serial number of hydrogen bonded atom 52 - 56 Integer serial Serial number of hydrogen bonded atom 57 - 61 Integer serial Serial number of salt bridged atom Details * Intra-residue connectivity within non-standard (HET) residues (excluding water) is presented on the CONECT records. * Inter-residue connectivity of HET groups to standard groups (including water) or to other HET groups are represented on the CONECT records. * Disulfide bridges specified in the SSBOND records have corresponding CONECT records. * Hydrogen bonds and salt bridges also have CONECT records. * No differentiation is made between donor and acceptor for hydrogen bonds. * No differentiation is made between atoms with excess negative or positive charge. * Atoms specified in the connectivity are presented by their serial numbers as found in the entry. * All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record. * If more than four fields are required for non-hydrogen and nonsalt-bridge bonds, a second CONECT record with the same atom serial number in columns 7 - 11 will be used. * These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order. * The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11. * For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional. * For hydrogen bonds, when the hydrogen atom is present in the coordinates, PDB generates a CONECT record between the hydrogen atom and its acceptor atom. Verification/Validation/Value Authority Control Connectivity is checked for unusual bond lengths. Relationships to Other Record Types CONECT records must be present in an entry that contains either non-standard groups or disulfide bonds. Example 1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 CONECT 1179 746 1184 1195 1203 CONECT 1179 1211 1222 CONECT 1021 544 1017 1020 1022 1211 1222 1311 Known Problems Only five digits are available for the atom serial number, but some structures have already been received with more that 99,999 atoms. Changing the field length would make earlier entries incorrect. CONECTs to atoms whose coordinates are not in the entry (e.g., symmetry-generated) are not given. ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Re: Double bonds Date: Wed, 24 Jul 1996 14:35:24 -0500 To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Will, I don't have the fumarate problem you describe with the unix version of Rasmol, but I have encountered wierdo phosphoryl groups from Brookhaven PDB files (oxygens linked together to form triangular bonds, pretty startling). Everything we put up we check pretty carefully for accuracy. We're not perfect, obviously, but something that egregious we probably would have spotted. [Well, I sure hope so!] However, we sure don't test browser/viewers on multiple platforms or combinations so I can't guarantee what one might see. Cheers, Toni "Double bonds" (Jul 23, 11:42pm) References: <9607240342.AA09245@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: Double bonds Date: Wed, 24 Jul 1996 17:51:36 -0400 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu Hi all, The PDB file format has historically not had provisions for specifying bond order (bonds either, for that matter). So, don't blame this one on Roger, he's just doing his best to make a silk purse out of a sow's ear. CONECT records in the PDB model have no intended semantic as what kind of bonds are used, and counting the number of instances of the same CONECT records to set a double bond is not a standard interpretation of the PDB spec. That RasMol is supposed to find redundant CONECT records and increase bond order based on the number of times it sees a CONECT record is clear from my inspection of the C code. Roger may have more to say on this. According to the PDB spec these CONECT records are *supposed* to be redundant (but are never validated to be such): "* The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11. " The only semantic that would not in conflict with the PDB spec would be to specify a double bond THREE times in the connect record, and FOUR times for a triple bond... But let's leave this alone - as none of this ever gets validated anyway. I have added a PDB file at the end that works. The best solution is to use a validated data file format that does include explicit bonding information, like ASN.1 or mmCIF. However I must confess that after seeing a DNA-protein complex in RasMol rendered with all the double bonds on (my test version of RasMol that reads ASN.1 MMDB records), it looks like there is too much information onscreen. For the small-molecule stuff, double bonds are desirable, but after looking at looking at a few larger structures with all the double-bonds on, I prefer them off. I will announce to the list when and where you can get ASN.1-aware versions of RasMol. Unfortunately it looks like the Win16 compile is not resolvable, but anyone with Win3.1 on a 386 can upgrade to be able to use Win32's. Chris Hogue. NCBI --------------- This modified version works for me on RasMol2.6 for SGI and on Win32. I have repeated the CONECT records for ATOM's 1 and 6, specifying their bonds to the Oxygens, for illustration. COMPND Fumarate. ATOM 1 C 1 1.608 0.736 0.700 1.00 0.00 ATOM 2 O 1 2.812 0.584 0.556 1.00 0.00 ATOM 3 O 1 1.176 1.600 1.524 1.00 0.00 ATOM 4 C 1 0.660 -0.084 -0.080 1.00 0.00 ATOM 5 C 1 -0.660 0.084 0.080 1.00 0.00 ATOM 6 C 1 -1.608 -0.736 -0.700 1.00 0.00 ATOM 7 O 1 -2.812 -0.584 -0.556 1.00 0.00 ATOM 8 O 1 -1.176 -1.600 -1.524 1.00 0.00 ATOM 9 H 1 1.028 -0.816 -0.780 1.00 0.00 ATOM 10 H 1 -1.028 0.816 0.780 1.00 0.00 TER 11 1 CONECT 1 2 3 4 0 CONECT 1 2 3 0 0 CONECT 4 0 5 9 0 CONECT 5 4 6 10 0 CONECT 6 0 7 8 0 CONECT 6 0 7 8 0 END ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Double bonds ONLY Date: Thu, 25 Jul 1996 10:09:48 -0400 To: rasmol@noc1.oit.umass.edu Regarding double bonds, further tests reveal an important difference between 2.6 beta-1 and beta-2, and one which is not mentioned in the update document. In order to show double bonds, 2.6 beta-1 requires that every bond for the entire molecule be specified in CONECT records. Thus, the deletion of just one of the carbon-to-hydrogen bonds causes beta-1 to stop showing double bonds. (As stated in Roger's documentation, beta-1 defaults to 'set bonds off' so must be explicitly told to display them with 'set bonds on'; beta-2 defaults to 'set bonds on'.) However, beta-2 displays double bonds when they are the ONLY bonds given in the CONECT records! Thus, it becomes easy to show the double bonds in any (small) molecule by adding the few CONECT records needed by hand, using a text editor, to the PDB file. (You can click on the relevant atoms and have RasMol report their numbers, while you enter the CONECT records in another window.) Also, it turn out that you do not need two separate CONECT records for a double bond; the second atom can be specified twice in the same record. For example, in the case of the fumarate PDB provided by Chris Hogue and included in my previous message, the following are the only CONECT records needed for beta-2: CONECT 1 2 2 CONECT 4 5 5 CONECT 6 7 7 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: Re: Double bonds Date: Wed, 24 Jul 1996 18:05:12 -0500 To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu I hesitate to say anything since I haven't down-loaded the new version that displays the double bonds (and won't until I finish this grant!), but I'd like to make a couple of more philosophical points. First, I think Chris Hogue is right about the semantics of CONECT records. Klotho's PDB files are ***generated*** by CONCORD, and I can't speak for Tripos or Bob Pearlman as to their intentions with the records. As readers may remember we've already encountered problems with other areas of the PDB records generated in this way (still unresolved --- gotta bug Tripos again). Second, Klotho generates an isomeric SMILES string to pass to CONCORD, but for fumarate her* internal representation has the electrons evenly distributed over the two Os in the carboxyls, since all structures are written at pH 7.0. (Klotho actually distinguishes among a number of different bond types, for example between C=C and C=O.) If we generated them directly, and if the conventions Chris describes were followed, I don't know how we would indicate the "bond and a half" that really occurs in the CONECT records --- bluntly, the representation is too impoverished to do it. By eyeball, my version of RasMol shows the Os equidistant, suggesting that CONCORD's minimization got the same result from a different direction (CONCORD may distinguish among even more bond types than Klotho, can't spot the manual just now. Obviously the C=C bond in oleate is relatively unshared, and seems a hair shorter than the C-Cs.) The way bond types are inferred is from crystal structure data which when interpreted positions atoms "closer" together. In fact if one looks at the data a whole range of bond lengths can be found, and the single-double-triple categorization is really a bunch of pretty fuzzy sets (and this is not meant as a pun on the quantum mechanics, but why not!). I'm therefore very uneasy about inferring bond types from CONECT records alone, and I'm not enthused about the set of descriptors to which I hear they're being mapped for display. This is surely a matter of taste, but I prefer to remember the pragmatic distinctions between our observations of the physical world and the interpretations of same. Cheers all, Toni *I just don't think of the program as an it --- probably has to do with the gender of goddesses and boats :-)! ++++------+------+------+------+------+------+------+------+------+------+ From: Joerg Gampfer Subject: printing quality Date: Thu, 25 Jul 1996 11:12:45 +0200 (MDT) To: rasmol@noc1.oit.umass.edu hello !! creating protein images, i have the problem that the printed output is not of very good quality. i am wondering if there is any chance to improve this. using the "vectps on" command does not change the prints ( at least not when printing them in corel draw). working with spheres the resolution of the created pictures is rather bad. is it possible to transfer the image completly to molscript, and then print it ?? i would be very thankful for help joerg gampfer ++++------+------+------+------+------+------+------+------+------+------+ From: cmn@biotec.uni-bremen.de (Christof M. Niemeyer) Subject: Introduction and Help Date: Thu, 25 Jul 1996 14:12:49 +0100 To: rasmol@noc1.oit.umass.edu Cc: cmn@alf.zfn.uni-bremen.de Dear All, allthough I just started to use RasMol (RasMac2.6=DF1 and RasMac 2.6-ucb1 versions), I am allready fascinated about the capabilities of the programm. (Just love it!). As I intend to use it mainly for teaching purposes, I am very keen to generate movies (scripts) for Macintosh plattforms, e.g. showing two biomolecules approaching (and docking to) each other. Is there someone out there willing to give some tips helping me to get started? =46urthermore, I did not yet find out, if it is possible to display subunits of multimeric proteins, related by crystallographic dyad axes. (e.g. streptavidin- tetramer from dimeric PDB file structure). Does anybody know how to to calculate and display the missing half of the molecule? Your help is greatly appreciated! Sincerely, Christof ************************************** Dr. Christof M. Niemeyer Universitaet Bremen, FB 02 - UFT Biotechnologie und Molekulare Genetik Leobener Str. 28359 Bremen, Germany Tel.: (49) 421-218 4911; Fax: (49) 421-218 7578 ************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Double Bonds: Success Date: Thu, 25 Jul 1996 14:51:02 -0500 (EST) To: rasmol@noc1.oit.umass.edu Using the fumarate.pdb provided by Chris Hogue with RasWin32 2.6 beta-2, I can indeed finally see double bonds. Thanks to Wade Freeman for looking up and reporting the correct interpretation of CONECT records, namely, that the first atom is connected to the others in the same record (line), but the 2nd thru Nth atoms are not connected to each other (by that record). I note the following peculiarities with RasMol's double bond display: 1. To get RasMol to show a double bond, the same atom must be in the first column in both CONECT records. This works: CONECT 4 5 CONECT 4 5 This does not work: CONECT 4 5 CONECT 5 4 This explains why the fumarate.pdb provided by Chris failed to show a double bond between the middle carbons 4 and 5. 2. Bonds are double only in the wireframe or stick (wireframe with larger diameter) representations. The plane defined by the two bonds remains parallel to the viewing screen surface as the molecule is rotated. That is, the bonds do not rotate with the molecule, so that you can always see their doubleness. 3. Bonds are double only if their diameter is not excessive. Thus, if you load the fumarate and can't see the double bonds in stick representation, reduce the size of the graphics window or zoom down. Similarly, by increasing the size of the graphics window or zooming up, you can always make the double bonds revert to single. Below is Hogue's fumarate.pdb revised and commented by yours truly, which shows only one double bond per carboxyl group, and shows the double bond between the middle carbons. COMPND Fumarate with double bonds. REMARK PDB file provided by Chris Hogue, edited and commented by Eric Martz. REMARK REMARK This file is to illustrate the rendering of double bonds by RasMol. REMARK The doubling of bonds is shown only by the wireframe/stick REMARK representation. In order to draw double bonds, the wires must not REMARK be excessive in diameter. Making the molecule larger by increasing REMARK the size of the graphics window, or zooming >100%, can cause stick REMARK double bonds to revert to single. REMARK Double bonds are always shown with the plane they define parallel REMARK to the viewing screen. As the molecule is rotated, the bonds do REMARK not rotate, so their doubleness can always be seen. REMARK ATOM 1 C 1 1.608 0.736 0.700 1.00 0.00 ATOM 2 O 1 2.812 0.584 0.556 1.00 0.00 ATOM 3 O 1 1.176 1.600 1.524 1.00 0.00 ATOM 4 C 1 0.660 -0.084 -0.080 1.00 0.00 ATOM 5 C 1 -0.660 0.084 0.080 1.00 0.00 ATOM 6 C 1 -1.608 -0.736 -0.700 1.00 0.00 ATOM 7 O 1 -2.812 -0.584 -0.556 1.00 0.00 ATOM 8 O 1 -1.176 -1.600 -1.524 1.00 0.00 ATOM 9 H 1 1.028 -0.816 -0.780 1.00 0.00 ATOM 10 H 1 -1.028 0.816 0.780 1.00 0.00 TER 11 1 REMARK REMARK The first atom in each CONECT record (line) is connected to each of REMARK the other atoms in the record. The 2nd through Nth atoms in each REMARK record are not connected by that record. Trailing zeros are optional. CONECT 1 2 3 4 0 CONECT 1 2 0 0 0 CONECT 4 5 9 0 0 CONECT 4 5 REMARK The reverse order, CONECT 5 4, fails to double the bond. CONECT 5 6 10 CONECT 6 0 7 8 0 CONECT 6 7 END But, this file does not generate double bonds in Chime. Tim Maffett, is it supposed to? I finally had the time to start a FAQ on my RasMol web site. I've included the above information there. Also there is a summary of mouse controls for Mac and Windows. If someone wants to send me the details for unix or X-windows, I'll add them. Look under "what's new" to find the FAQ. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: Making movies with docking Date: Thu, 25 Jul 1996 15:18:15 -0500 (EST) To: rasmol@noc1.oit.umass.edu, cmn@biotec.uni-bremen.de In message Thu, 25 Jul 1996 14:12:49 +0100, cmn@biotec.uni-bremen.de (Christof M. Niemeyer) writes: > (Just love it!). As I intend to use it mainly for teaching > purposes, I am very keen to generate > movies (scripts) for Macintosh plattforms, e.g. showing > two biomolecules approaching (and docking to) each other. > Is there someone out there willing to give some tips > helping me to get started? 1. Manually-generated RasMol and Chime scripts run equally well on Macintosh, Windows, and unix. There are no automated script generators at present (see document A. below). 2. Docking can presently only be done with UCB-RasMol (not RasMol nor Chime). There is a bug in UCB-RasWin which causes it to crash whenever it encounters a zap in a script, but this bug may not exist in UCB-RasMac. I would love to see a script with docking and I hope you succeed! I don't know of any docking scripts already on the web. 3. Resources for how to generate movies: A. Guide to "movie" script creation for RasMol and Chime http://www.umass.edu/microbio/scripts.htm B. Tutorial on Scripting for Chime and Rasmol (same URL) C. Use the existing scripts as models (same URL) 4. Don't miss the classroom page http://www.umass.edu/microbio/rasclass.htm Good luck! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ "Introduction and Help" (Jul 25, 2:12pm) References: <9607251213.AA00641@biotec.uni-bremen.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: Introduction and Help Date: Thu, 25 Jul 1996 18:32:33 -0400 To: rasmol@noc1.oit.umass.edu Cc: sussman@pdb.pdb.bnl.gov, abola1@bnl.gov Hi, I response to Christof's request for coordinates of complete functional proteins, I suggest that you check out our collection available via anonymous ftp (ftp.pdb.bnl.gov) or on the WWW at ftp://pdb.pdb.bnl.gov/user_group/biological_units/ (you can jump from the "Searching and Browsing the PDB" page to the "List of prepared Biological Molecules"). Although this is not yet a complete list, PDB will be generating these "biomolecules" on a regular basis. Until they have all been generated, if someone has a particular molecule of interest that they need, you may contact me and we will generate it for you upon request. I hope this information is helpful. Best regards, Nancy -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Outreach Program Coordinator Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: toni@athe.wustl.edu (Toni Kazic) Subject: [busemann@chemie.uni-wuerzburg.de: CCL:M:Warning: RasMol 2.6 Mopac import-filter] Date: Fri, 26 Jul 1996 10:56:44 -0500 To: rasmol@noc1.oit.umass.edu Errors-To: ccl@infomeister.osc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Stefan Busemann Subject: CCL:M:Warning: RasMol 2.6 Mopac import-filter Date: Fri, 26 Jul 1996 15:50:53 +0200 (MDT) To: chemistry@ccl.osc.edu !!! WARNING !!! Using the Mopac import-filter of the Molecule Visualizer Software RasMol 2.6 rasmol -mopac shows not the expected molecule but its ENANTIOMER! \\|// ( @ @ ) .---------------------oOOo----(_)----oOOo-----------------------------------. | Stefan Busemann | Institut fuer Organische Chemie | | Dipl.-Chem. | Computational Chemistry Group | | mail : busemann@chemie.uni-wuerzburg.de | Universitaet Wuerzburg | | voice: +49 0931/888-4750 | Am Hubland | | fax : +49 0931/888-4755 Oooo. | D-97074 Wuerzburg | | ( ) Oooo. | | .----------------------------\ (----( )-----------------------------------. \_) ) / (_/ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: busemann@chemie.uni-wuerzburg.de -- Original Sender From: Address: busemann@chemie.uni-wuerzburg.de CHEMISTRY@ccl.osc.edu: Everybody | CHEMISTRY-REQUEST@ccl.osc.edu: Coordinator MAILSERV@ccl.osc.edu: HELP CHEMISTRY or HELP SEARCH | Gopher: ccl.osc.edu 73 Anon. ftp: ccl.osc.edu | CHEMISTRY-SEARCH@ccl.osc.edu -- archive search Web: http://ccl.osc.edu/chemistry.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Printing in High Resolution Date: Fri, 26 Jul 1996 15:23:09 -0500 (EST) To: rasmol@noc1.oit.umass.edu Michael Conway, Ryan Hung, and S. Sridharan take note (and anyone else interested): I have taken a first stab at documenting the options available for high resolution printing from RasMol. See the FAQ on my web site, www.umass.edu/microbio/rasmol/faq.htm. I actually have no experience with this (I summarized it from the past email) so please send corrections and further details to me. A number of loose ends: Is 'write vectps' completely undocumented as it appears to me to be? (See www.umass.edu/microbio/rasmol/getras.htm#rasmanual for the complete list of documentation as I know it.) Do any of the Export menu options do a write vectps? Is EPSF raster (like PS) or vector (like VECTPS)? Can vector postscript somehow be written in monochrome, similar to the Export menu option? Am I correct in assuming that none of the Export menu methods provide control over landscape vs. portrait? Presumably the file generated could be printed either way by suitable print control software? How would this be done in Windows? On the Mac? Can anyone tell me what is good low-cost/free software for Macs to do the same things LviewPro does so nicely for Windows? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Laura A Andersson Subject: Re: Introduction and Help Date: Tue, 30 Jul 1996 17:36:37 -0500 (CDT) To: oeder@pdb.pdb.bnl.gov Cc: rasmol@noc1.oit.umass.edu, sussman@pdb.pdb.bnl.gov, abola1@bnl.gov Hi, can anyone tell me WHY some pdb files of metmyoglobin, which we all know has a water bound, will NOT display that water using any of the appropriate coommands? [e.g., select WAT, select HOH, etc]. I was able to see the water bound to the heme of cytochrome c peroxidase using these commands. Laura Andersson Thu, 25 Jul 1996, Nancy O. Manning wrote: > Date: Thu, 25 Jul 1996 18:32:33 -0400 > From: Nancy O. Manning > To: rasmol@noc1.oit.umass.edu > Cc: sussman@pdb.pdb.bnl.gov, abola1@bnl.gov > Subject: Re: Introduction and Help > > Hi, > > I response to Christof's request for coordinates of complete functional > proteins, I suggest that you check out our collection available via anonymous > ftp (ftp.pdb.bnl.gov) or on the WWW at > ftp://pdb.pdb.bnl.gov/user_group/biological_units/ (you can jump from the > "Searching and Browsing the PDB" page to the "List of prepared Biological > Molecules"). > > Although this is not yet a complete list, PDB will be generating these > "biomolecules" on a regular basis. > > Until they have all been generated, if someone has a particular molecule of > interest that they need, you may contact me and we will generate it for you > upon request. > > I hope this information is helpful. > > Best regards, > Nancy > > -- > _______________________________________________________________________ > > Nancy Oeder Manning Protein Data Bank > Outreach Program Coordinator Brookhaven National Laboratory > oeder@bnl.gov Biology Department, Bldg. 463 > (516) 344-5744 phone P.O. Box 5000 > (516) 344-5751 FAX Upton, NY 11973-5000 USA > _______________________________________________________________________ > ********************************************* laraheme@ksu.edu Laura A. Andersson, Ph.D., Assistant Professor Dept. Biochemistry, Kansas State University 103 Willard Hall, Manhattan, KS 66506 (913) 532-5118; FAX: (913) 532-7278 ********************************************** "Re: Introduction and Help" (Jul 30, 5:36pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: Introduction and Help Date: Wed, 31 Jul 1996 13:18:45 -0400 To: rasmol@noc1.oit.umass.edu, oeder@pdb.pdb.bnl.gov Cc: rasmol@noc1.oit.umass.edu, sussman@pdb.pdb.bnl.gov, abola1@bnl.gov Hi Laura Because a structure in the database has a name, like Myoglobin (met) or (Aquomet) this refers to the chemical content of the experiment (the crystal or the NMR tube), but you may not get XYZ coordinates for every single atom in that experiment. Hence you may not "see" everything you expect. These omissions are not considered database errors - they punctuate the experimental uncertainty in 3-D structure data. While one can crystallize a chemical form of a protein or biomolecular complex, one may not always get electron density data for all the atoms. Hence regions of the protein may be missing (e.g. 3TS1) owing to the fact that they are heterogenous within the crystal and do not refract x-rays. Solvent molecules won't refract x-rays if they are not ordered within the crystal. Water molecule placement requires good crystals with high resolution diffraction. Sometimes a remarkable number of solvent molecules are found (e.g. 3INS) owing to the methodology. I found waters in the file 1MYG, but not in 1MBS - but even if the crystallographic waters are present, there is no guarantee that the iron-coordinated water you are interested in will be present as well. One way to see the chemical content in a PDB database structure is to learn how to read the PDB text file. For example the structure 3INS has solvent - but it isn't water - it is DOD (D2O). So you may not find it with the usual RasMol commands unless the program knows that this is synonymous with solvent - or unless you have read the file yourself. If you need to find structures that display this aspect of aquomet-myoglobin the only recourse you may have is to try them out until you find one. Cheers, Christopher Hogue NCBI. http://www.ncbi.nlm.nih.gov/Structure >On Jul 30, 5:36pm, Laura A Andersson wrote: > Subject: Re: Introduction and Help > Hi, > can anyone tell me WHY some pdb files of metmyoglobin, which we all > know has a water bound, will NOT display that water using any of the > appropriate coommands? [e.g., select WAT, select HOH, etc]. I was able > to see the water bound to the heme of cytochrome c peroxidase using these > commands. > Laura Andersson > > Thu, 25 Jul 1996, Nancy O. Manning wrote: > > > Date: Thu, 25 Jul 1996 18:32:33 -0400 > > From: Nancy O. Manning > > To: rasmol@noc1.oit.umass.edu > > Cc: sussman@pdb.pdb.bnl.gov, abola1@bnl.gov > > Subject: Re: Introduction and Help > > > > Hi, > > > > I response to Christof's request for coordinates of complete functional > > proteins, I suggest that you check out our collection available via anonymous > > ftp (ftp.pdb.bnl.gov) or on the WWW at > > ftp://pdb.pdb.bnl.gov/user_group/biological_units/ (you can jump from the > > "Searching and Browsing the PDB" page to the "List of prepared Biological > > Molecules"). > > > > Although this is not yet a complete list, PDB will be generating these > > "biomolecules" on a regular basis. > > > > Until they have all been generated, if someone has a particular molecule of > > interest that they need, you may contact me and we will generate it for you > > upon request. > > > > I hope this information is helpful. > > > > Best regards, > > Nancy > > > > -- > > _______________________________________________________________________ > > > > Nancy Oeder Manning Protein Data Bank > > Outreach Program Coordinator Brookhaven National Laboratory > > oeder@bnl.gov Biology Department, Bldg. 463 > > (516) 344-5744 phone P.O. Box 5000 > > (516) 344-5751 FAX Upton, NY 11973-5000 USA > > _______________________________________________________________________ > > > > ********************************************* > laraheme@ksu.edu > Laura A. Andersson, Ph.D., Assistant Professor > Dept. Biochemistry, Kansas State University > 103 Willard Hall, Manhattan, KS 66506 > (913) 532-5118; FAX: (913) 532-7278 > ********************************************** >-- End of excerpt from Laura A Andersson ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMac help? Date: Wed, 31 Jul 1996 14:30:15 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: cmatte@student.umass.edu (Christy/BCRC) I normally use RasWin but now I'm using RasMac in preparation for a workshop next week which will be given in a mac lab we have here. Am I correct in thinking that the only built-in help in RasMac is the (clunky but better than nothing) 'help' command in the command-line window? Is it true that the excellent point-and-click built-in 'hypertext' manual which is accessible from the pull-down Help Menu in RasWin doesn't exist in RasMac? Or does this Mac novice just not know where to look? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: RasMac help? Date: Thu, 01 Aug 1996 10:58:07 -0500 (EST) To: Fergus.Doherty@nottingham.ac.uk, rasmol@noc1.oit.umass.edu In view of RasMac's lack of built-in hypertext help, a good alternative is to view the html manual (now revised up to 2.6 beta-2 on my RasMol Home Page) with Netscape on one side of the screen while using RasMac on the other side. This manual is a single html file, so can be viewed as a local file if the Mac is not networked, and of course can be bookmarked for quick access. In message Thu, 01 Aug 1996 12:00:57 +0100, Fergus Doherty writes: > Eric Martz wrote: >> Is it true that the excellent point-and-click >> built-in 'hypertext' manual which is accessible from the pull-down >> Help Menu in RasWin doesn't exist in RasMac? > > Unfortunately I don't think it is available. Maybe it is a Windows Help > file. What the mac version needs is an AppleGuide. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: 3DBbrowse is now available from PDB Date: Fri, 2 Aug 1996 21:48:29 -0400 To: rasmol@noc1.oit.umass.edu 3DBbrowse is now available: http://pdb.pdb.bnl.gov/3DBbrowser.html or from PDB Web page "Searching and Browsing the PDB". -------------------------- A new Web based browser, 3DBbrowse, makes now even simpler to search and retrieve data from the Protein Data Bank (PDB). The version of 3DBbrowse that is right now available on the Web allows the user to rapidly search through the contents of the entire PDB Archive for entries obeying certain constraints. A full text search (based on the Glimpse indexing and query system) can be made for any string appearing in the text of a PDB entry. A unique browsing tool: ---------------------- 3DB will perform for you the searches that before you used to do with o PDB's WWW Browser o Pending/Waiting List keyword search o On Hold List keyword search o Bibliographic header keyword search of all released entries A fast start: ------------ For a quick try enter zinc in the 'Full text query of PDB data' field and press 'Start a search'. User annotations: ---------------- In this new PDB era, users have the ability of annotate entries, adding textual or graphic information to make clear and/or complete the existing deposited information. Rasmol scripts are one of these annotation types. Starting from version 2.6, Rasmol accepts on-line scripts, describing the starting configuration for displaying a given PDB file. An explanation of what to do is at http://www.pdb.bnl.gov/rasmime.html A nice example on the 1ACJ PDB "Atlas" page. If you have suggestions or comments on this or another PDB tools, we would like to hear from you: pdbhelp@bnl.gov Dr. Jaime Prilusky Head, PDB Data Base Development Group ------------------------------------------------------------------------ Additional information on 1. The Protein Data Bank: Current Status and Future Challenges http://pdb.pdb.bnl.gov/papers/IUCr/ 2. Glimpse http://glimpse.cs.arizona.edu 3. 3DB database http://www.pdb.bnl.gov/opmbrowser.html -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Outreach Program Coordinator Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: "Mark J Howard (Bioc)" Subject: Compiling Rasmol 32(24) bit for Unix Date: Tue, 6 Aug 1996 08:31:09 +0100 (BST) To: rasmol@noc1.oit.umass.edu I have recently obtained the 2.6b release of Rasmol and I have successfully compiled the 8 bit version for use on our SGI's in our lab. We have just had an Indigo2 R10000 installed so I thought it would be a good idea to have the 24 bit version available for that machine. I have followed the INSTALL notes and modified the rasmol.h file before compiling on the R10000 but I still end up with the 8 bit version. Any advice would be very useful before I tear all my hair out!!!! Cheers Mark ******************************************************** Dr. Mark Howard Protein NMR Spectroscopy | Dept. of Biochemistry | University of Cambridge || | Tennis Court Road | || | | Cambridge, UK. || | ||| | | CB2 1QW ____|||||___/\__||||||||___|_|_ Tel: (01223) 333662 Fax: (01223) 333661 E-mail: mjh2@mole.bio.cam.ac.uk ******************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Joerg Gampfer Subject: solvent surface Date: Mon, 5 Aug 1996 11:36:08 +0200 (MDT) To: rasmol@noc1.oit.umass.edu hello !! another short question. with the dots command i can show the solvent accesible surface of a molecule (setting "solvent true"). is it possible to get a numeric size expressing the this surface ?? that would help me to compare different structures of the same protein. thanks for help joerg ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Double Bonds: Success Date: Thu, 8 Aug 1996 20:29:27 +0100 (BST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear All, Firstly, I must apologise for taking so long to reply to this thread but unfortunately I've spent the last two weeks attending conferences in Oregon and New Mexico. I see from my mail box that the topic of RasMol's double bonds has come up and I thought that I'd add my penny's worth. Everything you ever wanted to know about Double Bonds in RasMol. ================================================================ [1] Single Bonds ---------------- As mentioned in previous e-mails the Brookhaven Protein Databank conventions on CONECT records don't make any mention of bond order. Instead each CONECT record (coneptually) describes the neighbours of a given atom. Hence in Eric's original e-mail, the lines: > CONECT 1 2 3 4 0 > CONECT 2 1 0 0 0 > CONECT 3 1 0 0 0 > CONECT 4 1 5 21 22 indicate that: Atom 1 is bonded to atoms 2, 3 and 4; Atom 2 is bonded to atom 1; Atom 3 is bonded to atom 1 and Atom 4 is bonded to atoms 1, 5, 21 and 22. [Hence there is no bond between atoms 1 and 5!]. This issue was resolved in Wade Freeman's e-mail, which included the relevant portion of the PDB specification. That section contains the paragraph: > * The connectivity list given here is redundant in that each bond > indicated is given twice, once with each of the two atoms involved > specified in columns 7 - 11. Indeed if you look carefully at the example that is given above, it is clear that a given bond is described twice for example the bond linking atom 1 to 2 (on the first line) is same bond that links atom 2 to atom 1 (on the second line). To avoid processing each bond twice, RasMol contains the rule that it only processes bonds specified from an atom to a neighbour, if the neighbours serial number is higher than the source serial number. This should then explain Will McClure's e-mail that describes how he reduces the size of PDB files using RasMac by stripping out the superfluous CONECT entries. For example, reducing the example above to the two lines. > CONECT 1 2 3 4 0 > CONECT 4 0 5 21 22 And also explains why Eric was having problems specifying a double bond from atom 5 to atom 4 (which is ignored). [2] Double Bonds ---------------- Firstly, RasMol is happy reading double and triple bonds from Alchemy, MDL Mol file and Sybyl Mol2 format files as described in their specification. RasMol makes use of a strange pseudo-standard based upon the PDB file format that is supported by several other packages including DGEOM and Rubicon distance geometry programs. I'm not sure if "babel" supports this extension, but Pat Walters certainly knows of it. Bond orders are represented by representing a bond more than once, i.e. to create a double bond between atoms 1 and 2, RasMol allows either the full description: > CONECT 1 2 2 3 4 > CONECT 2 1 1 0 0 > CONECT 3 1 0 0 0 > CONECT 4 1 5 21 22 or alternatively the short-hand description: > CONECT 1 2 2 3 4 > CONECT 4 1 5 21 22 It is the distinction between these two forms of representing a bond twice that confused Chris Hogue when he claimed that RasMol's interpretation of the PDB CONECT format was incorrect. [Infact RasMol's interpretation of the CONECT record is incorrect but for a different reason. In order to read "Spartan", "MacSpartan" and (I believe) CONCORD format PDB files, RasMol allows 6 bonds to be specified in a CONECT record rather than 4. The last two fields are (by-the-book) conventionally reserved for hydrogen bonds. However so few PDB files contain explicit hydrogen bonds that more files break by treating them as h-bonds than by treating them as covalent bonds] [3] Future Work --------------- Finally as pointed out by Toni Kazic, the behaviour of electrons in real molecules results in non-integral bond orders. Hence the double, single or aromatic bond is purely an abstraction for chemists. However there is an interesting body of work that tries to determine bond orders and atom hybridization purely from the local geometry of a molecule. I suspect that such an algorithm will be implemented in RasMol in the near future (references given below, comments welcome). However in the meantime this functionality is implemented in "babel". Simply use "babel" to translate a PDB file into an MDL Mol file and load the MDL mol file into RasMol complete with double bonds. [4] References -------------- Elaine C. Meng and Richard A. Lewis, "Determination of Molecular Topology and Atomic Hybridization States from Heavy Atom Coordinates", Journal of Computational Chemistry, Vol. 12, No. 7, pp. 891-898, 1991. Jon C. Baber and Edward E. Hodgkin, "Automatic Assignment of Chemical Connectivity to Organic Molecules in the Cambridge Structural Database", Journal of Chemical Information and Computer Science, Vol. 32, pp. 401-406, 1992. I hope this answers those few questions that haven't been answered already. I'd love to hear from any chemists or programmers who have already attempted to use or implement a co-ordinates to bond order algorithm. Please let me know your sucesses or failures with babel. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol Manual Completed Date: Tue, 13 Aug 1996 15:41:42 -0400 To: rasmol@noc1.oit.umass.edu I've added the (formerly missing) General Operation section to the hypertext form of the RasMol Manual, plus a few other revisions including the summary of mouse controls. These were incorporated into the version recently updated to 2.6 beta-2 by Margaret Wong. Thus, the html version of the Manual is now, I believe, complete and up to date (140 Kbytes). All my changes are marked (see the html source). Corrections and suggestions for additions are welcome -- I intend to keep this form of the manual maintained. Roger Sayle has just provided me with an FAQ html which he created recently. I plan to incorporate that into the FAQ on my web site in the near future. http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ "RasMol Manual Completed" (Aug 13, 3:41pm) References: <9608131941.AA07683@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christoph Weber" Subject: Re: RasMol Manual Completed Date: Tue, 13 Aug 1996 18:28:34 -0700 To: rasmol@noc1.oit.umass.edu Eric, this is great! I really appreciate this work, since dealing with a 2.5 manual and two addenda has become rather difficult. I would suggest that you create a generic URL, i.e. /rasman.html, to which the most current version will always be linked, so that we can leave our links untouched while the manual may grow. Some criticism: The introductions states: "Finally, the rendered image may be written out in a variety of formats including either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script of Kinemage" Correct would be: "... or as a Molscript input script or a Kinemage." The table with mouse controls could be expanded to spell out the insight and quanta mouse bindings, since the 'set mouse' entry in the manula doesn't. What about moving the parts of the top portion of the document elsewhere such that the TOC appears in the first screen? Again, thanks for the great work. Cheers, Christoph -- *** > NEW PHONE NUMBER: 784-7459 < *** | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-784-7459 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RasMol Manual Completed Date: Wed, 14 Aug 1996 11:46:27 -0400 To: weber@scripps.edu, rasmol@noc1.oit.umass.edu >From: "Christoph Weber" >Tue, 13 Aug 1996 18:28:34 -0700 >To: rasmol@noc1.oit.umass.edu >Subject: Re: RasMol Manual Completed > >Eric, [snip] >I would suggest that you create a generic URL, i.e. /rasman.html, >to which the most current version will always be linked, so that we can leave >our links untouched while the manual may grow. Good idea, done. The link will remain http://www.umass.edu/microbio/rasmol/distrib/rasman.htm independent of new versions of RasMol. [snip] >Correct would be: "... or as a Molscript input script or a Kinemage." Done. >The table with mouse controls could be expanded to spell out the insight and >quanta mouse bindings, since the 'set mouse' entry in the manula doesn't. I would be happy to include these, as well as the X-windows/unix bindings, as soon as someone will provide the details to me. >What about moving the parts of the top portion of the document elsewhere such >that the TOC appears in the first screen? I think it important that new viewers be told about the supplementary documents and the searching possibility before they get into the manual itself. As a compromise I've put 'Jump to TOC' at the top for experienced users. Thanks for your feedback! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Dewey Williams Subject: script continuously running in win95 Date: Thu, 15 Aug 1996 10:36:39 -0400 To: rasmol@noc1.oit.umass.edu I recently (yesterday) downloaded the newest Raswin for Win95 and was playing around with the DNA script tutorial. Since attempting to run the DNA script I keep getting the message: Cannot find D:/raswin/scripts/dna1a.scr. I received this when I first tried to run the script. It seems that not only do all the scripts have to be in the same directory, but raswin has to be in that directory too. Win3.1 had a way to place a 'working directory' for a program but there is no provision in Win95. When I typed script d:\raswin\scripts\dna1.top in the command line, I received this message. 'Top' was ran, but it could not find the first script in its list. I have checked and the script is there. Doing a Ctrl-Alt-Del brings up the list of running tasks and DNA1A is listed. Pressing OK on the error message or End Task on the task list makes the message and task go away. However, it comes back every so often. I haven't timed the reoccurence, but it has been as short as 15 minutes and as long as 1 hour. I have rebooted Win95 and Shut down completely without any change. I cannot find any evidence of something running when the error message is NOT showing. I am running an AMD 5x86-133 with 16 meg Ram. Anyone seen this behavior? Anyone know how to remove this process? It doesn't seem to be doing any harm, just darn annoying. BTW, is there any way to change the font of the command line in Win95. It is so small that I can barely read it. Dewey Williams - Lab Manager williams@unccvm.uncc.edu UNC-Charlotte Chemistry Dept. http://www.chem.uncc.edu "These are my ideas and no one else will claim them." "If you are not part of the solution, you are part of the precipitate" ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RASMOL for OS/2 Date: Thu, 15 Aug 1996 21:17:53 -0400 To: rasmol@noc1.oit.umass.edu Cc: christopher.mcrae@mq.edu.au Chris' is the second request in recent days for OS/2 RasMol. Is anyone doing it or seriously considering it? -Eric >From: "Christopher McRae" >To: "emartz@microbio.umass.edu" >Date: Thu, 15 Aug 96 12:07:38 +1000 >Subject: RASMOL for OS/2 > >G'day Eric, > >I was wondering if you are considering/doing an OS/2 port of RASMOL. To >make the project more attractive :-), IBM provides,free of charge a set >of libraries which map Win32 APIs to OS/2 APIs (called Open32) to allow >the easy porting of Win32 apps to OS/2. (Lotus WordPro for OS/2 was >ported using these libraries from the Win95 version). > >Anyway, just a thought :-) > >Cheers, > > -- Chris >------------------------------- -------------------------------------- >Dr Christopher McRae _--_|\ Internet: christopher.mcrae@mq.edu.au >School of Chemistry / \ Voice: +61-2-9850-8288 >Macquarie University \_.--._* FAX: +61-2-9850-8313 >Sydney NSW 2109 v >Australia Micro$oft - Small and Limp? /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Envelope-To: rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Michael.Vork@FYS.RULIMBURG.NL Subject: Initializing RASMOL ??? Date: Thu, 15 Aug 1996 16:45:46 +0000 (EZT) To: rasmol@noc1.oit.umass.edu Hi there, Like all of us (I assume) I am a very enthousiastic RASMOL user. Because I use it a lot I get a little irritated sometimes. What is the problem ? Every time RASMOL is started (under windows 3.1), the graphic displaying window is put somewhere on the screen while the command window is present a an icon. I always have to resize and move the graphics window and open the command windows (and resize and move it) to get a satisfactory display of both windows. This is especially annoying when I want to play Eric's scripts. Question: Is it possible to make some kind of initialization file (which is read by RASMOL every time it is activated) in which the exact location of the two windows is stored together with additional information about a window being open or put on screen as an icon ? I would very much like to have this info in order to make it a perfect program. Michael Vork University of Limburg Dept. Physiology Maastricht Netherlands ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: printing quality Date: Thu, 15 Aug 1996 16:26:36 +0100 (BST) To: Joerg Gampfer Cc: rasmol@noc1.oit.umass.edu Dear Joerg, > creating protein images, i have the problem that the printed output is > not of very good quality. i am wondering if there is any chance to > improve this. using the "vectps on" command does not change the prints ( > at least not when printing them in corel draw). working with spheres the > resolution of the created pictures is rather bad. is it possible to > transfer the image completly to molscript, and then print it ?? Thanks very much for your e-mail. I'm sorry to take so long to reply but I've recently been attending conferences in the US and have fallen behind with my e-mail. Eric Martz's RasMol FAQ at "http://www.umass.edu/microbio/rasmol/faq.htm" contains a section on high resolution printing that may solve your problems. However, it is possible to export the current view of a protein as a MolScript input script using the RasMol "write molscript " command. When this script is run through Per Kraulis' Molscript program it should produce a ribbons view of the protein with the current viewpoint, scale and clipping planes with all atoms that are displayed as spheres in RasMol similarly displayed in Molscript. The protein secondary structure prediction uses RasMol current assignment, either the author's or RasMol's internal DSSP. RasMol is often used to generate Molscript input files, principally to avoid the time consuming tasks of typing in a protein secondary structure assignment and then iteratively running Molscript to establish the best viewpoint. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Printing in High Resolution Date: Thu, 15 Aug 1996 17:36:10 +0100 (BST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear Eric, Once again apologies for the backlog... > Do any of the Export menu options do a write vectps? I thought that both the Macintosh and Microsoft Windows versions of RasMol supported the selection of Vector PostScript in their "File Type" list boxes from "EPSF" on the Export menu. However, upon looking I discovered that the RasWin Export dialog file type box is a bit out of date. I've now updated it, but for the current version only the Macintosh can select "vectps" from the menus. > Is EPSF raster (like PS) or vector (like VECTPS)? In short, "epsf" is identical/synonymous to "ps". > Can vector postscript somehow be written in monochrome, similar to > the Export menu option? The "mono" option in RasMol PostScript driver is purely an attempt to reduce the file size of the PostScript file. i.e. a monochrome laser printer will happily print a RasMol generated colour PostScript file. However, it will be both slower and the file atleast three times larger. Vector PostScript files are small enough that "mono" versions don't make sense. I believe that they should print fine on all mono laser printers [but I stand to be corrected on very old printers...] > Am I correct in assuming that none of the Export menu methods provide > control over landscape vs. portrait? Presumably the file generated > could be printed either way by suitable print control software? > How would this be done in Windows? On the Mac? The user has no explicit control over the orientation of the PostScript images produced by RasMol. RasMol simply scales the image to fit the paper size in portrait. In EPSF Mode (but not in VectPS for some reason?), RasMol may also rotate the image to landscape if the window is wider than it is tall. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord <100412.1707@CompuServe.COM> Subject: New Web page Date: 16 Aug 96 01:00:47 EDT To: "Contrib. Rasmol" Dear Colleagues, I have started a Web page at the following URL : http://ourworld.compuserve.com/homepages/JDebord This page presents molecular models of drugs and other organic compounds. The models are stored as PDB files and may be easily visualized with RasMol. The geometries have been optimized by semi-empirical molecular orbital methods (MNDO or AM1) with HyperChem or MOPAC. The atomic charges have been stored in the temperature factor of the PDB files, so that the electrostatic potential may be viewed with RasMol. Most of the compounds presented here are related to our research work on esterase inhibition but they may be of interest for researchers in other fields. Please send your comments by e-mail. Sincerely, Jean Debord Laboratoire de Pharmacologie, Faculte de Medecine 2 Rue du Docteur Marcland, F-87025 Limoges, France 100412.1707@compuserve.com http://ourworld.compuserve.com/homepages/JDebord "RASMOL for OS/2" (Aug 15, 9:17pm) References: <9608160117.AA23196@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: RASMOL for OS/2 Date: Thu, 15 Aug 1996 22:36:17 -0400 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu Cc: christopher.mcrae@mq.edu.au Hi folks, Ah yes, the RasMol port to OS/2... I have spent quite a lot of my spare time on it. I cranked out "rasos2.c" and makefiles, resources, icons, etc. I can compile it all cleanly - but the executable dies mysteriously, shortly after putting up the window frame. It apparently needs more of my spare time, which is in increasingly short supply. (As an aside, I have also had, last week, similar problems trying to execute the OS/2 OpenGL sample programs made with standard makefiles, and without the DAPIE - perhaps I have a video driver problem...) Anyhow, I cannot say when (or if) I will complete this port. I appreciate the problem because there are no free OS/2 viewers for 3D structures. Chris Hogue. NCBI >On Aug 15, 9:17pm, Eric Martz wrote: > Subject: RASMOL for OS/2 > Chris' is the second request in recent days for OS/2 RasMol. Is anyone > doing it or seriously considering it? -Eric > > >From: "Christopher McRae" > >To: "emartz@microbio.umass.edu" > >Date: Thu, 15 Aug 96 12:07:38 +1000 > > >Subject: RASMOL for OS/2 > > > >G'day Eric, > > > >I was wondering if you are considering/doing an OS/2 port of RASMOL. To > >make the project more attractive :-), IBM provides,free of charge a set > >of libraries which map Win32 APIs to OS/2 APIs (called Open32) to allow > >the easy porting of Win32 apps to OS/2. (Lotus WordPro for OS/2 was > >ported using these libraries from the Win95 version). > > > >Anyway, just a thought :-) > > > >Cheers, > > > > -- Chris > >------------------------------- -------------------------------------- > >Dr Christopher McRae _--_|\ Internet: christopher.mcrae@mq.edu.au > >School of Chemistry / \ Voice: +61-2-9850-8288 > >Macquarie University \_.--._* FAX: +61-2-9850-8313 > >Sydney NSW 2109 v > >Australia Micro$oft - Small and Limp? > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor (Immunology) > Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 > 413-545-2325 FAX:545-1578. Web projects include: > RasMol Home Page, http://www.umass.edu/microbio/rasmol > Catalog of Free Flow Cytometry Software (includes MFI which I wrote), > http://www.bio.umass.edu/mcbfacs/flowcat.html > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ >-- End of excerpt from Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: script continuously running in win95 Date: Fri, 16 Aug 1996 13:25:06 +0100 (BST) To: Dewey Williams Cc: rasmol@noc1.oit.umass.edu Dear Dewey, > It seems that not only do all the scripts have to be in the same > directory, but raswin has to be in that directory too. Win3.1 had a > way to place a 'working directory' for a program but there is no > provision in Win95. When I typed script d:\raswin\scripts\dna1.top in > the command line, I received this message. 'Top' was ran, but it could > not find the first script in its list. I have checked and the script > is there. I must admit that I hadn't noticed that working directories had been dropped from Windows 95, and have never encountered the mysterious rogue process task you describe. However it now seems eminently sensible that all file names within RasMol script files should be treated by the program to be relative to the directory or folder holding the parent script. Why I never considered this previously I don't know. However this is now on the list of features expected in the next version of RasMol. Sorry for any inconvenience this oversight may have caused. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RASMOL for OS/2 Date: Fri, 16 Aug 1996 11:42:16 -0500 (EST) To: rasmol@noc1.oit.umass.edu ------------------------------ Fri, 16 Aug 96 11:49:34 +1000 From: "Christopher McRae" Subject: Re: RASMOL for OS/2 To: "Eric Martz" I posted the question to comp.os.os2.scitech and got a heap (27 to be precise) of 'If you find out let me know, I'd really like an OS/2 version of RasMol' type responses, but no-one saying they are doing the port. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: script continuously running in win95 Date: Fri, 16 Aug 1996 11:54:41 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Thu, 15 Aug 1996 10:36:39 -0400, Dewey Williams writes: > Anyone seen this behavior? Anyone know how to remove this process? I have no experience with Win95. However, with RasMac or RasWin on Win 3.1, if the script is left standing at a pause but has not finished executing (returning to the RasMol> prompt in the command line window) it is possible to close the windows but you can't terminate the program's execution. What is needed is to press Ctrl-D to kill script execution. (This only works with 2.6 beta-2! In beta-1 you must let the script run to completion, which sometimes may take quite a while!) Only then can you truly terminate RasMol. I hope that Roger will find a way to implement the Ctrl-D for unpaused scripts in the next release because I have wasted hours (cumulatively) during the writing/debugging of scripts due to the inability to kill an unpaused script after it has hit a bug and gone awry. One of my demo loops runs for 30 minutes unpaused. The only way to stop it is to kill the power to the computer! So you not only have to reboot but resize/reposition the RasMol windows after every snafu. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: Command line font size Date: Fri, 16 Aug 1996 11:59:12 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Thu, 15 Aug 1996 10:36:39 -0400, Dewey Williams writes: > BTW, is there any way to change the font of the command line in Win95. It > is so small that I can barely read it. Using RasWin32 2.6 beta-2 with a 1024 x 768 pixel screen under Win3.1, I have noticed that if you open RasWin32 before opening any other processes, you get a wonderfully large font in the command line window. If, however, you have some other windows running you get the teeny tiny illegible font. I don't know why but this seems consistent. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Command line font size Date: Fri, 16 Aug 1996 20:35:40 +0100 (BST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear All, > Using RasWin32 2.6 beta-2 with a 1024 x 768 pixel screen under Win3.1, I > have noticed that if you open RasWin32 before opening any other processes, > you get a wonderfully large font in the command line window. If, however, > you have some other windows running you get the teeny tiny illegible font. > I don't know why but this seems consistent. I believe that I have found the cause of the font problems within RasWin. It appears that RasMol requests the font for its terminal window by specifying the height of the characters. Requesting a 12pt Modern font on earlier versions of Windows was sufficient to get reasonable text. More recent versions, however, support multiple width fonts such that the default width of a 12pt font is probably determined by the set of fonts that are already in use. RasWin has now been fixed to request a Modern font that is 12pt high and 8pt wide... 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Kornhauser Subject: Script menu Date: Fri, 16 Aug 1996 17:11:16 -0600 (CST) To: Lista de Rasmol Hi! Everyone. First I would like to thank Roger Sayle, Eric Martz and everyone that has contributed to the creation and use of RasMol, it really is a great tool. This mail is to sugest something (which might be usefull). I use a lot of scripts in diferent directories, and combine them in different ways, it would be nice to be able to run them from a menu. Not that I am complainig!! But maybe in a future version it could be done if this is a usefull thing for everyone. Well, thanks again and regards to all. Adrian Kornhauser ++++------+------+------+------+------+------+------+------+------+------+ From: Dewey Williams Subject: Re: script continuously running in win95 Date: Mon, 19 Aug 1996 14:02:28 -0400 To: rasmol@noc1.oit.umass.edu At 01:25 PM 8/16/96 +0100, you wrote: > >Dear Dewey, > >> It seems that not only do all the scripts have to be in the same >> directory, but raswin has to be in that directory too. Win3.1 had a >> way to place a 'working directory' for a program but there is no >> provision in Win95. When I typed script d:\raswin\scripts\dna1.top in >> the command line, I received this message. 'Top' was ran, but it could >> not find the first script in its list. I have checked and the script >> is there. > >I must admit that I hadn't noticed that working directories had been >dropped from Windows 95, and have never encountered the mysterious >rogue process task you describe. > Ooops, I solved the mystery of the continuously running script! While working with the latest RasWin program I came upon a particularly interesting molecule. Having just downloaded a new screen capture program I ran it, and copied the dazzling RasWin molecule for use as a screen saver BMP. For some reason, the screen capture program placed a line in my SYSTEM.INI file that calls DNA1A for the screen saver. Since this was the same name aas the script I was running in RasWin, I thought RasWin was the problem. Deleting that line from System has solved the problem. Sorry about the confusion. Dewey Williams - Lab Manager williams@unccvm.uncc.edu UNC-Charlotte Chemistry Dept. http://www.chem.uncc.edu "These are my ideas and no one else will claim them." "If you are not part of the solution, you are part of the precipitate" ++++------+------+------+------+------+------+------+------+------+------+ From: Hamza Suria Subject: Chirality in Rasmol Date: Thu, 22 Aug 96 19:58:34 EDT To: rasmol@noc1.oit.umass.edu Hi, Does anyone know any method of changing the chirality of stereocenters in Rasmol? We have built numerous small organic molecules, mostly natural products chemistry oriented material, and we've discovered that some of the stereocenters are incorrect. Since we made these by specifying a SMILES string with the CORINA server, our only hope of changing stereochemistry is by Rasmol. Thanks. Hamza Suria. k93hs01@hobbes.kzoo.edu http://www.kzoo.edu/~k93hs01 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: hydrogen bonds avoiding hydrogens Date: Thu, 29 Aug 1996 13:24:32 -0400 To: ras32425@ggr.co.uk Cc: rasmol@noc1.oit.umass.edu It appears that even when a PDB file includes the hydrogens on the backbone nitrogens (e.g. 1ROG, 1LFA), RasMol 2.6 beta-2 still draws alpha helix hydrogen bonds from the N to the O. A suggestion for a future release would be to draw the bond from the H on the NH to the backbone O. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ "hydrogen bonds avoiding hydrogens" (Aug 29, 1:24pm) References: <9608291724.AA10243@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christoph Weber" Subject: arbitrary lines/bonds? Date: Thu, 29 Aug 1996 11:03:21 -0700 To: rasmol@noc1.oit.umass.edu Eric's last posting reminded me of a problem we had a while ago: Rasmol does not seem to have any command to draw a line/bond between user specified atoms. (Or are we missing something?) This would be very useful to visualize things like distances, unusual chemical bonds that Rasmol does not find by default and a variety of other stuff. Our application would be to visualize the distance difference matrix on the structure. (see Akke et al. JMB 252, 102 (1995)) My (long-term) plans include generating HTML with an image map of the distance difference matrix (that's a two-dimensional map with the two sequences being compared running along the axes and the distance difference between residues/atoms/whatever displayed on a color scale or as contours). On this image map one could then click and get the structure up in Rasmol with the distance highlighted as a (color-coded) vector. This would be very similar to the NOESY peak demo on the Hyperactive Molecules page (http://www.ch.ic.ac.uk/hm_first.html) I wonder if anyone on this list has comments and/or suggestions. Cheers, Christoph -- *** > NEW PHONE NUMBER: 784-7459 < *** | Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB2 619-784-7459 or -8754 (phone) | The Scripps Research Institute 619-554-3757 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: arbitrary lines/bonds? Date: Thu, 29 Aug 1996 20:51:56 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Thu, 29 Aug 1996 11:03:21 -0700, "Christoph Weber" writes: > Rasmol does not seem to have any command to draw a line/bond between user > specified atoms. (Or are we missing something?) See these commands: monitor color monitor set monitor set picking distance We believe these commands are fully and correctly documented in the newly revised hypertext manual http://www.umass.edu/microbio/rasmol/distrib/rasman.htm In addition to giving a distance readout, the monitor command does indeed provide a mechanism to show a bond between any two arbitrary atoms. At present, the 'bond' can only be shown as a dotted line. I've recently suggested to Roger Sayle that the cylindrical stick representation be enabled for monitor lines. For an example of the use of this command to show arbitrary inter-molecular hydrogen bonds, see Will McClure's Chime tutorial on protein secondary structure http://info.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: HTML Manual revised Date: Mon, 2 Sep 1996 22:13:30 -0400 (EDT) To: marg@chem1.chem.swin.edu.au, ras32425@ggr.co.uk, rasmol@noc1.oit.umass.edu I found and fixed a number of omissions, errors, and formatting problems in the hypertext version of the RasMol manual which Margaret Wong and I had worked on earlier to bring up to version 2.6 beta-2. Most of the latest changes are documented in the revision history included in the manual. http://www.umass.edu/microbio/rasmol/distrib/rasman.htm /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Hodgson's 6/96 article in Nature Biotech Date: Sat, 31 Aug 1996 21:27:26 -0400 (EDT) To: rasmol@noc1.oit.umass.edu I've added a reference to John Hodgson's 6/96 Nature Biotech article to the bibliography page at my web site, along with a commentary which corrects the factual errors in this unfortunate article. See 'What's new'. I am copying this message to Hodgson. BTW, this email list now has >210 subscribers! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: HTML Manual revised Date: Mon, 2 Sep 1996 22:13:30 -0400 (EDT) To: marg@chem1.chem.swin.edu.au, ras32425@ggr.co.uk, rasmol@noc1.oit.umass.edu I found and fixed a number of omissions, errors, and formatting problems in the hypertext version of the RasMol manual which Margaret Wong and I had worked on earlier to bring up to version 2.6 beta-2. Most of the latest changes are documented in the revision history included in the manual. http://www.umass.edu/microbio/rasmol/distrib/rasman.htm /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Hodgson's 6/96 article in Nature Biotech Date: Sat, 31 Aug 1996 21:27:26 -0400 (EDT) To: rasmol@noc1.oit.umass.edu I've added a reference to John Hodgson's 6/96 Nature Biotech article to the bibliography page at my web site, along with a commentary which corrects the factual errors in this unfortunate article. See 'What's new'. I am copying this message to Hodgson. BTW, this email list now has >210 subscribers! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Hamza Suria Subject: Introduction Date: Tue, 3 Sep 96 12:42:20 EDT To: rasmol@noc1.oit.umass.edu Hello all, I have posted messages to this list before but am guilty of not having introduced myself. I'm an undergrad Bio and Chem major at Kalamazo College, Kalamazoo, Michigan. Over the last 4 months I have been working with Chemlinks (a consortium of schools interested in improving the way chemistry is taught) to create a module for second year undergraduate organic chemistry classes. The general aim of the module is to help students visualize real-life organic chemistry by having them research a variety of natural drugs. They would investigate aspects such as synthesis, history, usage and structure. To help the structure part, I have been creating Rasmol pdb files of about 200 natural products using the CORINA server. The structures are located at: http://www.kzoo.edu/~k93hs01/chemlinks/ I would like to thank Eric Martz for helping me with this project also. Hamza Suria. k93hs01@hobbes.kzoo.edu http://www.kzoo.edu/~k93hs01 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Chirality in Rasmol Date: Wed, 4 Sep 1996 19:16:46 +0100 (BST) To: Hamza Suria Cc: rasmol@noc1.oit.umass.edu Dear Hamza, > Does anyone know any method of changing the chirality of stereocenters in > Rasmol? We have built numerous small organic molecules, mostly natural > products chemistry oriented material, and we've discovered that some of the > stereocenters are incorrect. Since we made these by specifying a SMILES > string with the CORINA server, our only hope of changing stereochemistry > is by Rasmol. Once again I'm sorry to take so long to answer this e-mail during the summer break. I've just looked at the corina page and was surprised to find that it doesn't implement either of the SMILES stereo conventions! Unfortunately, it is not possible to invert a chiral center within RasMol. However, a common trick is that if ALL of the chiral centers are incorrect, i.e. a molecule contains only a single chiral center, the file may be fixed by hand editting the XYZ (or PDB) file and negating the Z co-ordinate. Alas the corina algorithm is deterministic (unlike distance geometry) and will produce the same conformation and chiral invertions reproducibly. If anybody has a solution, I'd love to hear about it (I have similar problems myself). 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: RE: RasMol - stereo - for 16-bit Windows Date: Wed, 4 Sep 1996 21:05:47 +0100 (BST) To: Eric Martz Cc: rasmol@noc1.oit.umass.edu Dear All, My apologies for the delay. A 16 bit version of RasWin has been placed on the usual FTP site, ftp.dcs.ed.ac.uk in the directory /pub/v2.6beta. This has just been compiled and is atleast v2.6beta2. 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 References: ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Chirality in Rasmol Date: Wed, 4 Sep 1996 17:04:03 -0400 (EDT) To: rasmol@noc1.oit.umass.edu For some small molecule intermediates and cofactors in the TCA Cycle that I wanted to display, but which were not available at Klotho, I used a spreadsheet calculation to change the bond lengths and atom positions of selected lines in the original pdb files. The equations used, which I had to look up, all come from the first few pages of a vector algebra chapter. This worked fine for switching a methyl to a hydrogen position, converting a sulfur to an oxygen, etc. But "fine" means most viewers couldn't tell the difference. I don't think I would use such coordinates as the starting point for any real work! -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Chirality in Rasmol Date: Wed, 4 Sep 1996 14:11:46 -0700 To: rasmol@noc1.oit.umass.edu At 07:16 PM 9/4/96 +0100, you wrote: > >Dear Hamza, >> Does anyone know any method of changing the chirality of stereocenters in >> Rasmol? We have built numerous small organic molecules, mostly natural >> products chemistry oriented material, and we've discovered that some of the >>(snipped) I ran into the same thing - at least with corina, sometimes changing the order of the smiles string will give you the other enantiomer, for instance with a-methylphenethylamine you can write c1ccccc1CC(C)N or c1ccccc1CC(N)C or variations on that theme. Smiles seems to be flexible that way...just try different strings until you get the one you want....admittedly this is not easy with polycyclics, etc. ""It is forbidden to decry other sects; the true believer gives honor to whatever in them is worthy of honor" Asoka, Buddhist Emporer iof India (died 238 BCE) "There is no expedient to which man will not resort to avoid the real labor of thinking" Sir Joshua Reynolds ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: 16-bit RasWin Date: Wed, 4 Sep 1996 17:52:01 -0500 (EST) To: Thank you, Roger, for providing 16-bit RasWin 26 beta-2! Over the past few weeks, I've forwarded over a dozen requests for this to Roger so there is still significant demand for RasWin on 80286 computers. I have put it on the RasMol Home Page. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Hamza Suria Subject: Difficult Solution to Chirality Date: Thu, 5 Sep 96 10:07:32 EDT To: rasmol@noc1.oit.umass.edu Hello everyone, Thanks everyone who replied to my curiousity about chirality inversions within Rasmol. Turns out that is not possible unless if you want to sit down with a spreadsheet and invert atom coordinates all over the place. Therefore, molecules already built are difficult to invert. But when building new molecules, CORINA has implemented its stereochemistry interpreter(?) so that molecules can now be specified with stereochemistry in a SMILES string. The SMILES can be a little tricky when it comes to this the convention is generalized in the Daylight SMILES tutorial: http://www.daylight.com/dayhtml/smiles/smiles-intro.html The tutorial is informative but does not provide a couple of very interesting parameters. If anyone is interested, I can go through those and provide examples. CORINA itself is located at http://schiele.organik.uni-erlangen.de/services/3d.html and my site is: http://www.kzoo.edu/~k93hs01/chemlinks Thanks. Hamza Suria. k93hs01@hobbes.kzoo.edu http://www.kzoo.edu/~k93hs01 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: translate z? Date: Fri, 6 Sep 1996 08:47:27 -0400 (EDT) To: rasmol@noc1.oit.umass.edu, ras32425@ggr.co.uk What does 'translate z' do? Not only does it have no obvious effect, but neither does it affect the slabbed image nor the shadowed image (two cases where I could imagine it having an effect). Yet it is in the manual and is accepted. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: translate z? Date: Fri, 6 Sep 1996 20:04:59 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu > > What does 'translate z' do? Not only does it have no obvious effect, but > neither does it affect the slabbed image nor the shadowed image (two cases > where I could imagine it having an effect). Yet it is in the manual and is > accepted. I think "translate z " is ignoreinternally. The function to apply a transformation ignores the z-translation. A translation in z-direction would zoom the actual object, so the job is donene by the command "zoom". Perhaps the idea was to allow translation in all directions, and nobody did the programming for z-translation, however it would be the same as zooming. Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: translate z? Date: Mon, 9 Sep 1996 20:08:08 +0100 (BST) To: rasmol@noc1.oit.umass.edu Eric, > What does 'translate z' do? Not only does it have no obvious effect, but > neither does it affect the slabbed image nor the shadowed image (two cases > where I could imagine it having an effect). Yet it is in the manual and > is accepted. Currently, it doesn't do anything at all. However, because it may be used in a future release (to alter slabbing, lighting or perspective) and it is orthogonal to the "translate x" and "translate y" options, it has been supported (but not implemented) since the first version of RasMol. On the topic of future compatability, I have a few minor requests for RasMol users and script writers. [1] Although RasMol accepts strings without double quotes, please could you use them in file handling, echo and label commands. For example, I may wish to add "label bonds " in the near future. This may cause confusion if the first word of your atom label is "bond". [2] To be extra cautious, add the "pdb" file format specifier to the load command in scripts. I'm currently investigating the ability to "auto-detect" file formats in RasMol. This would then be the default option for load. Although RasMol should be able to correctly identify most PDB files (including all Brookhaven PDB files), those that begin with e-mail headers for example, may be mistaken for something else. [3] Finally, although never documented as such the keyword "residue" has been synonymous with the keyword "group", i.e. "colour group". Alas, the keyword "residue" is now no longer identical, and will refer to the NCBI's new "residue" amino acid colour scheme. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Medical Biochem via Chime/Shockwave Date: Mon, 9 Sep 1996 20:35:38 -0400 (EDT) To: rasmol@noc1.oit.umass.edu I forward this from George Helmkamp as he had technical difficulties getting it through. -Eric Martz ++++------+------+------+------+------+------+------+------+------+------+ From: George Helmkamp Date: Mon, 19 Aug 1996 12:23:50 -0600 To: rasmol@noc1.oit.umass.edu Dear RasMol enthusiasts: During the summer months, we tackled the problem of running RasMol scripts that consist of an interactive Graphics box and an accompanying text box in Netscape. To see what we have accomplished I direct your attention to the Medical Biochemistry site at the University of Kansas Medical Center (Kansas City, Kansas, USA). In the Index, you will find links to several Interactive Molecular Modeling Modules where our RasMol scripts reside. These were created using Java Script and the Chemscape Chime plugin. Therefore, Mac users will (most likely) be unable full interact with this site. We would very much appreciate your feedback and comments. Our URL is http://www.kumc.edu/research/medicine/biochemistry/bioc800/start.html Thank you. George Helmkamp and John Grant References: <199609100035.UAA00564@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Re: Medical Biochem via Chime/Shockwave Date: Tue, 10 Sep 1996 10:57:27 +0100 To: rasmol@noc1.oit.umass.edu George Helmkamp wrote: > During the summer months, we tackled the problem of running RasMol scripts > that consist of an interactive Graphics box and an accompanying text box in > Netscape. To see what we have accomplished I direct your attention to the > Medical Biochemistry site at the University of Kansas Medical Center (Kansas > City, Kansas, USA). In the Index, you will find links to several > Interactive Molecular Modeling Modules where our RasMol scripts reside. > These were created using Java Script and the Chemscape Chime plugin. > Therefore, Mac users will (most likely) be unable full interact with this > site. We would very much appreciate your feedback and comments. Our URL is > http://www.kumc.edu/research/medicine/biochemistry/bioc800/start.html > > Thank you. George Helmkamp and John Grant It worked with my Mac running Netscape 3.0 + Chime Fergus Doherty ++++------+------+------+------+------+------+------+------+------+------+ From: YIP CHRISTOPHER M Subject: Using RasMol Enhanced version - and rotating Date: Tue, 10 Sep 1996 12:41:14 +0000 (GMT) To: rasmol@noc1.oit.umass.edu A quick question.... Is there a manual out for the enhanced version from Berkeley?.. I'm trying to figure out how the Rotate Bond option works in the toolbox. I looked on the WWW site but it didn't have explicit instructions on which bonds could be rotate or where to click etc.... Thanks Chris. ++++------+------+------+------+------+------+------+------+------+------+ From: Erik Lindahl Subject: Intro, and: is anyone working on "real" 3d? Date: Wed, 11 Sep 1996 10:08:21 +0200 To: rasmol@noc1.oit.umass.edu Hi, I'm new to the list - my name is Erik Lindahl, and I'm a grad student at Theoretical Physics, Royal inst. of Technology, Stockholm, Sweden. We have used the software for quite a period and really like it! However, with one of the new computers we bought, we got a pair of stereo glasses; that is, real colour stereo with LCD's in the glasses and fast switching of two different pictures on the screen. I know this is currently not implemented in RasMol, but since the basic stereo is, it wouldn't be too hard to write, would it? I'm planning on doing it myself, but I'd like to hear from other people possibly working on the same problem. The computer I'm using is a Sparc Ultra 1 with Creator 3D graphics and the glasses are called "CrystalEYES stereographics". I'm planning on writing the display code in OpenGL, for portability reasons. Any opinions on this, esp. concerning speed? sincerely, Erik Lindahl ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Intro, and: is anyone working on "real" 3d? Date: Wed, 11 Sep 1996 14:54:59 +0100 (BST) To: Erik Lindahl Cc: rasmol@noc1.oit.umass.edu Dear Erik, > I know this is currently not implemented in RasMol, but since the basic > stereo is, it wouldn't be too hard to write, would it? I'm planning on > doing it myself, but I'd like to hear from other people possibly working > on the same problem. The computer I'm using is a Sparc Ultra 1 with > Creator 3D graphics and the glasses are called "CrystalEYES > stereographics". Thanks very much for your e-mail. Support for hardware stereo has become a frequently asked question by the x-ray crystallographers here at Glaxo-Wellcome, but this is one of the first times I've heard it requested externally. You'll be pleased to hear that I was given first pair of LCD glasses just two weeks ago, with the hope of adding stereo to RasMol. There are several potential methods of achieving hardware support: [1] Develop an OpenGL implementation of x11win.c, using the GLX library and using "glDrawPixels" rather than "XPutImage" or "XShmPutImage". This still would use RasMol to perform rendering, but OpenGL to put the resulting bitmap on the screen. [2] Add Platform specific hardware stereo support using old-style "tall" screen support, overlaying two normal X Windows in the top and bottom halves of the screen. [3] Add platform specific support using undocumented "vendor" X Windows server extensions, such as "SGIFullScreenStereo", "SUN_DGA" or "Multi-Buffering". I had originally planned to use option [3], but on a recent visit to Silicon Graphics, it became evident that although in theory this approach should work, they'd never considered the possibility of non-GL stereo. Hence the required few lines of code in their X server are missing. The approach that I currently consider most promising is [1]. I'd be interested from hearing from anybody with similar interests. Has anybody heard of a stereo MPEG viewer? 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: My Ubiquitin pages, your chymotrypsin? Date: Wed, 11 Sep 1996 16:53:50 +0100 To: rasmol@noc1.oit.umass.edu You are welcome to try out my WWW pages on the ubiquitin system, which include pdb files for display with Chime in frames. On my Mac these work OK with Netscape 3.0 and Chime 0.9. http://www.ccc.nottingham.ac.uk/~mbzmail/students/ub/ubindex.html Let me know what you think (fear and trepidation). But note: these pages are still very much under contruction, only sections 1,2,3 are complete (nearly), and section 1 and 2 contain links to the images. In return: Does anyone know of a good source of images (preferably pdb) or pages on enzyme mechanisms, especially using chymotrypsin as a model. I think there are MAGE files that deal with this, perhaps that is the best way to go, but advice would be appreciated. A MAGE plug-in might be interesting. Fergus Doherty, Biochemistry, Nottingham University, UK ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: rasmol script&win95 Date: Wed, 11 Sep 1996 14:30:26 -0400 To: rasmol@noc1.oit.umass.edu Could someone please tell me how to run a rasmol script using winows 95? I have the latest version (2.6) of rasmol. When I try to run the rasmol script: script dna3.top I get error messages saying: RASWIN caused a general protection fault in module RASWIN.EXE at 0002:0000d3b0. Registers: EAX=00000000 CS=0ee7 EIP=0000d3b0 EFLGS=00000256 EBX=00007250 SS=0fe7 ESP=0000cbf8 EBP=0000cc24 ECX=04170001 DS=0fe7 ESI=00000000 FS=0000 EDX=00000cde ES=01c7 EDI=00000000 GS=012f Bytes at CS:EIP: 26 88 41 29 8a 84 a0 9d 8b 3e be 83 c1 e7 02 c4 Stack dump: d5a5000f 0fef97e8 8bfecc64 05be0000 9999999a 3fd99999 0000d5a5 00000000 00103ff0 00000000 3ff00000 9972cc32 a0990ff7 cc640ff7 cc548bfe 18170e91 ************************** * Brian Pratt * * 7278A Lunitas Ln * * Perrysburg, OH 43551 * * (419) 666-2579 * * bboru@glasscity.net * ************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: My Ubiquitin pages, your chymotrypsin? Date: Wed, 11 Sep 1996 11:36:37 -0700 To: Fergus.Doherty@nottingham.ac.uk, rasmol@noc1.oit.umass.edu At 04:53 PM 9/11/96 +0100, Fergus Doherty wrote: >You are welcome to try out my WWW pages on the ubiquitin system, which >include pdb files for display with Chime in frames. On my Mac these >work OK with Netscape 3.0 and Chime 0.9. > >http://www.ccc.nottingham.ac.uk/~mbzmail/students/ub/ubindex.html > >Let me know what you think (fear and trepidation). But note: these >pages are still very much under contruction, only sections 1,2,3 are >complete (nearly), and section 1 and 2 contain links to the images. > very nice! Just a couple of comments which I think might 'add' to your pages for some users. These are really minor things, but I think that it will make your pages appear/function better for some users. 1) Chime allows files being viewed to be gzipp'ed on the server. This is transparent to the user, but allows for *much* faster download times. The user is still free to save the PDB/MOL files to disk, and the saved files are NOT gzip'ed. examples of 'byte savings' for structures in your page: Name Filename Type Normal Gzipped ubiquitin ubq.pdb pdb 60,185 17,139 di-ubiquitin diubq.pdb pdb 81,787 21,975 tetra-ubiq. tetraubq.pdb pdb 158,466 45,456 adenylate adenylate.mol mol 2,968 563 thiolester thiolester.mol mol 1,338 272 ---------------------------------------------------------- Totals 304,744 85,405 The savings if over 200k overall, but for large files, like the tetra-ubiquitin , there is a savings of 100k. I think that for low-bandwidth links, like over a 14k modem, or over the atlantic, the smaller file sizes add the 'useability' of your pages. GZip is available for all platforms, including the mac, and you can just gzip the files and change names back to original name (ie. remove the '.gz' extension . (you can leave the gzip extension on the files, but this requires changing MIME type configs for your HTTP server) 2) For Chime users that are forced to use Windows on PC's it is nice to include a 'palette=foreground' so that the colors come out nice on spacefill/ribbon images. [note: there can only be one plugin on a page with the 'palette=foreground' tag, and because of a bug in the 0.9 version of Chime on window's it does *NOT* handle multiple palette=foreground tags well (this has been fixed in the soon-to-be-released version] I think the inclusion of Chime 'buttons' to highlight features of the proteins is a great feature (although I wish you had more of these). I also want to complement you on your ending of your RASMol scripts with 'select all'. This allows the user to use the display menu items even after your had selected some sub-region of the display to highlight. (this is something I forgot in my CSML script parser, although it has been added now.) >In return: > >Does anyone know of a good source of images (preferably pdb) or pages on >enzyme mechanisms, especially using chymotrypsin as a model. I think >there are MAGE files that deal with this, perhaps that is the best way >to go, but advice would be appreciated. A MAGE plug-in might be >interesting. I have been researching MAGE support for Chime off and on for quite sometime. My current thoughts are this: A MAGE file could be represented as an HTML file with Chime plugins and Chime buttons/toggle buttons. The 'Text window' becomes the text of the html file, and then for each kinemage you have a chime plugin with buttons for each view, and then a 'control' panel with the kinemage specific toggles. Captions could be displayed in a frame... (the above is overly simplified, there are obviously MAGE features that would need to be added to Chime) If the original PDB file was supplied then that could be used to generate the backbone, and the user would still have the entire PDB file available if they wished. So my current thinking is along two lines: a) create a "stand alone" program that produces a HTML file based on a MAGE file as input. This program would have to be used by authors of MAGE files to make then accessible within a browser. Some of the neat benefits of this approach is that this file could be edited and further enhanced to take advantage of some of the additional options available within HTML/Chime. b) Take the 'a' processor and build it into Chime, so that if a MAGE file was encountered the Chime plugin would essentially 'redirect' the netscape browser to an HTML file created on the fly that would allow the user to view the MAGE file. I arrived at these thoughts because: 1) the multiple window architecture of MAGE doesn't make sense within a browser plugin. 2) it would not make sense to try and incorporate all of the text display features of MAGE within a plugin when the plugin is sitting *within* a browser that has all these features plus many more. I would be interested on anyone's thoughts on MAGE file support 'within' a web browser, via a plugin or whatever... Does any of this make sense ? -tim (Principal Architect - Chemscape/Chime, MDL Info Sys.) ps. please forgive any typos (and other nonsense), I threw this message together rather quickly. > >Fergus Doherty, >Biochemistry, >Nottingham University, UK > References: <3.0b11.32.19960911113629.00c43930@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: My Ubiquitin pages, your chymotrypsin? Date: Thu, 12 Sep 1996 09:12:20 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Excerpts from mail: 11-Sep-96 Re: My Ubiquitin pages, you.. by Tim Maffett@mdli.com > I would be interested on anyone's thoughts on MAGE file support > 'within' a web browser, via a plugin or whatever... Does any of this > make sense ? > Since MAGE can be launched with a click on a web page link to produce its own (resizable) windows, putting those windows into an HTML (e.g. frames) format seems redundant, or even constraining. In a real sense, Chime is both similar and complementary to MAGE in allowing web page authors to choose coordinate files, emphasize key features (buttons), and add explanatory text. The big plus for Chime is that it allows the user to manipulate the displays with a RasMol-like menu. As such, it also makes for a terrific transition for those students who will make their own RasMol displays and write their own scripts. So, Tim, I hope the Chime-team will continue to focus all of its time and creative energies on adding more plug-in features to the current and future improvements of RasMol. -Will McClure PS. A plug for a Chime-based Protein Architecture tutorial: It is linked from: http://info.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html or reached directly at: http://info.bio.cmu.edu/Courses/BiochemMols/ProtG/ProtGMain.htm ++++------+------+------+------+------+------+------+------+------+------+ From: BRIGGS STEPHEN L Subject: stereo locked Date: Thu, 12 Sep 1996 15:03:04 +0000 (GMT) To: rasmol@noc1.oit.umass.edu I loaded the newest version 9/4/96 Berkeley-enhanced RasMol-2.6-ucb-beta for Windows/ The stereo button is locked and I am unable to display the stereo application> PC Computer: Intel pentium 120 24 megab of ram Steve ++++------+------+------+------+------+------+------+------+------+------+ From: b_duke@lacebark.ntu.edu.au Subject: A Masters degree in Comp Chem over the internet. Date: Sat, 14 Sep 1996 09:06:25 +1100 (EETDT) To: rasmol@noc1.oit.umass.edu (Rasmol list) Greetings to all on the Rasmol list. I am posting this to the Rasmol list, because the materials we are using in this proposal makes use of Rasmol and are likely to make more use of it in future. We express out thanks to Roger Sayle for making this excellent software available. I am posting to several lists, so please accept my apologies if you receive it several times. Four Australian Computational Chemists have come together to offer a taught Masters degree in Computational Chemistry which will be taught in part entirely in distance education mode using the World Wide Web. We believe this proposal to be highly innovative and possibly unique. The four chemists are Brian Salter-Duke (Brian Duke in the literature) from the Northern Territory University, Margaret Wong from the Swinburne University of Technology, Ted LLoyd from the Victorian College of Pharmacy, Monash University and Brian Yates from the University of Tasmania. The course will take a very full 12 months to complete. The first 8 months will consist of six core units:- The Scope of Computational Chemistry Molecular Modelling Approximate Quantum Chemistry Basic QSAR Ab initio Quantum Chemistry Molecular Mechanics and Dynamics and one out of three electives:- Advanced Molecular Modelling Advanced ab initio Quantum Chemistry Advanced QSAR This part of the course will be taught entirely over the web. It can be completed part-time over a period up to 20 months. The second part of the course is a four month project carried out as a full time student in one of the four universities. The course starts in Febuary 1997. Fees have not yet been finally determined, but they are likely to be around AUS$12,000 (about US$9,500) for the whole course. Accreditation for the course as a Master of Science in Computational Chemistry has already been obtained at the Northern Territory University. Accreditation is close to being obtained for a Master of Applied Science in Computational Chemistry at Swinburne University of Technology. The accreditation process is still being followed at Monash University. Students will be able to take out any of the degrees offered. The university where the project is carried out will be the normal degree to be obtained. The project can be done in any of the four universities but for various reasons the degree will only be offered by some of the four universities in 1997. Students from all over the world are welcome. You will need good internet access and a graphics browser. Materials have been designed to suit a range of browsers. Other software will be made available over the internet from our home sites. For more information go to the Home page of the project that resulted in this development:- http://www.chem.swin.edu.au/CAUT.html or direct to a page that describes the degree:- http://lacebark.ntu.edu.au/msc/ We welcome expressions of interest and comments on this proposal. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89410460 e-mail: b_duke@lacebark.ntu.edu.au WWW http://lacebark.ntu.edu.au/chemistry ++++------+------+------+------+------+------+------+------+------+------+ From: Yoshiteru Wakabayashi <50mrm012@is.icc.u-tokai.ac.jp> Subject: Greeting and Question Date: Fri, 13 Sep 96 09:53:47 JST To: rasmol@noc1.oit.umass.edu Hi, I'm new to this list . My name is Yoshiteru Wakabayashi, grad student for Tokai Univ. school of medicine JAPAN. Actually, I first subscribed to this list few months ago and I'm afraid that my greeting was so late to all of you, and this is my first message to this mailing list. I want to know about the PDB format. In the PDB file format the document goes like this.(example) ATOM 211 CA LEU A 91 12.911 -6.255 11.578 1.00 13.00 1ABO 352 ATOM 212 C LEU A 91 14.075 -5.463 12.168 1.00 13.62 1ABO 353 ATOM 213 O LEU A 91 15.111 -6.036 12.509 1.00 14.99 1ABO 354 ATOM 214 CB LEU A 91 13.166 -6.517 10.085 1.00 13.39 1ABO 355 ATOM 215 CG LEU A 91 12.038 -7.272 9.364 1.00 17.55 1ABO 356 ATOM 216 CD1 LEU A 91 12.132 -7.079 7.861 1.00 19.53 1ABO 357 ATOM 217 CD2 LEU A 91 12.066 -8.745 9.743 1.00 15.77 1ABO 358 ATOM 218 N GLY A 92 13.920 -4.147 12.267 1.00 12.34 1ABO 359 ATOM 219 CA GLY A 92 14.994 -3.328 12.803 1.00 11.85 1ABO 360 ATOM 220 C GLY A 92 14.672 -1.845 12.788 1.00 10.93 1ABO 361 And in the command window typing 'hbonds' command shows me the hydrogen bonding of the protein molecule's backbone. I want to know where's the information for the 'hbonds' in this PDB format. I'm investigating for structure's characteristics, especialy for Beta strands, and I'd like to calculate the distance between the atoms, which are related to the hydrogen bonds. Could anybody tell me about this PDB format? ======================================================================= Yoshiteru Wakabayashi; Tokai Univ. School of Medicine, Dept. of Biomedical Engineering Kanagawa,JAPAN 50mrm012@is.icc.u-tokai.ac.jp ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Greeting and Question Date: Thu, 12 Sep 1996 19:14:20 -0700 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu At 09:53 AM 9/13/96 JST, Yoshiteru Wakabayashi wrote: >Hi, > >I'm new to this list . >My name is Yoshiteru Wakabayashi, >grad student for Tokai Univ. school of medicine JAPAN. > >Actually, I first subscribed to this list few months ago > and I'm afraid that my greeting was so late to all of you, and this is > my first message to this mailing list. > >I want to know about the PDB format. >In the PDB file format the document goes like this.(example) > >ATOM 211 CA LEU A 91 12.911 -6.255 11.578 1.00 13.00 1ABO 352 >ATOM 212 C LEU A 91 14.075 -5.463 12.168 1.00 13.62 1ABO 353 >ATOM 213 O LEU A 91 15.111 -6.036 12.509 1.00 14.99 1ABO 354 >ATOM 214 CB LEU A 91 13.166 -6.517 10.085 1.00 13.39 1ABO 355 >ATOM 215 CG LEU A 91 12.038 -7.272 9.364 1.00 17.55 1ABO 356 >ATOM 216 CD1 LEU A 91 12.132 -7.079 7.861 1.00 19.53 1ABO 357 >ATOM 217 CD2 LEU A 91 12.066 -8.745 9.743 1.00 15.77 1ABO 358 >ATOM 218 N GLY A 92 13.920 -4.147 12.267 1.00 12.34 1ABO 359 >ATOM 219 CA GLY A 92 14.994 -3.328 12.803 1.00 11.85 1ABO 360 >ATOM 220 C GLY A 92 14.672 -1.845 12.788 1.00 10.93 1ABO 361 > >And in the command window typing 'hbonds' command shows me the hydrogen >bonding of the protein molecule's backbone. I want to know where's the >information for the 'hbonds' in this PDB format. >I'm investigating for structure's characteristics, especialy for Beta strands, >and I'd like to calculate the distance between the atoms, which are related to >the hydrogen bonds. There are no bonds specified in this PDB file either, but Rasmol will display bonds as well. The bonds AND the hydrogen-bonds are generated by rasmol 'on the fly' by doing distance calculations. The routine within rasmol that does both of these functions is CreateMoleculeBonds(). The second argument to this routine specifies if covalent radii should be used (if True) or if hydrogen bonding rules should be used (False). This routine also used several other routines, the main one being TestBonded(), which also takes a flag argument that means the same as the arg coming into CreaetMoleculeBonds(). The CreateMoleculeBonds() looks fairly complicated at first, but it is really just comparing distances between 'all atoms which might be bonded' by calling TestBonded(). Because this would be a order n^2 problem, where n is the number of atoms, it uses a 'trick' of sub dividing the 3D space into 'voxels' which keep track the atoms within their 'cube' of space. Once space is divided into voxels you only need to look at the atoms in the adjacent voxels that are within a reasonable distance for bonding. This greatly reduces the total number of check that you must perform. That may be more info that you wanted, but I thought I would point it out because you said you were interested in doing your own calculations. >Could anybody tell me about this PDB format? You can find lots of info on the PDB file format at: http://www.pdb.bnl.gov/ -tim > >======================================================================= >Yoshiteru Wakabayashi; >Tokai Univ. School of Medicine, Dept. of Biomedical Engineering >Kanagawa,JAPAN >50mrm012@is.icc.u-tokai.ac.jp ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: chime plug-in Date: Thu, 12 Sep 1996 23:29:11 -0400 To: rasmol@noc1.oit.umass.edu I recently created some *.htm documents and incorporated some of the *.pdb files in the pages. The site is to act as a supplement to my course material in biochemistry and medicinal chemistry. Unfortunately, when I access the site (despite having netscape 3.0 and chime plug-in installed correctly) the *.pdb files will not load. Either large icons representing the embedded files are displayed or netscape looks for the plug-in and cannot find it. If I double click the large icons representing the embedded files rasmol opens as an external program (helper application). Any ideas as to why I am having problems? Is this a server compatibility issue. Our university is using Netscape Enterprise server. Thank you in advance. ************************** * Brian Pratt * * 7278A Lunitas Ln * * Perrysburg, OH 43551 * * (419) 666-2579 * * bboru@glasscity.net * ************************** Yoshiteru Wakabayashi <50mrm012@is.icc.u-tokai.ac.jp> ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Greeting and Question Date: Fri, 13 Sep 1996 11:33:34 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: Tim Maffett , Dear Yoshiteru, > >And in the command window typing 'hbonds' command shows me the hydrogen > >bonding of the protein molecule's backbone. I want to know where's the > >information for the 'hbonds' in this PDB format. > >I'm investigating for structure's characteristics, especialy for Beta > >strands, and I'd like to calculate the distance between the atoms, > >which are related to the hydrogen bonds. > The bonds AND the hydrogen-bonds are generated by rasmol 'on the fly' > by doing distance calculations. The routine within rasmol that does > both of these functions is CreateMoleculeBonds(). Close by not quite right. The hydrogen bonds are calculated by RasMol in the routine "CalcHydrogenBonds()" which in turn calls one of the two routines "CalcProteinHBonds()" or "CalcNucleicHBonds()". The protein backbone hydrogen bond calculation that you refer to is based upon Kabsch and Sander's DSSP algorithm, which is described in detail in the paper: ! Wolfgang Kabsch and Christian Sander, "Dictionary of Protein ! Secondary Structure: Pattern Recognition of Hydrogen-Bonded and ! Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983. This paper also describes RasMol's algorithm to determine the locations of protein secondary structural elements. For example, one of the rules for an antiparallel beta-sheet is that residues i and j form a beta sheet if i is hbonded to j and i+1 is hbonded to j-1. Another rules is that residues i+1 and i+2 form a 3/10 helix if i is bonded to i+3 and i+1 is hbonded to i+4. ! There is no generally corrected H bond definition, as there is no sharp ! border between the quantum-mechanical and electrostatic regimes (wave ! function overlap dominates at short distances and electrostatic ! interaction at larger distnaces) and no discontinuity of the interaction ! energy as a function of distance or alignment. ! ! Main chain hydrogen bonds, used in determining secondary structure, ! may be described by an electrostatic model. The electrostatic ! interaction energy between two H-bonding groups is calculated by placing ! patial charges on the C, O (+q_1,-q_1) and N, H (+q_2,-q_2) atoms. ! This produces the energy equation ! ! E = q_1 q_2 ( 1/r(ON) + 1/r(CH) - 1/r(OH) - 1/r(CN) ) * f ! ! with q_1 = 0.42e and q_2 = 0.20e, e being the unit electron charge ! and r(AB) the interatomic distance from A to B. In chemical units, ! r is in angstroms, the dimension factor f = 322, and E is in kcal/mol. ! Typically a good hydrogen bond has a binding energy of -3 kcal/mol. ! ! The default cutoff value is -0.5 kcal/mol, as described in Kabsch and ! Sander's paper. This generous limit permits bifurcated H-bonds and ! errors in coordinates. One of the features of Kabsch and Sander's hydrogen bond definition is that it only applies to protein backbone hydrogen bonds. This means that RasMol is unable to calculate and display sidechain-sidechain or sidechain-backbone hydrogen bonds in proteins, on inter- and intra- molecular hydrogen bonds with small molecules. This deficiency may be corrected in a future version of RasMol. I hope this answers your question. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Dewey Williams Subject: Re: chime plug-in Date: Fri, 13 Sep 1996 12:52:55 -0400 To: rasmol@noc1.oit.umass.edu At 11:29 PM 9/12/96 -0400, you wrote: >I recently created some *.htm documents and incorporated some of the *.pdb files > in the pages. The site is to act as a supplement to my course material in bioc >hemistry and medicinal chemistry. Unfortunately, when I access the site (despit >e having netscape 3.0 and chime plug-in installed correctly) the *.pdb files wil >l not load. Either large icons representing the embedded files are displayed or > netscape looks for the plug-in and cannot find it. If I double click the large > icons representing the embedded files rasmol opens as an external program (help >er application). Any ideas as to why I am having problems? Is this a server co >mpatibility issue. Our university is using Netscape Enterprise server. Thank y >ou in advance. The server must be told what MIME type the pdb files are and how to handle them. This is referred to as setting 'content types' amoung other things. Speak with your server administrator. I believe pdb (and other files of this type) should be set as chemical/x-pdb (or x-mol, etc). That is the way I have it set on my Website server. Dewey Williams - Lab Manager williams@unccvm.uncc.edu UNC-Charlotte Chemistry Dept. http://www.chem.uncc.edu "These are my ideas and no one else will claim them." "If you are not part of the solution, you are part of the precipitate" ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: home site Date: Fri, 13 Sep 1996 13:19:55 -0400 To: rasmol@noc1.oit.umass.edu If anyone is interested take a look at: http://www.onu.edu/user/fs/dkinder This is still in an embryonic stage, but I am looking forward to learning more and developing it. It is meant to help students with course material in biochemistry and medicinal chemistry. We are still working on server configs etc. Download time is terrible on this server (depending on the time of day it could be worse). Having some files in cache will help tremendously. None the less, I am excited about its potential and would warmly embrace criticisms in any manner. ************************** * Brian Pratt * * 7278A Lunitas Ln * * Perrysburg, OH 43551 * * (419) 666-2579 * * bboru@glasscity.net * ************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: chime plug-in Date: Fri, 13 Sep 1996 10:32:04 -0700 To: rasmol@noc1.oit.umass.edu At 12:52 PM 9/13/96 -0400, you wrote: >At 11:29 PM 9/12/96 -0400, you wrote: >>I recently created some *.htm documents and incorporated some of >>the *.pdb files in the pages. The site is to act as a supplement to my >>course material in biochemistry and medicinal chemistry. Unfortunately, >>when I access the site (despite having netscape 3.0 and chime plug-in >>installed correctly) the *.pdb files will not load. Either large icons >>representing the embedded files are displayed or netscape looks for the >>plug-in and cannot find it. If I double click the large icons >>representing the embedded files rasmol opens as an external program >>(helper application). Any ideas as to why I am having problems? Is >>this a server compatibility issue. Our university is using Netscape >>Enterprise server. >> >>Thank you in advance. > >The server must be told what MIME type the pdb files are and how to handle >them. This is referred to as setting 'content types' amoung other things. > >Speak with your server administrator. I believe pdb (and other files of >this type) should be set as chemical/x-pdb (or x-mol, etc). That is the way >I have it set on my Website server. > >Dewey Williams - Lab Manager williams@unccvm.uncc.edu For information on configuring your HTTP server with the correct MIME types, and information of the MIME types Chime supports, see: 0 0, 0 0,ffff http://www.mdli.com/chemscape/chime/chimehelp.html#Ref5 The chemical MIME types used by chime are the 'official' chemical MIME types specified at: http://www.ch.ic.ac.uk/chemime/chemime_id.html which can be found off of the 'Chemical MIME Home Page': http://www.ch.ic.ac.uk/chemime/ One additional MIME type that Chime supports, that is of particular interest to this mailing list, is the Rasmol script MIME type. For this we use the MIME type that was informally agreed upon in this group, which is 'application/x-spt' Some sites also use 'application/x-rasmol', and I am considering adding this, for compatibility reason, to future versions of Chime. -tim References: <3.0b11.32.19960913103038.00b8c650@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Chime plug-in version 1.0? and gzip? Date: Sun, 15 Sep 1996 14:37:05 +0100 To: rasmol@noc1.oit.umass.edu Tim, Two questions: Any idea when Chime 1.0 will be available? I gziped my pdb files as you suggested recently, and indeed file size was reduced markedly, this seems to help loading even over the campus nEthernet from the server. But how does this work? Does the UNIX WWW server decompress on the fly? Or does Netscape do this (I don't think it does it needs a helper?) Or does Chime? TIA Fergus Biochemistry, Nottingham University. ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Chime plug-in version 1.0? and gzip? Date: Sun, 15 Sep 1996 21:54:34 -0700 To: Fergus.Doherty@nottingham.ac.uk, rasmol@noc1.oit.umass.edu At 02:37 PM 9/15/96 +0100, Fergus Doherty wrote: >Tim, > >Two questions: > >Any idea when Chime 1.0 will be available? With any luck it will be within the next month... We are coordinating several things to make get the release done. I am sorry I can give and exact date, it should be worth the wait though (I hope!) > >I gziped my pdb files as you suggested recently, and indeed file size >was reduced markedly, this seems to help loading even over the campus >nEthernet from the server. But how does this work? Does the UNIX WWW >server decompress on the fly? Or does Netscape do this (I don't think it >does it needs a helper?) Or does Chime? Chime is the one that is decompressing the files as it receives them. It is, as you see, transparent to the user, and there is really no way to tell if the file was downloaded compress/uncompressed once it is at the user's machine. I am glad that it worked for you. I think it is a really useful feature, and that's why I added it. Our web server has been very slow at times, and it has really helped there. The www's 3D 'environment' standard, VRML, also use gzip for the standard compression for files being transmitted over the net, and it has also been well accepted there. -tim > >TIA > >Fergus > >Biochemistry, Nottingham University. > > rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Chime plug-in version 1.0? and gzip? Date: Mon, 16 Sep 1996 15:25:39 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: Fergus.Doherty@nottingham.ac.uk, Tim Maffett , > Chime is the one that is decompressing the files as it receives them. > It is, as you see, transparent to the user, and there is really no way to > tell if the file was downloaded compress/uncompressed once it is at the > user's machine. > I am glad that it worked for you. I think it is a really useful > feature, and that's why I added it. The ability to decompress "gzip" .gz files and uncompress UNIX "compress" .Z files is also available in UNIX RasMol. This functionality was originally added for sites wishing to maintain complete local copies of PDB. The mechanism in RasMol differs from that in Chime. RasMol spawns the locally installed version of gzip as a helper application, rather than include gzip source code. This allows easy support for multiple decompression algorithms, including future, more efficient compression algorithms, such as "bzip", as well as bug fixes and performance improvements. The disadvantage is that such a mechanism isn't available under Microsoft Windows, Apple Macintosh or other platforms. To conclude: In addition to Chime, .pdb.gz files can also be viewed using RasMol, but only on UNIX workstations. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Cerpovicz Subject: front end links? Date: Mon, 16 Sep 1996 17:11:58 -0400 To: rasmol@noc1.oit.umass.edu Greetings all. Does anyone have any experience linking front ends to RasMol using Visual Basic or other similar programs? I don't know too much about this yet but I was told it could probably be done. Any information would be greatly appreciated. Paul ----------------------------------------------------------------------------- Dr. Paul Cerpovicz paulcerp@gsaix2.cc.gasou.edu Department of Chemistry Herty Building, L.B. 8064 Tel: (912) 871-1883 Georgia Southern University Fax: (912) 681-0699 Statesboro, GA 30460 ++++------+------+------+------+------+------+------+------+------+------+ From: ozgur.huner@utoronto.ca (Ozgur Huner) Subject: Re: is anyone working on "real" 3d? Date: Tue, 17 Sep 1996 02:51:18 -0400 To: rasmol@noc1.oit.umass.edu Dear Erik and Roger: I think you guys would be onto a good thing, making a virtual macromolecular structure modeler! I saw this web site (http://www.pc.chemie.th-darmstadt.de/vrml/) had a downloadable PDB-to-VRML converter. Would this be a good start? I would like to know myself and would be ecstatic to contribute in any way I can. Sincerely, Ozgur Ozgur Huner graduate student Clinical Biochemistry University of Toronto Toronto, ON, Canada ozgur.huner@utoronto.ca ________________________________ H. Ozgur Huner Banting and Best Diabetes Centre The Toronto Hospital MBRC4-909 200 Elizabeth Street Toronto, ON, Canada M5G 2C4 tel.: (416) 340-3165 e-mail: ozgur.huner@utoronto.ca X-Confirm-Reading-To: "Andrew Coulson" X-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Coulson" Subject: Re: front end links? Date: Tue, 17 Sep 1996 11:03:59 +0000 To: rasmol@noc1.oit.umass.edu > Does anyone have any experience linking front ends to RasMol using Visual > Basic or other similar programs? I don't know too much about this yet but I > was told it could probably be done. Any information would be greatly > appreciated. > > Paul Using VisualBasic, it's easy but hard... Like a lot of modern windows-type programming, there is a lot of jargon, it is difficult to get the general idea of what you're trying to do, and it is hard to find the information you really need in the manual, but actually driving RasMol from a VB program only needs about 3 lines of code. How to do it: Get a Visual Basic book which has a chapter about DDE and linking to other applications. Write a couple of Visual Basic programs which put text into boxes, make buttons appear and disappear, set colours, etc. Read the bit in the book which tells you how to turn the text in a Visual Basic window into a command for another application -- in this case, RasMol -- and how to display what the application sends back, and then do it. As I say, three lines of code should be enough. Be warned that (at least when I last looked) DDE will not work with the 32-bit version of Rasmol for Windows. I _think_ that Roger told me that this is a Microsoft problem. Well, I'm sure he told me that; what I only think I remember is that he had discovered a way of circumventing the deep plots of Bill Gates's minions, and that he was going to implement it. Perhaps he already has? Andrew Coulson ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Greeting and Question Date: Tue, 17 Sep 1996 19:40:14 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu > > > Dear Yoshiteru, > > >And in the command window typing 'hbonds' command shows me the hydrogen > > >bonding of the protein molecule's backbone. I want to know where's the > > >information for the 'hbonds' in this PDB format. > > >I'm investigating for structure's characteristics, especialy for Beta > > >strands, and I'd like to calculate the distance between the atoms, > > >which are related to the hydrogen bonds. > > > The bonds AND the hydrogen-bonds are generated by rasmol 'on the fly' > > by doing distance calculations. The routine within rasmol that does > > both of these functions is CreateMoleculeBonds(). > > Close by not quite right. The hydrogen bonds are calculated by RasMol > in the routine "CalcHydrogenBonds()" which in turn calls one of the two > routines "CalcProteinHBonds()" or "CalcNucleicHBonds()". > > The protein backbone hydrogen bond calculation that you refer to is based > upon Kabsch and Sander's DSSP algorithm, which is described in detail in > the paper: > > ! Wolfgang Kabsch and Christian Sander, "Dictionary of Protein > ! Secondary Structure: Pattern Recognition of Hydrogen-Bonded and > ! Geometrical Features", Biopolymers, Vol.22, pp.2577-2637, 1983. > > This paper also describes RasMol's algorithm to determine the locations > of protein secondary structural elements. For example, one of the rules > for an antiparallel beta-sheet is that residues i and j form a beta sheet > if i is hbonded to j and i+1 is hbonded to j-1. Another rules is that > residues i+1 and i+2 form a 3/10 helix if i is bonded to i+3 and i+1 is > hbonded to i+4. > > ! There is no generally corrected H bond definition, as there is no sharp > ! border between the quantum-mechanical and electrostatic regimes (wave > ! function overlap dominates at short distances and electrostatic > ! interaction at larger distnaces) and no discontinuity of the interaction > ! energy as a function of distance or alignment. > ! > ! Main chain hydrogen bonds, used in determining secondary structure, > ! may be described by an electrostatic model. The electrostatic > ! interaction energy between two H-bonding groups is calculated by placing > ! patial charges on the C, O (+q_1,-q_1) and N, H (+q_2,-q_2) atoms. > ! This produces the energy equation > ! > ! E = q_1 q_2 ( 1/r(ON) + 1/r(CH) - 1/r(OH) - 1/r(CN) ) * f > ! > ! with q_1 = 0.42e and q_2 = 0.20e, e being the unit electron charge > ! and r(AB) the interatomic distance from A to B. In chemical units, > ! r is in angstroms, the dimension factor f = 322, and E is in kcal/mol. > ! Typically a good hydrogen bond has a binding energy of -3 kcal/mol. > ! > ! The default cutoff value is -0.5 kcal/mol, as described in Kabsch and > ! Sander's paper. This generous limit permits bifurcated H-bonds and > ! errors in coordinates. > > > One of the features of Kabsch and Sander's hydrogen bond definition is > that it only applies to protein backbone hydrogen bonds. This means that > RasMol is unable to calculate and display sidechain-sidechain or > sidechain-backbone hydrogen bonds in proteins, on inter- and intra- > molecular hydrogen bonds with small molecules. This deficiency may be > corrected in a future version of RasMol. > Hm, I've examined InsightII and MolMol2.2. In these programs hbonds are calculated simply by testing the distance between donor and acceptor AND the angle "atom bonded covalently to donor -- donor -- acceptor" which must be ~ 0..30 degrees. It wouldn't be so hard to implement this in the actual RasMol-code. I know this way of determining hbonds is not the best, but It's a starting-point for developing a system in RasMol for exact hbonds- calcualtion between backbone and sidechain, sidechain-sidechain, ... . At the moment you could uses DSSP for the backbone, distance and angles for the rest. thank you, Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: gzip Date: Wed, 18 Sep 1996 23:44:55 -0400 To: rasmol@noc1.oit.umass.edu I am currently working with some chime examples on my home page which is serving as a supplement to class/lecture material. I was made aware of gzip software to decrease the size of *.pdb files, but I am not sure which version to download. Our server, Netscape Enterprise, runs Windows NT I believe. Should I use the DOS based version of gzip? Incidentally, the gzip download site is pretty meager on documentation and I have had no luck each time I have tried to download it. The server seems to be unstable and I get errors during or after the download. ************************** * Brian Pratt * * 7278A Lunitas Ln * * Perrysburg, OH 43551 * * (419) 666-2579 * * bboru@glasscity.net * ************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: gzip Date: Wed, 18 Sep 1996 22:09:14 -0700 To: rasmol@noc1.oit.umass.edu At 11:44 PM 9/18/96 -0400, Brian Pratt wrote: >I am currently working with some chime examples on my home page which is serving as a supplement to class/lecture material. I was made aware of gzip software to decrease the size of *.pdb files, but I am not sure which version to download. Our server, Netscape Enterprise, runs Windows NT I believe. Should I use the DOS based version of gzip? >Incidentally, the gzip download site is pretty meager on documentation and I have had no luck each time I have tried to download it. The server seems to be unstable and I get errors during or after the download. > Any version of gzip can be used to compress the file. The output of gzip is platform independent, a file compressed with gzip on unix can be decompress on windows, mac, etc. Using gzip is very easy, from MS-DOS you can simply type: gzip and the file will be compressed, and renamed with a 'z' appended to the filename. (the extension on the file being compressed must be only two characters, so there is room for the 'z'. If the file has a 3 character extension the dos gzip will fail.) So, for a dos example of compressing 'mystruct.pdb' you would: ren mystruct.pdb mystruct.pd (this makes room for 'z' extension) gzip mystruct.pd (compresses file and creates 'mystruct.pdz') ren mystruct.pd mystruct.pdb (change back to original name, so http server will still map .PDB -> MIME type for pdb) The unix version of gzip appends a '.gz' to the filename, so you would get 'mystruct.pdb.gz' when you compress 'mystruct.pdb'. I would assume that the mac version does the name thing, because there is no '8.3' limit on the mac filenames (like unix). Hope that helps. It really is pretty easy, just make sure you have backups of your pdb files in case something does go wrong. -tim > > >************************** >* Brian Pratt * >* 7278A Lunitas Ln * >* Perrysburg, OH 43551 * >* (419) 666-2579 * >* bboru@glasscity.net * >************************** > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: Re: gzip Date: Thu, 19 Sep 1996 09:50:42 -0400 To: rasmol@noc1.oit.umass.edu Thanks! That helped alot! ++++------+------+------+------+------+------+------+------+------+------+ ++++------+------+------+------+------+------+------+------+------+------+ From: Lee Liolios Subject: UNIX rasmol problems Date: Fri, 20 Sep 1996 11:51:12 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Hello: I work at a University and just recently installed the rasmol viewer. It works very well for the most part. However, there is a URL (www.cs.stedwards.edu/contrib/Chemistry/Biotext/helix.pdb) that doesn't launch the rasmol helper from netscape on our SUNs, but works fine on our PCs running netscape. Any ideas? It seems strange that this only happens for this URL and the file in fact ends with pdb so I'm really confused as to why netscape doesn't launch rasmol? Any insight into why this is would be greatly appreciated. Thanks -- Lee Liolios UNIX Systems Administrator University Libraries State University of New York at Buffalo liolios@acsu.buffalo.edu voice: 716-645-3961 fax: 716-645-3844 http://www.acsu.buffalo.edu/~liolios ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: UNIX rasmol problems Date: Fri, 20 Sep 1996 09:46:12 -0700 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu At 11:51 AM 9/20/96 -0400, Lee Liolios wrote: >Hello: > >I work at a University and just recently installed the rasmol >viewer. It works very well for the most part. However, there is >a URL (www.cs.stedwards.edu/contrib/Chemistry/Biotext/helix.pdb) >that doesn't launch the rasmol helper from netscape on our >SUNs, but works fine on our PCs running netscape. > The problem is that the MIME type that the server is sending for the pdb file is 'chemistry/x-pdb' instead of 'chemical/x-pdb'. The MIME type configuration file of your HTTP server needs to be edited to send the correct 'chemical/...' MIME types instead of 'chemistry/...'. There is some general information on our web site about configuring different HTTP servers with the standard chemical MIME types: http://www.mdli.com/chemscape/chime/chimehelp.html#Ref5 Note: the MIME type list at the above URL is not a comprehensive 'chemical/..' list, it only includes those that Chime supports. The reason the 'broken' MIME type still works on the PC is that if you do *not* have a helper app 'registered' within Netscape Navigator then Netscape goes to the Windows OS and asks for any program that has said that it will handle the '.pdb' file extension. Rasmol does handle the .pdb file extension, so Windows tells Netscape to go ahead and load the Rasmol program. (I hope that made sense...) -tim >Any ideas? It seems strange that this only happens for this URL >and the file in fact ends with pdb so I'm really confused as to >why netscape doesn't launch rasmol? > >Any insight into why this is would be greatly appreciated. > > >Thanks >-- >Lee Liolios >UNIX Systems Administrator >University Libraries >State University of New York at Buffalo >liolios@acsu.buffalo.edu >voice: 716-645-3961 fax: 716-645-3844 >http://www.acsu.buffalo.edu/~liolios > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: kinemage->HTML->Chime? Date: Fri, 20 Sep 1996 20:59:54 -0500 (EST) To: Tim Maffett (Chime development team at MDLI) recently proposed a kinemage to HTML converter to enable Chime to display kinemages. Will McClure (Carnegie-Mellon U) responded: > Since MAGE can be launched with a click on a web page link to produce >its own (resizable) windows, putting those windows into an HTML (e.g. >frames) format seems redundant, or even constraining. Actually, a disadvantage I feel with MAGE is that it has only wireframe and very limited ball representations. For example, you can't show students how a spacefilling model looks -- atomic contacts appear separated by too much space in MAGE's representation. Since there are HUNDREDS of excellent kinemages already available (http://www.prosci.uci.edu), it would be advantageous to be able to view them in Chime where a full range of representations are available. Contrast the availability of kinemages with the dozen or so RasMol and Chime scripts in existence. Indeed, with the proposed converter, one could then expand/modify/adapt kinemages for Chime. Will continued: > So, Tim, I hope the Chime-team will continue to focus all of its time >and creative energies on adding more plug-in features to the current and >future improvements of RasMol. I have to second that. I'd very much like to see Chime 1.0 and perhaps even 1.1 (or at least 1.01) before the Chime-team gets distracted with a kinemage->HTML converter. However, after Chime 1.1, maybe it would be a great idea ... /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: kinemage->HTML->Chime? Date: Mon, 23 Sep 1996 15:57:15 -0500 (EST) To: Cc: (Will McClure) I forward this from Will who meant to send it to the list. -Eric ------------------------------ Sat, 21 Sep 1996 12:19:30 -0400 (EDT) From: William R Mcclure Subject: Re: kinemage->HTML->Chime? To: emartz@microbio.umass.edu Excerpts from mail: 20-Sep-96 kinemage->HTML->Chime? by "Eric Martz"@microbio.um > Actually, a disadvantage I feel with MAGE is that it has only > wireframe and very limited ball representations. For example, you > can't show students how a spacefilling model looks -- atomic contacts > appear separated by too much space in MAGE's representation. "Almost, but not quite". Clearly, 1) RasMol is more versatile in the display and coloring of molecules, and 2) most kinemages use only wireframe. However, any kinemage you've written or downloaded can be modified to put Ball & Sticks or Spacefill in all or in only a selected part of the display. The "@balllist" line sets the color, label, and radius of the selected atoms. Making these changes with a text editor in existing kinemages is easy after doing one of the PREKIN_2.5 tutorials. I don't disagree with the main point offered by Eric, but only want to emphasize that existing kinemages can easily be changed to suit one's specific purposes including text and caption alterations. -Will /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: rendering 2d Date: Mon, 23 Sep 1996 21:27:18 -0400 To: rasmol@noc1.oit.umass.edu I have a friend who is creating our molecules in hyperchem. He is saving them in *.pdb and *.mol format. However, when I incorporate these files into htm documents and view them thru netscape and chime plug-in, a few of them display in 2d until I manually convert them to 3d. Why is this the case and can it be changed. In my embed options I have display set to 3d. ************************** * Brian Pratt * * 7278A Lunitas Ln * * Perrysburg, OH 43551 * * (419) 666-2579 * * bboru@glasscity.net * ************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: rendering 2d Date: Tue, 24 Sep 1996 03:31:39 -0700 To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu At 09:27 PM 9/23/96 -0400, Brian Pratt wrote: >I have a friend who is creating our molecules in hyperchem. He is saving them >in *.pdb and *.mol format. However, when I incorporate these files into htm >documents and view them thru netscape and chime plug-in, a few of them display >in 2d until I manually convert them to 3d. Why is this the case and can it be >changed. In my embed options I have display set to 3d. The likely cause is that all of the Z coordinates are 0 for some of the files, and so chime is deciding to display these in 2D. (Examples of structures whose 3D coordinates still have 0 for all Z coords are any planar structure, such as benzene.) This behavior of Chime is *supposed* to be overridden by the 'display3d=' argument, but there is a bug in the current (downloadable) version of chime which is not making 'display3d=' force the 3d display. This has been fixed for the next release of chime, but in the mean time there is a work around of adding a 'spiny=30' tag, or any of the other spin parameters. You do NOT have to start spinning or anything, but the presence of a 'spin#=' tag will force 3d display, even on molecules where all of the Z coordinates are 0. (Note 'spiny=30' is a good one because that is the default spin axis/rate, so adding it does not really change anything.) sorry for the inconvenience caused by this little bug... -tim > >************************** >* Brian Pratt * >* 7278A Lunitas Ln * >* Perrysburg, OH 43551 * >* (419) 666-2579 * >* bboru@glasscity.net * >************************** > > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: 30,000 viewed RasMol Date: Tue, 24 Sep 1996 14:50:53 -0500 (EST) To: I've just tallied up the visiting statistics for the past 9 months at my RasMol Home Page. In brief, over 30,000 people (IP addresses) have visited, and over 5,000 downloaded RasWin (2/3) or RasMac (1/3) after the 2.6 beta-2 releases, from my site alone (I'm sure many copies were downloaded also from other sites, such as Roger Sayle's site in UK and Brookhaven in US). 49% of the visitors were from the USA, and the others from 66 other countries. >1,500 downloaded my RasMol scripts. I don't have any data for Henry Brzeski's lac repressor script which I'm sure is also popular. About 4,000 people have viewed Roger's gallery images. 600 people have looked at the 'Guide to script creation ...' since it was put up 4 months ago, and in the 2 months since Margaret Wong and I brought the html manual up to 2.6 beta-2, 600 people have used it. There are plans to translate scripts or parts of the web site into French, Korean, and Spanish, though I I don't think any of the translations are finished yet. And I'm having fun :-)! More details are at http://www.umass.edu/microbio/rasmol/rastats.htm /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: Workshops for Faculty Date: Tue, 24 Sep 1996 15:35:35 -0500 (EST) To: On August 7, I gave a one-day workshop to train 19 faculty from my University how to use RasMol and Chime (also demonstrated MAGE). Each participant had a computer and got hands-on experience on each topic in the workshop. The goal was to increase use of molecular visualization in our biological science classes. I won't know how well this succeeded until I've polled the participants at the end of the semester. I'd like to hear from anyone interested in having such a workshop at your institution. I'll be happy to share notes whether or not it is possible for me to travel to help present such workshops. I've added a new web page on this, http://www.umass.edu/microbio/rasmol/workshop.htm /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Kornhauser Subject: Question with define Date: Tue, 24 Sep 1996 19:51:21 -0600 (CST) To: RasMol List Hi! I was definig some sets of atoms with a script file, but some of them seem to be too long for example with this line: define cons6 7,15,19,33,38,43,55,56,61,65,72,79,86,101,104,109,113,114,119,122,126,129,130,132,134,137,143,145,146,152,161,170,176,180,185,192,204,205,209,212,219,226,228,234,238,242,248,259,275,279,285,286,289,296,297,302,303,305,307,308,312,323,338,340,354,356,362 I get tis error: line6: Script command line too long! The cons6 set is used afterwards by other scripts. These other scripts are "standart scripts" they are used with various "defining" script files so it would be nice if I could actually make define lines as long as I want. Is this possible? Regards Adrian Kornhauser ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Question with define Date: Tue, 24 Sep 1996 22:49:03 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Here is how I would handle Adrian Kornhauser's problem with defining long lines, but perhaps someone else knows a more elegant method. select 7,15,19,33,38,43,55,56,61,65,72,79 define temp1 selected select 130,132,134,137,143,145,146,152,161 define temp2 selected ...etc... define cons6 (temp1 or temp2 or ...etc...) By the way, I should think the above lists would select residue numbers, not atom numbers. The syntax I know for atom numbers is select atomno=7 or atomno=15 or atomno=19 and so forth (which gets really cumbersome). Actually, I didn't know that commas would substitute for or's, but on checking I find that they do. Thanks! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology) Dept Microbiology, Univ Massachusetts, Amherst MA 01003-5720 413-545-2325 FAX:545-1578. Web projects include: RasMol Home Page, http://www.umass.edu/microbio/rasmol Catalog of Free Flow Cytometry Software (includes MFI which I wrote), http://www.bio.umass.edu/mcbfacs/flowcat.html - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Pratt Subject: colors Date: Wed, 25 Sep 1996 12:55:38 -0400 To: rasmol@noc1.oit.umass.edu When I incorporated some new *.mol files into my web documents the cpk color was purple. The only other color available for me to change to was monochrome. Is this a problem that was created when I made the molecules and saved them in hyperchem? ************************** * Brian Pratt * * 7278A Lunitas Ln * * Perrysburg, OH 43551 * * (419) 666-2579 * * bboru@glasscity.net * ************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: colors Date: Thu, 26 Sep 1996 18:16:10 +0100 (BST) To: Brian Pratt , Tim Maffett Cc: rasmol@noc1.oit.umass.edu Hi Brian, > >> When I incorporated some new *.mol files into my web documents the cpk color > >> was purple. The only other color available for me to change to was > >> monochrome. Is this a problem that was created when I made the molecules > >> and saved them in hyperchem? Thanks very much for your e-mail. I've had a look at the suspect mol files and concluded that RasMol reads them perfectly. The problem lies with Chime. It seems that Chime uses MDL's own library for reading MDL mol files, and this isn't quite as forgiving as RasMol's routines. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Kornhauser Subject: Problem with help. Date: Tue, 1 Oct 1996 16:42:33 -0600 (CST) To: RasMol List Hi! I was looking for help on selecting all carbons, so I went to the html manual, It said to type help expressions in the command line of rasmol. I quote from this help: "Atom expressions are composed of either primitive expressions, (for more details type "help primitives")" But when I type this rasmol responds with: "No available help on requested topic!" Am I doing something wrong, or is this help not yet available? Thanks Adrian Kornhauser ++++------+------+------+------+------+------+------+------+------+------+ From: Mitchell Miller Subject: Re: Problem with help. Date: Tue, 01 Oct 1996 21:07:59 -0600 To: rasmol@noc1.oit.umass.edu Cc: RasMol List You can select all carbons by typing RasMol> select *.c ... At 04:42 PM 10/1/96 -0600, Adrian Kornhauser wrote: > >Hi! I was looking for help on selecting all carbons, so I went to the >html manual, It said to type help expressions in the command line of rasmol. >I quote from this help: > >"Atom expressions are composed of either primitive expressions, (for more >details type "help primitives")" > >But when I type this rasmol responds with: > >"No available help on requested topic!" > >Am I doing something wrong, or is this help not yet available? > >Thanks > >Adrian Kornhauser > Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Dean Waldow Subject: Rasmol and molecules on a square lattice Date: Thu, 3 Oct 1996 12:29:51 -0700 (PDT) To: rasmol@noc1.oit.umass.edu Hello, I am new to this list and hope this is a reasonable question for the group. I would like to use rasmol to display results from monte carlo simulations of polymers on a square lattice. I have tried using pbd and xyz formats but have not found a lot of information about the file formats. I am curious to see if anyone could point me to information about generating these formats or even if using a square lattice arrangment of beads and bonds would work in rasmol? Thanks Dean W. ----------------------------------------------------------------------------- Dean Waldow, Assistant Professor (206) 535-7533 Department of Chemistry (206) 536-5055 (FAX) Pacific Lutheran University waldowda@plu.edu Tacoma, WA 98447 USA http://www.chem.plu.edu/waldow.html ----------------------------------------------------------------------------- ---> CIRRUS and the Chemistry homepage: http://www.chem.plu.edu/ <--- ----------------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Rasmol and molecules on a square lattice Date: Fri, 4 Oct 1996 12:06:35 +0100 (BST) To: rasmol@noc1.oit.umass.edu Cc: Dean Waldow Hi Dean, > I would like to use rasmol to display results from monte carlo simulations > of polymers on a square lattice. I have tried using pbd and xyz formats > but have not found a lot of information about the file formats. I am > curious to see if anyone could point me to information about generating > these formats or even if using a square lattice arrangment of beads and > bonds would work in rasmol? Thanks very much for your e-mail. I'll answer the easiest part of your question first: Yes, RasMol is quite happy displaying lattice models of proteins and other molecules. Appended to this e-mail is a PDB file mailed to me by Bill Hart at Sandia National Labs that contains an example lattice model of a protein. [For those interested it also includes "user colours", using COLOR records]. The definitive information on the Brookhaven Protein Databank file format can be found on Brookhaven National Labs' WWW site at the URL "http://www.pdb.bnl.gov/Format.doc/Contents_Guide_2.html". The definitive guide to Minesota Computer Center's is the UNIX man page xyz(5) provided with the program XMol, "http://www.msc.edu/msc/docs/xmol/XMol.html". The XYZ file format is without doubt the simplest of all molecular file formats, but may not be suitable for lattice models as the connectivity is implied by the proximity of atoms. The file format is a free-format ASCII text file consisting of two header lines followed by a single line for each atom in the molecule. The first line contains a count of the number of atoms in the file, the second line contains the name of the molecule (which can optionally be left blank), and each atom line contains four fields, the atomic symbol of the atom followed by the cartesian x, y and z co-ordinates of the atom in Angstroms. These fields may be separated by spaces (preferred), tabs or commas. A better bet for lattice models is to use a PDB file similar to that described below. Note the large number of explicit CONECT records that precisely specify bonding. Don't worry about the large number of different fields, RasMol only needs the ATOM and CONECT records. I hope this answers your question. 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 == lattice.pdb ========================================================= HEADER Tortilla PDB File ######### HI## TITLE Automatically generated by pf software COMPND Artificial sequence SOURCE See COMPND KEYWRD NONE EXPDTA Tortilla Software AUTHOR W.E.HART,S.ISTRAIL REVDAT 1 DATE HI## 0 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.E.HART,S.ISTRAIL REMARK 1 TITL FAST PROTEIN FOLDING IN THE HYDROPHOBIC-HYDROPHILIC REMARK 1 TITL 2 MODEL WITH THREE-EIGHTHS OF OPTIMAL REMARK 1 REF J.COMPUTATIONAL BIOLOGY, SPRING 1996 SEQRES 1 40 GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY SEQRES 2 40 GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY SEQRES 3 40 GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY GLY SEQRES 4 40 GLY CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ATOM 1 Z2 GLY 1 18.000 27.000 0.000 1.00 0.00 ATOM 2 Z2 GLY 2 15.000 27.000 0.000 1.00 0.00 ATOM 3 Z1 GLY 3 12.000 27.000 0.000 1.00 0.00 ATOM 4 Z1 GLY 4 9.000 27.000 0.000 1.00 0.00 ATOM 5 Z2 GLY 5 9.000 30.000 0.000 1.00 0.00 ATOM 6 Z2 GLY 6 12.000 30.000 0.000 1.00 0.00 ATOM 7 Z1 GLY 7 12.000 33.000 0.000 1.00 0.00 ATOM 8 Z2 GLY 8 9.000 33.000 0.000 1.00 0.00 ATOM 9 Z2 GLY 9 6.000 33.000 0.000 1.00 0.00 ATOM 10 Z1 GLY 10 6.000 36.000 0.000 1.00 0.00 ATOM 11 Z1 GLY 11 3.000 36.000 0.000 1.00 0.00 ATOM 12 Z2 GLY 12 3.000 33.000 0.000 1.00 0.00 ATOM 13 Z2 GLY 13 3.000 30.000 0.000 1.00 0.00 ATOM 14 Z2 GLY 14 6.000 30.000 0.000 1.00 0.00 ATOM 15 Z2 GLY 15 6.000 27.000 0.000 1.00 0.00 ATOM 16 Z1 GLY 16 6.000 24.000 0.000 1.00 0.00 ATOM 17 Z1 GLY 17 6.000 21.000 0.000 1.00 0.00 ATOM 18 Z2 GLY 18 6.000 18.000 0.000 1.00 0.00 ATOM 19 Z2 GLY 19 9.000 18.000 0.000 1.00 0.00 ATOM 20 Z1 GLY 20 9.000 15.000 0.000 1.00 0.00 ATOM 21 Z2 GLY 21 6.000 15.000 0.000 1.00 0.00 ATOM 22 Z2 GLY 22 3.000 15.000 0.000 1.00 0.00 ATOM 23 Z2 GLY 23 3.000 12.000 0.000 1.00 0.00 ATOM 24 Z1 GLY 24 6.000 12.000 0.000 1.00 0.00 ATOM 25 Z1 GLY 25 6.000 9.000 0.000 1.00 0.00 ATOM 26 Z2 GLY 26 3.000 9.000 0.000 1.00 0.00 ATOM 27 Z1 GLY 27 3.000 6.000 0.000 1.00 0.00 ATOM 28 Z1 GLY 28 6.000 6.000 0.000 1.00 0.00 ATOM 29 Z1 GLY 29 6.000 3.000 0.000 1.00 0.00 ATOM 30 Z2 GLY 30 3.000 3.000 0.000 1.00 0.00 ATOM 31 Z1 GLY 31 3.000 0.000 0.000 1.00 0.00 ATOM 32 Z1 GLY 32 0.000 0.000 0.000 1.00 0.00 ATOM 33 Z2 GLY 33 0.000 3.000 0.000 1.00 0.00 ATOM 34 Z2 GLY 34 0.000 6.000 0.000 1.00 0.00 ATOM 35 Z2 GLY 35 0.000 9.000 0.000 1.00 0.00 ATOM 36 Z2 GLY 36 0.000 12.000 0.000 1.00 0.00 ATOM 37 Z2 GLY 37 0.000 15.000 0.000 1.00 0.00 ATOM 38 Z2 GLY 38 0.000 18.000 0.000 1.00 0.00 ATOM 39 Z2 GLY 39 3.000 18.000 0.000 1.00 0.00 ATOM 40 Z1 GLY 40 3.000 21.000 0.000 1.00 0.00 TER 41 GLY 40 CONECT 1 2 CONECT 2 3 CONECT 3 4 CONECT 4 5 CONECT 5 6 CONECT 6 7 CONECT 7 8 CONECT 8 9 CONECT 9 10 CONECT 10 11 CONECT 11 12 CONECT 12 13 CONECT 13 14 CONECT 14 15 CONECT 15 16 CONECT 16 17 CONECT 17 18 CONECT 18 19 CONECT 19 20 CONECT 20 21 CONECT 21 22 CONECT 22 23 CONECT 23 24 CONECT 24 25 CONECT 25 26 CONECT 26 27 CONECT 27 28 CONECT 28 29 CONECT 29 30 CONECT 30 31 CONECT 31 32 CONECT 32 33 CONECT 33 34 CONECT 34 35 CONECT 35 36 CONECT 36 37 CONECT 37 38 CONECT 38 39 CONECT 39 40 COLOUR#######Z0############### 0.400 0.400 0.000 1.000 COLOUR#######Z1############### 0.200 0.800 1.000 1.000 COLOUR#######Z2############### 1.000 0.000 0.250 1.000 MASTER 5 0 0 0 0 0 0 0 40 1 39 0 END References: ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Rasmol and molecules on a square lattice Date: Fri, 4 Oct 1996 08:27:17 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Converting between file formats (PDB, XYZ, and many others) is very easy using the MacBabel program: http://mercury.aichem.arizona.edu/babel_mac_install.html Among other things, it's easy to create or edit an XYZ file on a spreadsheet; convert it to a plain text file; and then to a PDB file (MacBabel) for RasMol viewing. I don't whether similar pgms exist for Windows or Unix. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Andrea Bernini Subject: Write command in script file Date: Tue, 8 Oct 1996 09:50:18 +0100 (GMT+0100) To: Rasmol mailing list Hi, i'm a chemistry student at the university of Siena, in Italy,and i use every day Rasmol for mac for visualization of "my" protein. Now i'm interested in making quicktime movies of proteins and i I would like to use the rasmol graphic potential to produce a large amount of numbered picture of a step by step rotation of a protein using a script like this: rotate x 1 write pict prot1 rotate x 1 write pict prot2 etc ... unfortunately, the write command is disabled in script. Does everyone know if there are any porting, version, or programs similar to Rasmol or any other way to do this? Thanks. ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Write command in script file Date: Tue, 08 Oct 1996 11:41:13 -0700 To: rasmol@noc1.oit.umass.edu At 09:50 AM 10/8/96 +0100, Andrea Bernini wrote: >Hi, i'm a chemistry student at the university of Siena, in Italy,and i >use every day Rasmol for mac for visualization of "my" protein. Now i'm >interested in making quicktime movies of proteins and i I would like to >use the rasmol graphic potential to produce a large amount of >numbered picture of a step by step rotation of a protein using a script >like this: > >rotate x 1 >write pict prot1 >rotate x 1 >write pict prot2 >etc ... > >unfortunately, the write command is disabled in script. Does everyone know >if there are any porting, version, or programs similar to Rasmol or any >other way to do this? Thanks. You can type the command 'set write true' in the command window of rasmol, and this will enable your scripts to use write commands. For security reasons write commands are disabled in rasmol scripts by default. Our Netscape plugin, Chemscape Chime, can be also used to present Rasmol scripts within a Netscape Browser window to users over the internet. This can be a powerful way to present scripts, rather than quicktime movies, because the bandwidth required is (typically) smaller and the chemical information is retained. The user can manipluate the structure and trigger rasmol scripts using buttons. Chime is FREE to all users, and if you have not taken a look at it I think it would be worth your while. You can download Chime at http://www.mdli.com/chemscape/chime and you can also find links to many examples here as well. Good luck, and let us know your progress! -tim Tim Maffett tim@mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord <100412.1707@CompuServe.COM> Subject: Re: Rasmol and molecules on a square lattice Date: 09 Oct 96 23:34:57 EDT To: "Contrib. Rasmol" On Fri, 4 Oct 1996, William R Mcclure wrote: > Converting between file formats (PDB, XYZ, and many others) is very easy using the MacBabel program: http://mercury.aichem.arizona.edu/babel_mac_install.html [...] > I don't whether similar pgms exist for Windows or Unix. DOS, Unix and Mac versions of Babel are available at: ftp://joplin.biosci.arizona.edu/pub/Babel/ Also of interest is MolEdit, a DOS program to edit chemical data files: http://pctc.chemie.uni-erlangen.de/~gedeck/moledit.html Sincerely Jean Debord Lab. Pharmacologie, Fac. Medecine 2 Rue du Docteur Marcland, F-87025 Limoges, France http://ourworld.compuserve.com/homepages/JDebord ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RasMac bugs fixed Date: Fri, 11 Oct 1996 14:51:55 -0500 (EST) To: At the end of September, Roger Sayle provided an update to RasMac 2.6 beta-2 (which I shall call 2.6 beta-2a). It appears to me that this has not been announced to this list. I've just gotten around to making it available from http://www.umass.edu/microbio/rasmol/getras.htm#rasmac Here is Roger's explanation (also on the above web site): "There are no major changes in the functionality, but a number of niggling Macintosh specific bugs have been cleared and the performance probably improved. The most notable bug fix is that 'pause' commands in RasMol scripts now work when launched by double clicking on a scriptfile icon. Netscape should now be able to launch RasMac with a script and I'm not sure if it was fixed in the previous release but 'File Save As' and 'Export' options should no longer crash the system when `certain' directory assistants (Macintosh extensions) are running." (Running a script file by double clicking requires that the script file have the correct signature; see http://www.umass.edu/microbio/rasmol/distrib/macsigs.htm) /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology 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: Win95 script installation? Date: Tue, 15 Oct 1996 10:44:43 -0500 (EST) To: jat190@psu.edu, I do not yet have a Win95 system on which to work out the details requested by Mr. Thomson below. Can someone please give us a blow-by-blow? I'll then include it in the 00SPTDOC.HTM which provides generic instructions for all RasMol scripts. Under Win3.1, RasMol will not find the script files unless they are in the 'working directory'. In other words, if one issues the command 'script dna3.top', RasMol will reply something to the effect 'can't find script file' unless the working directory has been specified as that containing dna3.top, and the pdb files it loads and subscripts it calls. How is this achieved in Win95? ------------------------------ Sat, 12 Oct 1996 23:12:14 -0700 From: James Thomson Subject: script To: emartz@microbio.umass.edu Hello, my name is James Thomson and I am a student a Penn State Universtiy. I am trying to get a script to work on my computer. I have win95. I am having trouble with the part of your instructions where it is written,"Now, in Windows, with the RasWin icon selected, select File, Preferences, and change the Working Directory to the one containing the unpacked script files." In Windows 95, I cannot perform this task. There is no file/ preference menu to change the working directory, I can view the directory, but cannot change it. Am I missing something or is there something different to do? James jat190@psu.edu /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Kornhauser Subject: Wouldn`t it be nice? Date: Tue, 15 Oct 1996 11:34:10 -0600 (CST) To: Lista de Rasmol On Tue, 15 Oct 1996, Eric Martz wrote: > Under Win3.1, RasMol will not find the script files unless they are in > the 'working directory'. In other words, if one issues the command > 'script dna3.top', RasMol will reply something to the effect 'can't find > script file' unless the working directory has been specified as that > containing dna3.top, and the pdb files it loads and subscripts it calls. > How is this achieved in Win95? It would be nice to have a menu command to run scripts, and be able to selec the directory from which to run it in a dialog box. Just an opinion. Adrian Kornhauser ++++------+------+------+------+------+------+------+------+------+------+ From: Andrea Bernini Subject: Thanks and another question Date: Thu, 17 Oct 1996 12:25:37 +0100 (GMT+0100) To: Rasmol mailing list First, thanks to Roger Sayle and Tim Maffett for explanations on write command and Chime, now i'm making movies! Now i have two more question ( i've searched all the manuals and mailing list archives before ask you, but find nothing): how can i hide selected atom expression and set the work area to a determinate size? Thanks ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Thanks and another question Date: Thu, 17 Oct 1996 13:36:31 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu > > First, thanks to Roger Sayle and Tim Maffett for explanations on write > command and Chime, now i'm making movies! Now i have two more question > ( i've searched all the manuals and mailing list archives before ask you, > but find nothing): how can i hide selected atom expression and set the > work area to a determinate size? > > Thanks > Hello Andrea, the keyword "restrict" selectes a part of your molecule and hides the rest. example: Rasmol> restrict polar ... would select and display ONLY the polar aminoacids you can also select all atoms in a specified work area using the "within" command: Rasmol> restrict within(4.0, 1) this shows you only the atoms in a radius of 4.0A around the center of residue 1. chiao, Arne ++++------+------+------+------+------+------+------+------+------+------+ From: "Suzanne W. Slayden" Subject: Re: Win95 script installation? Date: Thu, 17 Oct 1996 16:39:59 -0400 (EDT) To: Eric Martz Cc: jat190@psu.edu, rasmol@noc1.oit.umass.edu > I am trying to get a script to work on my computer. I have > win95. I am having trouble with the part of your instructions where it > is written,"Now, in Windows, with the RasWin icon selected, select File, > Preferences, and change the Working Directory to the one containing the > unpacked script files." The instructions for Windows 95 are: -Make a shortcut icon to RasMol on the Desktop or a folder -Select the RasMol icon and then simultaneously press ALT-ENTER (or right-click the icon and select "Properties") - Click on the "Shortcut" tab in the Properties dialog box -In the box "Start in:", enter the path for the desired working directory. Suzanne Slayden |---------------------------| | Suzanne W. Slayden | | Chemistry Department 3E2 | | George Mason University | | Fairfax, VA 22030-4444 | | sslayden@gmu.edu | |---------------------------| References: <38684.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Neil Millar Subject: Re: Win95 script installation? Date: Thu, 17 Oct 1996 22:29:59 +0100 To: rasmol@noc1.oit.umass.edu Dear James, In Windows 95 it's all done with shortcuts. There are about a grillion ways to make a shortcut, but perhaps the simplest is to drag rasmol to the desktop with the right mouse button and select make shortcut. Then click on the shortcut icon you've just made with the right mouse button and select the last item from the list - properties. In the properties dialog box select the shortcut tab,and enter the directory you want in the "Start in" box. When you double-click the icon it will run your script, so long as there's a rasmol.ini file in the directory which points to the top script. You can make a shortcut icon this way for each directory/movie. Of course the command window text is still tiny... Hope this helps, Neil Millar. ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Thanks and another question Date: Thu, 17 Oct 1996 22:46:33 -0700 To: rasmol@noc1.oit.umass.edu At 12:25 PM 10/17/96 +0100, Andrea Bernini wrote: >First, thanks to Roger Sayle and Tim Maffett for explanations on write >command and Chime, now i'm making movies! Now i have two more question >( i've searched all the manuals and mailing list archives before ask you, >but find nothing): how can i hide selected atom expression and set the >work area to a determinate size? You can use the 'restrict' command to limit what is displayed. I am not sure what you mean you say 'determinate size', but with the next version of Chime, due out any day now (v 0.99), you can set the angstroms per inch for a Chime plugin, allowing you to have several Chime plugins on a page, all displaying molecules in the same absolute scale. This is currently done with an tag argument, but I may be adding a rasmol script command for this as well. There are variety of exciting enhancements to Chime that will become available with the 0.99 version, and I will try to give an overview here when we make the new version available. I am happy to hear that you have been able to get started on your movie making, and I look forward to seeing your work! -tim > >Thanks > > ++++------+------+------+------+------+------+------+------+------+------+ From: Dean Waldow Subject: Re: Rasmol and molecules on a square lattice Date: Sun, 20 Oct 1996 22:16:24 -0700 (PDT) To: rasmol@noc1.oit.umass.edu Hello, A couple weeks ago I asked about having Rasmol display results from a monte carlo simulation. Thanks to all who replied! I am now very close to a working solution and will summarize what I now understand (or at least, do) so far as well as ask another question. First the question: When I try to display the following pdb file with rasmol 2.6.1 it only shows atoms 5 atoms but no bonds. It states that there are five atoms, and 3 bonds, and prints out the bonds line again but with bonds equal to zero. Where as, if I try to display this file using rasmol 2.6beta ucb it shows the file as I expect it: with bonds between atoms 1-2 2-3 and 4-5. Any ideas why the difference between the two versions of rasmol? Am I constructing the file incorrectly, maybe? HETATM 1 Z0 GLU A 1 0.000 3.000 0.000 1.00 HETATM 2 Z0 GLU A 2 0.000 6.000 0.000 1.00 HETATM 3 Z1 GLU A 3 3.000 6.000 0.000 1.00 HETATM 4 Z1 GLU A 4 3.000 3.000 0.000 1.00 HETATM 5 Z1 GLU A 5 3.000 3.000 -3.000 1.00 TER 5 GLU 5 CONECT 1 2 CONECT 2 3 CONECT 4 5 COLOUR#######Z0############### 0.400 0.400 0.000 1.000 COLOUR#######Z1############### 0.200 0.800 1.000 1.000 COLOUR#######Z2############### 1.000 0.000 0.250 1.000 Summary: This may be very simple for most who are used to pdb files but it might be nice to have a summary for this type of application. I am displaying a ternary polymer blend consisting of an "A" polymer, a "B" polymer, and a copolymer of A and B monomers on a square lattice. I color each monomer based on whether it is an A or a B monomer. I have been able to display a box with 1106 separate molecules each 10 atoms long (total atoms 11,060). The size of the continuous boundary box is 24x24x24 in this case. The general approach uses the the following pdb keywords: HETATM, TER, CONECT, and COLOUR. Example lines as follows: HETATM 1 Z0 GLU A 1 0.000 3.000 0.000 1.00 | | | | | \_________ ________/ Atom number | | | | \/ Atom color---| | | | | I use the amino | | | | acid label the | | | | the type of | | | | molecule | | | | (A, B, or A/B)--| | | | Molecule label-------| | | (swith to a new letter | | when starting a new | | molecule) | | Atom label within molecule | (I set it to the same as the | atom number) | Lattice cordinates except multiplied by 3---| ( e.g. 0,1,0 --> 0,3,0 - I don't understand why - but it works) Then I add the termination line as follows (including the previous line) e.g. HETATM 15 Z1 ASP C 15 6.000 9.000 -6.000 1.00 TER 15 ASP 15 I add connectivity information CONECT 1 2 This connects atoms 1 and 2 with a bond. I then don't connect bonds between atoms as well as no connection the bond for part of the molecule that has left the box and re-entered on the opposite side. (continuous boundary conditions) And lastly, I add user defined colors. (green, blue, and red) COLOUR#######Z0############### 0.400 0.400 0.000 1.000 COLOUR#######Z1############### 0.200 0.800 1.000 1.000 COLOUR#######Z2############### 1.000 0.000 0.250 1.000 Other useful information: PDB file information: http://www.pdb.bnl.gov/Format.doc/Contents_Guide_2.html XYZ file information: http://www.msc.edu/msc/docs/xmol/XMol.html Babel (translating between file formats) DOS, Unix and Mac versions of Babel are available at: ftp://joplin.biosci.arizona.edu/pub/Babel/ MolEdit (a DOS program to edit chemical data files) http://pctc.chemie.uni-erlangen.de/~gedeck/moledit.html VMD (for the visualization of simulation trajectories, SGI's only) http://www.ks.uiuc.edu/Research/vmd/ Suggestions, corrections, etc are Welcome. Thanks again! Dean W. ----------------------------------------------------------------------------- Dean Waldow, Assistant Professor (206) 535-7533 Department of Chemistry (206) 536-5055 (FAX) Pacific Lutheran University waldowda@plu.edu Tacoma, WA 98447 USA http://www.chem.plu.edu/waldow.html ----------------------------------------------------------------------------- ---> CIRRUS and the Chemistry homepage: http://www.chem.plu.edu/ <--- ----------------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: AUTODEP 1.0 IS RELEASED BY THE PDB Date: Thu, 24 Oct 1996 14:41:11 -0500 (EST) To: -- From -- "PDB Help Desk" -- Date -- Thu, 24 Oct 1996 12:06:16 -0400 **** AUTODEP 1.0 IS RELEASED BY THE PDB **** The PDB is pleased to announce the release of AutoDep Version 1.0. AutoDep Version 1.0 is a World Wide Web-based graphical interface to the deposition form which leads the author through the entire submission process. The PDB also announces release of the new Electronic Deposition Form V. 3.30 which must be used for submitting structures to the PDB if AutoDep cannot be used. However, we strongly encourage authors to use AutoDep, as it greatly simplifies the submission process and also helps avoid many potential errors before submission. AutoDep may be accessed at from the PDB Web site (http://www.pdb.bnl.gov) by clicking on the page entitled "Submitting Data to the PDB" and then clicking on "AutoDep - PDB's New Web-based Submission Tool". The new Electronic Dep Form and the Submission Policy are also accessed from this Web page. AutoDep's most important features include the following: * It preserves data security and confidentiality through use of a password mechanism. * AutoDep may be initially populated from an existing PDB entry or a previous deposition. * Program output files may be merged into AutoDep. For example, the new releases of X-PLOR and SHELXL write refinement details in a format which can be read by the program and used to populate the relevant sections. * Help files, examples, and links to related documentation and useful URLs are provided in every section. * You may interrupt your AutoDep session at any time and return to it later in the day (or even days or weeks later) by restarting it with your session id number and password. * The SUBMIT button provided initiates the following: * the coordinates are passed through a syntax checker * if they fail, you are asked to correct the problem and resubmit the coordinates * if they pass, you are immediately sent an acknowledgement letter containing your PDB ID code * your entry enters the PDB processing flow Improvements to AutoDep will be made on a continuing basis. We gladly welcome your comments and suggestions. Questions on using AutoDep or the new Deposition Form should be sent to the PDB Help Desk at pdbhelp@pdb.pdb.bnl.gov. -- _______________________________________________________________________ Help Desk Protein Data Bank pdbhelp@bnl.gov Brookhaven National Laboratory (516) 344-5751 FAX Biology Department, Bldg. 463 (516) 344-6356 Phone P.O. Box 5000 http://www.pdb.bnl.gov Upton, NY 11973-5000 USA _______________________________________________________________________ /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Preston Garrison Subject: RasMol vs Molscript Date: Mon, 28 Oct 1996 23:12:14 -0600 (CST) To: rasmol@noc1.oit.umass.edu I'm forwarding Bill Pearson's question from bionet.software. Preston Garrison ----- Forwarded news article follows ----- Newsgroups: bionet.xtallography,bionet.software Path: netnews.uthscsa.edu!geraldo.cc.utexas.edu!cs.utexas.edu!news.sprintlink.net! news-peer.sprintlink.net!newsfeed.internetmci.com!in2.uu.net!hearst.acc.Virg inia.EDU!murdoch!usenet X-Nntp-Posting-Host: alpha0.bioch.virginia.edu X-Newsreader: Gnus v5.1 Lines: 10 Xref: netnews.uthscsa.edu bionet.xtallography:1256 bionet.software:4836 ++++------+------+------+------+------+------+------+------+------+------+ From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) Subject: RasMol vs Molscript Date: Tue, 29 Oct 1996 01:46:59 GMT I am having problems getting Molscript to provide the same view of a molecule that RasMol does. I can have RasMol tell me its coordinate system (via write script or using rotate commands), but when I use those values in Molscript, I do not get the correct orientation of my structure. How do I convert RasMol rotations to Molscript rotations? Bill Pearson ----- End of Forwarded news article ----- Preston Garrison, Ph.D. garrisonp@uthscsa.edu Biochem. Dept. Univ of Texas Health Sci Ctr San Antonio, Tx 78284-7760 USA 210-567-3702 ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: RasMol vs Molscript Date: Tue, 29 Oct 1996 10:16:37 +0100 (MEZ) To: rasmol@noc1.oit.umass.edu > > I'm forwarding Bill Pearson's question from bionet.software. > > Preston Garrison > > ----- Forwarded news article follows ----- > > Newsgroups: bionet.xtallography,bionet.software > Path: > netnews.uthscsa.edu!geraldo.cc.utexas.edu!cs.utexas.edu!news.sprintlink.net! > news-peer.sprintlink.net!newsfeed.internetmci.com!in2.uu.net!hearst.acc.Virg > inia.EDU!murdoch!usenet > From: wrp@alpha0.bioch.virginia.edu (William R. Pearson) > Subject: RasMol vs Molscript > X-Nntp-Posting-Host: alpha0.bioch.virginia.edu > Message-ID: > Sender: wrp@alpha0.bioch.Virginia.EDU > Organization: University of Virginia > X-Newsreader: Gnus v5.1 > Date: Tue, 29 Oct 1996 01:46:59 GMT > Lines: 10 > Xref: netnews.uthscsa.edu bionet.xtallography:1256 bionet.software:4836 > > > I am having problems getting Molscript to provide the same view of > a molecule that RasMol does. I can have RasMol tell me its > coordinate system (via write script or using rotate commands), but > when I use those values in Molscript, I do not get the correct > orientation of my structure. > > How do I convert RasMol rotations to Molscript rotations? > > Bill Pearson I've the same problems working with molscript. In my I opinion at the moment it's not possible to convert the RasMol coordiante system exactly to the molscript system. To change this you've to do some changes in the RasMol code. Maybe the code that creates the molscript file is a little experimental. At the moment I've always to do some hacking by hand in the molscript file to get may favorite view, colors, ... . sorry if I could help I'd do so. Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol vs Molscript Date: Tue, 29 Oct 1996 14:51:28 +0000 (GMT) To: wrp@alpha0.bioch.virginia.edu Cc: rasmol@noc1.oit.umass.edu Hi William, > I am having problems getting Molscript to provide the same view of > a molecule that RasMol does. I can have RasMol tell me its > coordinate system (via write script or using rotate commands), but > when I use those values in Molscript, I do not get the correct > orientation of my structure. > > How do I convert RasMol rotations to Molscript rotations? Thanks very much for your e-mail. Luckily RasMol contains a function to make precisely this task a bit easier. RasMol's "write molscript " command can be used to generate a MolScript input script containing the appropriate co-ordinate transformation. This command also outputs the appropriate scaling and z-clipping commands, and will even write out the current secondary structure defintion of the loaded protein. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: RasMol vs Molscript Date: Tue, 29 Oct 1996 17:11:03 +0100 (MEZ) To: rasmol@noc1.oit.umass.edu Hello All, > > > Hi William, > > I am having problems getting Molscript to provide the same view of > > a molecule that RasMol does. I can have RasMol tell me its > > coordinate system (via write script or using rotate commands), but > > when I use those values in Molscript, I do not get the correct > > orientation of my structure. > > > > How do I convert RasMol rotations to Molscript rotations? > > Thanks very much for your e-mail. Luckily RasMol contains a function to > make precisely this task a bit easier. RasMol's "write molscript " > command can be used to generate a MolScript input script containing the > appropriate co-ordinate transformation. This command also outputs the > appropriate scaling and z-clipping commands, and will even write out the > current secondary structure defintion of the loaded protein. > I also use this function generating molscript files. The problem is the exact translation of the _ACTUAL_ view of the molecule in RasMol to the appropiate view in Molscript. THThe view is not exact the same. Often it's not relevant to get1;2c the exact position of the protein, but if so you've to try some manipulation in the translation matrix of the generated molscript file. ... only for people who wonder about this. Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Garbett <106322.1423@compuserve.com> Subject: Running rasmol on 486SX computers and networks Date: Tue, 29 Oct 1996 16:43:56 -0500 To: Rasmol Hi, I am a new subsciber to the list having just discovered the pleasures of rasmol thanks to Neil Millar's article in the School Science Review (thanks again Neil!). I am hoping to use rasmol and some of Eric's scripts to help my A-level (17-18 yr old pre-university) students to understand the 3-D structure of nucleic acids, proteins and lipid bilayers. Rasmol runs perfectly on my 486 DX computer at home but refuses to run on the machines in my department at school. An 'Application Error - floating-point error: stack under' is generated whenever I attempt to run rasmol on the RM 486SX machines. Is this caused by the lack of a co-processor? If so, is there a version of rasmol available which will run on 486SX ? I would like to run rasmol on our LAN Network (486DX machines). Has anyone experience of this? Any advice would be gratefully received! Thanks, Mike Garbett Head of Science The Aldridge School Aldridge England ++++------+------+------+------+------+------+------+------+------+------+ From: Terry Walsh Subject: Re: Running rasmol on 486SX computers and networks Date: Wed, 30 Oct 1996 10:16:31 +1000 (EST) To: rasmol@noc1.oit.umass.edu At 16:43 29/10/96 -0500, you wrote: >Hi, > >I am a new subsciber to the list having just discovered the pleasures of >rasmol thanks to Neil Millar's article in the School Science Review (thanks >again Neil!). I'm also new to the list, which I've found a treasure chest of info. I think I can help you with this question, though, 'cos I've been doing the same thing here. > >I am hoping to use rasmol and some of Eric's scripts to help my A-level >(17-18 yr old pre-university) students to understand the 3-D structure of >nucleic acids, proteins and lipid bilayers. > >Rasmol runs perfectly on my 486 DX computer at home but refuses to run on >the machines in my department at school. > An 'Application Error - floating-point error: stack under' is generated >whenever I attempt to run rasmol on the RM 486SX machines. >Is this caused by the lack of a co-processor? Yep. I had the same response here when I first tried it on a hastily collected group of stand-alone computers. >If so, is there a version of rasmol available which will run on 486SX ? > I'm not sure about this one, but I think not. >I would like to run rasmol on our LAN Network (486DX machines). Has anyone >experience of this? We now have two labs of 36 and 20 486DX33s (maths coprocessors) running it beautifully from a Pentium133 NT box on a LAN network. I'm not sure of all the techno details btu my systems man could supply them if you need more information. > >Any advice would be gratefully received! > >Thanks, >Mike Garbett >Head of Science >The Aldridge School >Aldridge >England > > ******************************************************************************** Terry Walsh PhD Program Leader CRC for Diagnostic Technologies S/Lecturer Biochemistry & Molecular Biology, School of Life Science Queensland University of Technology, GPO Box 2434, Brisbane, 4001 AUSTRALIA Phone +61 7 3864 2347 Fax +61 7 3864 1534 ******************************************************************************** Content-MD5: r4TV5CEy+ntnNAZqsCCKwQ== ++++------+------+------+------+------+------+------+------+------+------+ From: Erik Lindahl Subject: Re: Running rasmol on 486SX computers and networks Date: Wed, 30 Oct 1996 08:31:37 +0100 To: rasmol@noc1.oit.umass.edu Hi, [Stuff deleted about lack of co-processor] If the problem indeed is lack of the numeric co-processor, it can be fixed by just recompiling it with floating point emulation turned on as a compiler option. However, I'm not sure this is the case, since most compilers include emulation code as default. (I haven't looked at the PC code myself) Good luck anyhow - it's really a nice program. Regards, Erik ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Running rasmol on 486SX computers and networks Date: Wed, 30 Oct 1996 12:18:51 +0100 (MEZ) To: rasmol@noc1.oit.umass.edu > > Hi, > > [Stuff deleted about lack of co-processor] > > If the problem indeed is lack of the numeric co-processor, it can > be fixed by just recompiling it with floating point emulation turned > on as a compiler option. However, I'm not sure this is the case, since > most compilers include emulation code as default. > > (I haven't looked at the PC code myself) ...I'm sure this is the probelm. I've had the same problems on a 486SX. As I remember the project-fiel for the borland compiler 3.1 defines no emulation, so recompiling the code would solve this poblem. I'm not an experienced dos/ windows- programmer. I was able to compile RasMol with emulation but couldn't link the program, there are problems with the stack-size. If I solve this problem I'll mail it to this group. Perhaps somebody of youou is confident about the bc3.1 compiler and gives me a tip ... Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol Date: Thu, 31 Oct 1996 20:32:39 +0000 (GMT) To: Viton Heera Cc: rasmol@noc1.oit.umass.edu Dear Viton, > Unfortunately I failed in producing high resolution post script files. I > used the commands "set vectps on" and "write ps ". However, > neither the wanted resolution nor the "black outlines" around spheres > and cylinders were produced. How can I manage this problem? I am > interested to depict the atoms by empty circles with black outlines. Are > there any possibilities to do this in your code? Thanks very much for your e-mail. The problem is that you need to use the "write vectps " command rather than the "write ps " command. The way to produce exactly the images that you are looking for is to also use the command "set ambient 100". This tells RasMol to make the darkest side of a sphere as bright as the brightest side. i.e. when combined with ball & stick, and "set vectps true", it should produce filled circles as spheres. Its probably best to ignore the strange looking images that you get on the screen, and enjoy the printouts! 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Bernhard Vogler Subject: "Double bonds" Date: Tue, 05 Nov 1996 10:33:14 -0800 To: rasmol@noc1.oit.umass.edu Dear Rasmol-users, for our "organic" teaching I would like to implement Rasmol, however so far I wasn't able to implement the "double" bonds into the structure. How can I manage to do that ? Which statements in PDB-files ? Which other settings ? Thanks in advance for helping ------------------------------------------------ Bernhard Vogler Institut fuer Chemie Universitaet Hohenheim Garbenstrasse 30 70599 Stuttgart Tel.: (49)711 - 459 - 2944 - 2963 (NMR) - 3908 (Computer Raum) FAX:(49)711 - 459 - 2951 e-mail: chemvogl@uni-hohenheim.de ------------------------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: "Double bonds" Date: Tue, 5 Nov 1996 07:55:09 -0500 (EST) To: rasmol@noc1.oit.umass.edu Bernhard Vogler asks: >> for our "organic" teaching I would like to implement Rasmol, however >>so far I wasn't able to implement the "double" bonds into the structure. How >>can I manage to do that ? Please see http://www.umass.edu/microbio/rasmol/faq.htm where there is a complete explanation with examples and a stereo GIF image of alprazolam showing double bonds. ++++------+------+------+------+------+------+------+------+------+------+ From: LEVY SAM Subject: rasmol script within netscape Date: Tue, 5 Nov 1996 09:36:47 -0700 (MST) To: rasmol@noc1.oit.umass.edu Cc: levy@beagle.colorado.edu I am trying to invoke the execution of RasMol from Netscape by ultimately providing a PDB file and a RasMol script file. Both of these data links would be simultaneously submitted to RasMol by the user clickng on a single link within an HTML interpretted script. I have tried to do this (unsuccessfully) in the following manner. The netscape browser opens a page with a link of the following kind

Then display.spt would contain load "molecule.pdb" select 1-9 color red I adjusted a new mime (in .mime.types) type definition to be chemical/spt spt and in the .mailcap file chemical/spt;xterm -T RasMol-e~/rasmol -script %s Then when one clicks on the link

we obtain load "xg17mc6.fig2.conf10.pdb" select 1-9 color red in browser window. Not the desired intent! Has anyone ever tried to do run Rasmol scripts within netscape (or any other web browser for that matter)? I would be interested to know if this can be made to work. Sincerely, Sam Levy X-Confirm-Reading-To: "Markus Stamm" X-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Markus Stamm" Subject: Re: rasmol script within netscape Date: Tue, 5 Nov 1996 20:10:42 +0100 To: rasmol@noc1.oit.umass.edu Hi Sam, > I am trying to invoke the execution of RasMol from Netscape > by ultimately providing a PDB file and a RasMol script file. > Both of these data links would be simultaneously submitted > to RasMol by the user clickng on a single link within an HTML > interpretted script. > > I have tried to do this (unsuccessfully) in the following manner. > The netscape browser opens a page with a link of the following kind > >

> > Then display.spt would contain > > load "molecule.pdb" > select 1-9 > color red > > I adjusted a new mime (in .mime.types) type definition to be > > chemical/spt spt > > and in the .mailcap file > > chemical/spt;xterm -T > RasMol-e~/rasmol -script %s > > Then when one clicks on the link > >

> > we obtain > > load "xg17mc6.fig2.conf10.pdb" > select 1-9 > color red > > in browser window. Not the desired intent! > > Has anyone ever tried to do run Rasmol scripts within netscape > (or any other web browser for that matter)? I would be interested > to know if this can be made to work. > > Sincerely, > > Sam Levy > It can, but the problem is that you have to edit the mime.types configuration file of the web server. Every document not covered by the mime-file of the server is set to text/plain, so your browser (any browser, not only netscape) will display it. Hope this helps. Markus Stamm "rasmol script within netscape" (Nov 5, 9:36am) References: <199611051636.JAA10009@beagle.colorado.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: rasmol script within netscape Date: Tue, 5 Nov 1996 16:23:21 -0500 To: rasmol@noc1.oit.umass.edu Dear Sam, You might want to look at http://www.pdb.bnl.gov/cgi-bin/pdbmain, which is PDB's 3DB Browser. Do a search on the PDB ID code 1acj. There are 2 scripts provided which open a Rasmol window and display certain views of the acetylcholinesterase molecule. You can also open a Rasmol display of the molecule as it appears in the PDB window. I hope that this might be of use to you. Best regards, Nancy On Nov 5, 9:36am, LEVY SAM wrote: > Subject: rasmol script within netscape > I am trying to invoke the execution of RasMol from Netscape > by ultimately providing a PDB file and a RasMol script file. > Both of these data links would be simultaneously submitted > to RasMol by the user clickng on a single link within an HTML > interpretted script. > > I have tried to do this (unsuccessfully) in the following manner. > The netscape browser opens a page with a link of the following kind > >

> > Then display.spt would contain > > load "molecule.pdb" > select 1-9 > color red > > I adjusted a new mime (in .mime.types) type definition to be > > chemical/spt spt > > and in the .mailcap file > > chemical/spt;xterm -T > RasMol-e~/rasmol -script %s > > Then when one clicks on the link > >

> > we obtain > > load "xg17mc6.fig2.conf10.pdb" > select 1-9 > color red > > in browser window. Not the desired intent! > > Has anyone ever tried to do run Rasmol scripts within netscape > (or any other web browser for that matter)? I would be interested > to know if this can be made to work. > > Sincerely, > > Sam Levy >-- End of excerpt from LEVY SAM -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Head User Support Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: New Chime Resources Date: Thu, 7 Nov 1996 18:16:32 -0500 (EST) To: I've placed drafts of several new web branches using Chime 0.99 at http://www.umass.edu/microbio/chime Chime 0.99 is presently available for Win3.1 and Win95, but not yet for Macs. Included are new help pages on how to use Chime, and how to write web pages for Chime, as well as tutorials on protein secondary structure and DNA structure. See especially the latter which is nonlinear and unlike others I've seen. These are not yet linked into the RasMol Home Page, but will be soon. /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: owens@garnet.berkeley.edu (Christine Owens) Subject: residue ID and annotation Date: Fri, 8 Nov 1996 10:47:07 -0800 To: rasmol@noc1.oit.umass.edu Hi, I've just started using Rasmol and I am interested in being able to click on a residue on the screen and have the name appear on the display window. I know that the name will appear in the command window but I was wondering if there was a way to ID specific residues on the screen? I've been working my way through a lot of help pages on the web, but I was wondering if anyone here could help me. Thanks in advance! Christine Owens ++++------+------+------+------+------+------+------+------+------+------+ From: michnick@BCH.UMontreal.CA (Stephen MICHNICK) Subject: Re: residue ID and annotation Date: Sat, 9 Nov 1996 02:58:28 GMT To: rasmol@noc1.oit.umass.edu type "set picking label" *-------------------------------------------------------* | | | Stephen Michnick | | Professeur | | Departement de Biochimie | | Universite de Montreal | | Case Postale 6128 | | Succursale Centre-Ville | | Montreal, Quebec | | Canada H3C 3J7 | | | *-------------------------------------------------------* | | | Tel: (514) 343-5849 (bureau) | | Tel: (514) 343-6111 X 1932 (labo) | | Fax: (514) 343-2210 | | Local: D-508 Pavillon principal | | | | | *-------------------------------------------------------* ++++------+------+------+------+------+------+------+------+------+------+ From: Vicki Bragin Subject: Question from a NEXTSTEP RasMol user Date: Mon, 11 Nov 96 13:50:02 -0800 To: rasmol@noc1.oit.umass.edu I use RasMol2.6 on a NEXTSTEP/Intel machine and I cannot seem to use the "set picking" command. I gather that I should be able to measure bond distances and bond angles through a set of picking commands. However, when I type "set picking on" the cursor remains an arrow and not the crosshair, as I understand it is supposed to be. Is this capability disabled on tne NEXTSTEP version? Thanks. Vicki Bragin ++++------+------+------+------+------+------+------+------+------+------+ From: Randy Bumgardner Subject: refresh command Date: Wed, 13 Nov 1996 16:35:19 -0800 To: rasmol@noc1.oit.umass.edu Cc: randyb@mdli.com Good Day, I'm curious if the 'refresh' command is recognized in windows but not on the Mac. Any help would be greatly appreciated! Thanks, Randy **************************************************** Randy Bumgardner MDL Information Systems (510) 895-1313, ext. 1172 Voice:(510) 357-2222, x1172 randyb@mdli.com **************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: E.J.Milner-White@bio.gla.ac.uk (James Milner-White) Subject: Re: refresh command Date: Thu, 14 Nov 1996 10:47:32 +0100 To: rasmol@noc1.oit.umass.edu The refresh command works for RasMol on the Mac just as it does in Windows, James >Good Day, > >I'm curious if the 'refresh' command is recognized in windows but not on >the Mac. Any help would be greatly appreciated! > >Thanks, >Randy >**************************************************** >Randy Bumgardner >MDL Information Systems >(510) 895-1313, ext. 1172 Voice:(510) 357-2222, x1172 >randyb@mdli.com >**************************************************** 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: E.J.Milner-White@bio.gla.ac.uk FAX: +44(0)141-330-4620 Tel.: +44(0)141-330-5283 ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Re: Question from a NEXTSTEP RasMol user (picking) Date: Fri, 15 Nov 1996 17:13:12 -0500 (EST) To: ------------------------------ Fri, 15 Nov 1996 11:56:02 -0500 windemut@cumbnd.bioc.columbia.edu From: awindemu@guarneri.curagen.com Subject: Re: Fw: Re: Question from a NEXTSTEP RasMol user To: emartz@microbio.umass.edu, tsengel@cip.informatik.uni-erlangen.de, Cc: rasmol@ggr.co.uk The sad story of the picking implementation is that I did it and then lost it. It was not much code at all, and I used most of the existing code (the X-windows version, I believe). The idea was that in "mouseDown:", after the mouse dragging loop, a test was made to determine if there was any dragging and if not, the apropriate RasMol picking routine was called with the mouse coordinates and the proper flags for depressed keys. It works very nice and full-featured. Alas, there is only an executable left in existence and I do not have time to redo it. Andreas Windemuth /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Neil Millar Subject: Opening PDB files in Win95 Date: Sun, 17 Nov 1996 18:35:25 +0000 To: rasmol@noc1.oit.umass.edu I've just discovered a really odd problem with Rasmol and Windows 95, and I was wondering if anyone else has it, or if it's just gremlins in my PC. Rasmol (2.6) opens PDB files OK when they're in a parent directory, or a "sibling" directory (ie at the same level), but not when they're in "child" or "nephew" directories (ie one level down). It doesn't give an error message, but behaves as if the file doesn't exist. Any reason why Rasmol should do this? Neil References: <328F5AEC.47B@thenet.co.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Neil Millar Subject: Re: Opening PDB files in Win95 Date: Sun, 17 Nov 1996 22:22:29 +0000 To: rasmol@noc1.oit.umass.edu OK, I've just played some more, and I've redefined the problem. It now seems that rasmol won't open files if they're in a directory/folder with a space in its name. That's a bit less odd, but it's still curious. Surprisingly 16-bit rasmol does it OK, but 32-bit rasmol can't cope with sapces in the path name. ho hum, Neil ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Opening PDB files in Win95 Date: Sun, 17 Nov 96 15:53:02 PST To: rasmol@noc1.oit.umass.edu Neil, I haven't directly noticed the problem you describe, but I'm wondering if what you describe relates to directory and file name limitations. I have noticed a similar problem when, for example, a Netscape helper application is set up to launch RasMol whenever a pdb file is downloaded over the net. If the directory structure that links the Netscape program to the RasMol program includes directory names with spaces or directory names that exceeed the "eight-plus-three" name size limitation imposed by DOS, the computer gets lost in much the way you describe. In other words, it seems that the newer versions of RasMol still don't allow for the more complex directory and file name structure permitted by Windows 95 and this hopefully will be fixed in future versions of RasMol; a similar problem does not occur with Mac versions of RasMol persumably because complex file and directory names have always been standard with Mac operating systems. Duane At 06:35 PM 11/17/96 +0000, you wrote: >I've just discovered a really odd problem with Rasmol and Windows 95, >and I was wondering if anyone else has it, or if it's just gremlins in >my PC. > >Rasmol (2.6) opens PDB files OK when they're in a parent directory, or a >"sibling" directory (ie at the same level), but not when they're in >"child" or "nephew" directories (ie one level down). It doesn't give an >error message, but behaves as if the file doesn't exist. > >Any reason why Rasmol should do this? > >Neil > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | 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 | | E-mail addresses: | | Faculty: sears@lifesci.lscf.ucsb.edu | | Academic: bioimages@lifesci.lscf.ucsb.edu | | WWW homepages: | | http://mentor.lscf.ucsb.edu/mcdb108a/ | | http://mentor.lscf.ucsb.edu/mcdb133/ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Rasmol for 486SX PC's Date: Mon, 18 Nov 1996 16:57:56 +0000 (GMT) To: Mike Garbett Cc: rasmol@noc1.oit.umass.edu > I have recently discovered your superb programme and have subscibed to > the RASMOL mailing list run by Eric Martz. > Having downloaded some of Eric's scripts, analysed them and started to > write simpler versions I was looking forward to using them with my A- > level Biology and Chemistry students. > However, (here comes the bad news!) on trying the programme on several > computers at my school (all 486SX machines) I became well aquainted with > the 'floating point error: stack under' experience! > I suspected that the lack of a co-processor was the problem and posted a > query to the mailing list hoping for confirmation. > Two people seemed to confirm my suspicion and one suggested that it > could be overcome by 're-compiling the source code'. > I have little (make that no) experience with C programming - (my > background is in BASIC and some machine code on long obsolete chips) but > would be willing to try anything to get Rasmol working on the stand- > alone 486SX machines at my disposal (or preferably on our LAN network). > > I would be grateful if you could: > a)confirm that the process is possible/sensible. > b)tell me where/if I could obtain the source code. > c)suggest a compiler and suitable settings. > > I know of several secondary schools in my area who would be very keen to > make use of Rasmol as a teaching resource but would have the same > problem with machine availability: the standard local Education > Authority installation of RM 486SX 33's made some 18 months ago. > > I realise that the main thrust of your work is towards research where > these mundane problems do not apply (or do they?), but I feel very > strongly that Rasmol has much to offer in the field of pre-university > education. > > Any suggestions/information would be gratefully received! > -- > Mike Garbett > Head of Science > The Aldridge School > Tynings Lane > Aldridge > WS9 0BG > ENGLAND > -- 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Rasmol for 486SX PC's Date: Mon, 18 Nov 1996 17:45:35 +0000 (GMT) To: Mike Garbett Cc: rasmol@noc1.oit.umass.edu Dear All, > However, (here comes the bad news!) on trying the programme on several > computers at my school (all 486SX machines) I became well aquainted with > the 'floating point error: stack under' experience! > I suspected that the lack of a co-processor was the problem and posted a > query to the mailing list hoping for confirmation. Sorry about the previous message. Hopefully this second attempt will be more meaningful. You'll be pleased to hear that I've just updated the version of "raswin.exe" on the anonymous FTP site at the University of Edinburgh. In addition, I've also deposited the file "raswinsx.exe" which use floating point emulation and should run on 386SX and 486SX computers. My apologies for any inconvenience this may have caused. I recently decided to update the RasWin compilation options to drop support for the 286, and make use of the 32bit instructions of 386s and higher. Unfortunately, at the same time I also assmumed that virtually all 386's had a co-processor and those that hadn't would emulate a maths coprocessor under Microsoft Windows. I hope this corrects the problems. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Opening PDB files in Win95 Date: Tue, 19 Nov 1996 11:23:30 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Hi Duane & Neil, > In other words, it seems that the newer versions of RasMol still don't > allow for the more complex directory and file name structure permitted > by Windows 95 and this hopefully will be fixed in future versions of > RasMol; a similar problem does not occur with Mac versions of RasMol > persumably because complex file and directory names have always been > standard with Mac operating systems. This was exactly the problem. However, it was noted that RasWin was able to handle the Windows' 95 filenames, but that RasWin32 was not. The reason for this was that the Windows '95/Windows NT filename problem was corrected in the source code earlier in the year, and only the 16bit executable has been recompiled and distributed since then. I've now just placed a new "raswin32.exe" in the FTP directory with the "raswin.exe" and "raswinsx.exe" that I put there yesterday. This means that all versions are less than two months old: -rw-r--r-- 1 rasmol local 754458 Oct 31 20:13 RasMol26.tar.gz -rw-r--r-- 1 rasmol local 660262 Sep 25 20:28 rasmac26.sit.hqx -rwxr-xr-x 1 rasmol local 287376 Nov 15 18:07 raswin.exe -rwxr-xr-x 1 rasmol local 349696 Nov 19 11:14 raswin32.exe -rw-r--r-- 1 rasmol local 325392 Nov 15 18:07 raswinsx.exe Share and enjoy, 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Dewey Williams Subject: RASMOL use in General Chemistry Date: Thu, 21 Nov 1996 10:55:44 -0500 To: rasmol@noc1.oit.umass.edu I know many of you use RASMOL in advanced chemistry, biochemistry and research but we are looking for ways to use it for our first semester chemistry majors. If anyone has ideas, scripts, web pages or other information on how we can utilize RASMOL in general chemistry, please let me know. Thanks in advance. Dewey Williams - Lab Manager williams@unccvm.uncc.edu UNC-Charlotte Chemistry Dept. http://www.chem.uncc.edu "These are my ideas and no one else will claim them." "If you are not part of the solution, you are part of the precipitate" ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RE: RASMOL use in General Chemistry Date: Thu, 21 Nov 1996 14:30:23 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear Dewey: I have been reluctant even to try to list chemistry molecular visualization resources at my web site because it seems a bottomless task -- I can't even keep up with the biology resources but I will keep trying. (I'm about to start hiring my first student assistants.) Anyway, if you find any sites which are really outstanding or which list other sites, please email them to me and eventually links will be put on my site. Thanks. In message Thu, 21 Nov 1996 10:55:44 -0500, Dewey Williams writes: > I know many of you use RASMOL in advanced chemistry, biochemistry and > research but we are looking for ways to use it for our first semester > chemistry majors. > > If anyone has ideas, scripts, web pages or other information on how we can > utilize RASMOL in general chemistry, please let me know. > > Thanks in advance. > > Dewey Williams - Lab Manager williams@unccvm.uncc.edu > UNC-Charlotte Chemistry Dept. http://www.chem.uncc.edu > "These are my ideas and no one else will claim them." > "If you are not part of the solution, you are part of the precipitate" > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Jason Cole Subject: Rasmol Titles Date: Fri, 22 Nov 1996 09:13:15 +0000 To: rasmol@noc1.oit.umass.edu Hi there, I have a brief (and probably stupid) question for all you rasmolphiles out there. Does anyone know of a whether its possible to configure a rasmol window so that a specific title is given either in the Window title bar (i.e. the space that says "RasMol Version XX") or in the window itself? Jason ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Downloading Chime Resources Date: Mon, 25 Nov 1996 21:50:58 -0500 (EST) To: On November 25, 1996, I have made it possible to download all the UMass Chime Resources which have been on the web since November 7, 1996. This will make it easy to run these Chime pages faster from your local hard disk, to examine how they were built and modify or extend them as you wish, and to project them to classes from computers not on the Internet. Please visit http://www.umass.edu/microbio/chime and note the new downloading invitation at the bottom of the page. These resources include: 1. How to use Chime (in Chime!) 2. Protein Secondary Structure (linear presentation for lecture) 3. DNA Structure (nonlinear, for self-directed exploration) 4. Raul Cacheau's XYZ animation (thermal motion of alpha helix) 5. Chime vs. RasMol (pros and cons for educational tutorials) 6. How Chime Works 7. Command-Line Interface Demonstration for Chime 8. Creating Chime Web Pages (tutorial in Chime) 9. Chime's New Script Commands (partial draft manual for Chime 0.99) Enjoy! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor of Immunology emartz@microbio.umass.edu Molecular visualization (free!): http://www.umass.edu/microbio/rasmol Flow cytometry (free software!): http://www.bio.umass.edu/mcbfacs Immunology at UMass/Amherst: http://www.bio.umass.edu/immunology Dept Microbiology Voice: 413-545-2325 FAX: 413-545-1578 Morrill IVN 203, Box 35720, Univ Massachusetts, Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Christer Jansson Subject: Rasmol scripts Date: Tue, 26 Nov 1996 07:02:31 +0100 To: rasmol@noc1.oit.umass.edu Hi! I have a couple questions regarding Rasmol scripts. 1. When I open a protein structure in Rasmol and execute various commands such as selecting, restricting, coloring, etc, the corresponding changes in the structure occur very rapidly. If I collect these commands in a script by typing, "write script structure1.spt" I am hoping that next time I open the structure and type "script structure1.spt" the response would be as immediate as when I type the commands one by one. However, this is not the case. It takes a very long time for the changes to take place. Just as long, if not longer, as it takes to open the structure to begin with! Why is this? 2. The other problem I've encountered is that I do not seem to be able to copy or move the scripts to another drive or location. When I try to execute the scripts I get a response saying that they can not be found, or rather, that the original path for the script location canno be accessed. What am I dong wrong here? I would be very grateful for any comments. Thank you! Christer Christer Jansson Professor of Biochemistry Biochemistry Dept, Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden E mail: christer@biokemi.su.se Fax: +46 8 153679 Phone: +46 8 162592 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Rasmol scripts Date: Tue, 26 Nov 1996 09:57:39 -0500 (EST) To: rasmol@noc1.oit.umass.edu At 07:02 AM 11/26/96 +0100, Christer Jansson wrote: > >1. When I open a protein structure in Rasmol and execute various commands >such as selecting, restricting, coloring, etc, the corresponding changes in >the structure occur very rapidly. If I collect these commands in a script >by typing, "write script structure1.spt" I am hoping that next time I open >the structure and type "script structure1.spt" the response would be as >immediate as when I type the commands one by one. However, this is not the >case. It takes a very long time for the changes to take place. Just as >long, if not longer, as it takes to open the structure to begin with! Why >is this? Scripts generated automatically by RasMol (with 'write script filename') are extremely long (atom by atom) and slow to process. If you want a quick result, you can usually write a script to generate the same image with relatively few commands, typed into a script file by hand. The limiting factor then becomes the time needed to load the PDB file. See the 'Guide' (ref below) for more information on how to do this. >2. The other problem I've encountered is that I do not seem to be able to >copy or move the scripts to another drive or location. When I try to >execute the scripts I get a response saying that they can not be found, or >rather, that the original path for the script location canno be accessed. >What am I dong wrong here? RasMol-generated scripts contain an absolute path name in the load command which loads the PDB file. Find the load command, and delete the path, leaving only the filename itself. This means 'find the PDB file in the local directory'. Provided you have RasMol's working directory set to the one containing the PDB file (Windows) or provided you dragged RasMac into the folder containing the PDB file before starting RasMac, it will work. See http://www.umass.edu/microbio/rasmol/distrib/00sptdoc.htm for details on how to start up scripts in various operating systems. This path business is explained in more detail with examples in my Guide to Script Creation in RasMol and Chime, http://www.umass.edu/microbio/rasmol/makescrp.htm where you will also find many other useful tips about writing RasMol scripts. I would also suggest that people writing RasMol scripts consider whether the final product should be delivered in a series of Chime web pages. For most purposes this has very substantial advantages, as explained at http://www.umass.edu/microbio/chime/chimvras.htm It still may be best to develop most of your script in RasMol before porting it to Chime. In Chime you can take advantage of hardware-independent delays and movements, so you don't have to worry about timing in the RasMol draft of the script. For some examples of Chime presentations (scripts w/ html) see http://www.umass.edu/microbio/chime /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Christer Jansson Subject: Re: Rasmol scripts Date: Wed, 27 Nov 1996 06:57:28 +0100 To: rasmol@noc1.oit.umass.edu Dear Dr Martz, Thank you very much for your comments and recommendations regarding Rasmol scripts. I realize now that what I need to do, at least with scripts for large proteins, is to write them manually and save them as a .spt file. However, when it comes to rotating I find it very tedious to find exactly the right orientation by trying different commands one after the other. Is there any way to first use the mouse to do this and then ask Rasmol to display the various rotating commands that correspond to the mous operation? That would be a very good help. Kind regards, Christer Jansson Professor of Biochemistry Stockholm University >At 07:02 AM 11/26/96 +0100, Christer Jansson wrote: >> >>1. When I open a protein structure in Rasmol and execute various commands >>such as selecting, restricting, coloring, etc, the corresponding changes in >>the structure occur very rapidly. If I collect these commands in a script >>by typing, "write script structure1.spt" I am hoping that next time I open >>the structure and type "script structure1.spt" the response would be as >>immediate as when I type the commands one by one. However, this is not the >>case. It takes a very long time for the changes to take place. Just as >>long, if not longer, as it takes to open the structure to begin with! Why >>is this? > >Scripts generated automatically by RasMol (with 'write script filename') are >extremely long (atom by atom) and slow to process. If you want a quick >result, you can usually write a script to generate the same image with >relatively few commands, typed into a script file by hand. The limiting >factor then becomes the time needed to load the PDB file. See the 'Guide' >(ref below) for more information on how to do this. > >>2. The other problem I've encountered is that I do not seem to be able to >>copy or move the scripts to another drive or location. When I try to >>execute the scripts I get a response saying that they can not be found, or >>rather, that the original path for the script location canno be accessed. >>What am I dong wrong here? > >RasMol-generated scripts contain an absolute path name in the load command >which loads the PDB file. Find the load command, and delete the path, >leaving only the filename itself. This means 'find the PDB file in the >local directory'. Provided you have RasMol's working directory set to the >one containing the PDB file (Windows) or provided you dragged RasMac into >the folder containing the PDB file before starting RasMac, it will work. See >http://www.umass.edu/microbio/rasmol/distrib/00sptdoc.htm for details on how >to start up scripts in various operating systems. > >This path business is explained in more detail with examples in my Guide to >Script Creation in RasMol and Chime, >http://www.umass.edu/microbio/rasmol/makescrp.htm > >where you will also find many other useful tips about writing RasMol scripts. >I would also suggest that people writing RasMol scripts consider whether the >final product should be delivered in a series of Chime web pages. For most >purposes this has very substantial advantages, as explained at >http://www.umass.edu/microbio/chime/chimvras.htm >It still may be best to develop most of your script in RasMol before porting >it to Chime. In Chime you can take advantage of hardware-independent delays >and movements, so you don't have to worry about timing in the RasMol draft >of the script. For some examples of Chime presentations (scripts w/ html) see >http://www.umass.edu/microbio/chime >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, >Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, >http://www.umass.edu/microbio/rasmol; other web projects listed at >http://www.umass.edu/microbio/rasmol/em-web.htm >- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ Christer Jansson Bitr. professor Biokemiska inst., Arrheniuslaboratorierna, Stockholms universitet, 106 91 Stockholm E mail: christer@biokemi.su.se Fax: 08 153679 Telefon: 08 162592 References: ++++------+------+------+------+------+------+------+------+------+------+ From: Greg Flack Subject: Re: Rasmol scripts Date: Wed, 27 Nov 1996 00:23:46 -0700 To: rasmol@noc1.oit.umass.edu Professor Jansson; Once you have obtained the view you like with the mouse, try saving this view as a script; then read this script with a word processor to see which rotations are needed to recreate that view. The commands should be among the first in the script written by RasMol. You may want to use the "cut" and "paste" commands from your word processor to save time in transferring this information to your manually written script. Respectfully, Gregory Flack ++++------+------+------+------+------+------+------+------+------+------+ From: Mueller Mr A Subject: Re: Rasmol scripts Date: Wed, 27 Nov 1996 09:02:59 +0000 (GMT) To: Rasmol mailing list Hi all, especially for writing scripts by hand it would be usefull to add a new feature to the rasmol code that shows you the current value of internal variables. example: "show ambient" would tell you the current ambient value "show rotate" would tell you the current rotation for x,y,z ... I think this is a good idea for the next rasmol version. Thanks, Arne ----------------------------------------------------------------------- | Arne Mueller | email: am27627@ggr.co.uk | | Glaxo Wellcome Medicines Research Centre, | Tel: +44 (0)1438 763419 | | Gunnels Wood Road, Stevenage, | | | Hertfordshire, SG1 2NY, U.K. | | ----------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord <100412.1707@CompuServe.COM> Subject: Re: RASMOL use in General Chemistry Date: 27 Nov 96 12:29:46 EST To: Rasmol List On Thu, 21 Nov 1996 Eric Martz wrote: > Anyway, if you find any sites which are really outstanding or which list other sites, please email them to me and eventually links will be put on my site. Thanks. I have collected some links on my web page: http://ourworld.compuserve.com/homepages/JDebord/models.htm I hope you will find them interesting. Best regards Jean Debord Faculte de Medecine, Limoges, France ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Rasmol scripts Date: Wed, 27 Nov 1996 11:27:53 -0800 To: rasmol@noc1.oit.umass.edu At 01:02 AM 11/27/96 -0800, Mueller Mr A wrote: > >Hi all, > >especially for writing scripts by hand it would be usefull to add a new >feature to the rasmol code that shows you the current value of internal >variables. > >example: "show ambient" would tell you the current ambient value > "show rotate" would tell you the current rotation for x,y,z > ... > >I think this is a good idea for the next rasmol version. The current Chime 0.99 release for windows has a new command which adds this capability. Chime has a new command 'view' which can be used in several ways, one of which is: view show user which displays a series of 'rotate', 'translate', 'zoom' and 'slab' commands needed to reproduce the current 'view' of the molecule. (The commands which are output can all be used in Rasmol to reproduce the current 'view' there as well.) The idea of having a 'show rotate' command which just shows the rotation values would also be useful. I will try to remember to add this to the next version of Chime. (and Show Ambient (!)) Chime 0.99 also has full command line capabilities from within the web browser page, so you can set directly interact with Chime using the command line mode (take a look at Eric's example). The other things that the 'view' command can be used for are view set X(theta) Y(phi) Z(psi) zoom xtrans ytrans ztrans slab cenX cenY cenZ - allows you to set the current view with a single command [note quite 'user' friendly, but this one is more intended for automatic script generation programs, like the movie generator Eric is working on] view save [#] : saves the current view into numbered slot [0-15] view restore [#] : restores current view from slow [0-15] view show view : outputs a single 'view set' command to restore the current view There are several other new commands which I have added to Chime to facilitate Eric's (and others) ability to easy create move scripts which are platform independent. I have some brief notes on these which are available at Eric's web site in his off of his Chime page. Eric also has some script examples there that use most of these new commands. -tim > > Thanks, > > > Arne > > ----------------------------------------------------------------------- >| Arne Mueller | email: am27627@ggr.co.uk | >| Glaxo Wellcome Medicines Research Centre, | Tel: +44 (0)1438 763419 | >| Gunnels Wood Road, Stevenage, | | >| Hertfordshire, SG1 2NY, U.K. | | > ----------------------------------------------------------------------- > > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Andy Bates Subject: Incremental zoom/trans? Date: Fri, 29 Nov 1996 09:29:08 GMT To: rasmol@noc1.oit.umass.edu Dear All, This is my first contribution. I am in the process of writing some Rasmol scripts for use in a lecture. Firstly, thanks to Eric Martz for the inspiration provided by some of his scripts on the Web site, and specifically for the opportunity to steal the ideas for some of his routines! I am writing some scripts which involve starting with a view of a whole molecule (or protein -DNA complex in this case) and dynamically zooming in to see some detail. I presume this is not original, but I have not seen it discussed. These routines involve translations and rotations as well as zooms. The problem is that they are inelegant and laborious to code; a simple iterative approach will not work since zoom and translate are absolute and not relative measures. I divide the change in zoom, rotx, roty.. etc into a suitable number of steps with a refresh after each step. I would like to be able to write 'zoom (+5)' or something to go from zoom 100 to zoom 105, then also from zoom 105 to zoom 110, so that iteration is possible. Is there such a command, or would there be popular support for it if it did exist? These same considerations apply to a dynamic 'inflation' of spacefill to full size, which is smoother than having spacefill springing suddenly into place. I suppose somebody (Tim Maffett?) is going to tell me that I should be using Chime, then all will be possible! I will, I promise, when I'm not under time pressure, and I can get to grips with it! Finally, I had to remind myself of my trigonometry to arrange a rotation about an axis other than x, y, z, which was ok, but would there be any call for a simple way of defining a new axis to rotate around (with angles, for example). I guess this just puts the trig in the program, rather than in the scripter's brain, so maybe there's no point... Thanks for reading my ramblings... Andy Bates. (note new address) __________________ Dr Andrew D. Bates School of Biological Sciences University of Liverpool Life Sciences Building Crown Steet Liverpool L69 7ZB UK Tel-(+44) (0)151 794 4322 Fax-(+44) (0)151 794 4349 Email-bates@liv.ac.uk http://www.liv.ac.uk/Biochem/Genes.html#ADB1 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Incremental zoom/trans? Date: Fri, 29 Nov 1996 17:03:37 -0500 (EST) To: rasmol@noc1.oit.umass.edu At 09:29 AM 11/29/96 GMT, Dr Andrew D. Bates wrote: > Firstly, thanks to Eric Martz for the >inspiration provided by some of his scripts on the Web site, and >specifically for the opportunity to steal the ideas for some of his >routines! You're very welcome. That's why I provided them. I don't regard it as stealing (assuming you do acknowledge the resources upon which you build) but rather as a collaboration in the best sense, and a very enjoyable way to 'meet' new friends. >I am writing some scripts which involve starting with a view of a whole >molecule (or protein -DNA complex in this case) and dynamically zooming in >to see some detail. I presume this is not original, but I have not seen it >discussed. These routines involve translations and rotations as well as >zooms. The problem is that they are inelegant and laborious to code; I've been there!! > a >simple iterative approach will not work since zoom and translate are >absolute and not relative measures. I divide the change in zoom, rotx, >roty.. etc into a suitable number of steps with a refresh after each step. That is correct for RasMol at present. Chime has enabled relative changes. >I would like to be able to write 'zoom (+5)' or something to go from zoom >100 to zoom 105, then also from zoom 105 to zoom 110, so that iteration is >possible. Is there such a command, or would there be popular support for >it if it did exist? >I suppose somebody (Tim Maffett?) is going to tell me that I should be >using Chime, then all will be possible! I will, I promise, when I'm not >under time pressure, and I can get to grips with it! Tim may tell you, and I (as an independent and relatively unbiased party) definitely will do so. Yes, it will take you a few hours to become familiar with how to use Chime. That is the price for the wonderful power of Chime. I have tried to make this as easy as possible by providing a series of examples into which you can substitute your molecules and scripts (http://www.umass.edu/microbio/chime). I have spent that much time merely adjusting the timing in an already completed and debugged RasMol script, just to allow it to work satisfactorily on different hardware. Therefore, I recommend that you invest the time to use Chime NOW because it will save you a lot of time in the future. Remember, Chime supports ALL RasMol commands, so if you've learned how to do things in RasMol you're more than half-way there. Chime's command language is a superset of RasMol commands which includes a few new ones that make script-writing a great deal easier. Chime's 'move' command does indeed allow you to do a RELATIVE zoom, even simultaneously with rotations and translations, smoothly and with machine-independent timing (you specify the total number of seconds you want for the entire move) -- all in a single one-line command! (See examples in my DNA or protein secondary structure scripts, and the 'move' command in the draft Chime manual at http://www.umass.edu/microbio/chime/manual/chimeman.htm) >Finally, I had to remind myself of my trigonometry to arrange a rotation >about an axis other than x, y, z, which was ok, but would there be any call >for a simple way of defining a new axis to rotate around (with angles, for >example). I guess this just puts the trig in the program, rather than in >the scripter's brain, so maybe there's no point... I'm not sure what the advantage is here, vs. the simpler approach of first orienting the molecule so the desired rotation can then occur around e.g. X or Y, making it easy to do. > These same considerations apply to a dynamic >'inflation' of spacefill to full size, which is smoother than having >spacefill springing suddenly into place. I've never felt the need for this. It is an interesting idea. At present it would have to be 'inelegantly' hand coded in either RasMol or Chime. I should remind however that such 'inelegant' coding needs be done only once, and can thenceforth be called as a sub-script whenever desired. Moreover, if this idea gains popularity we can probably persuade Tim Maffett to provide such a command in Chime. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: German version of RasMol Date: Fri, 29 Nov 1996 17:12:28 -0500 (EST) To: ukrueger@BIOMED.MED.YALE.EDU Cc: rasmol@noc1.oit.umass.edu I have not received any emails from individuals providing or interested in providing German translations of RasMol resources. All non-English resources I know about are listed at http://www.umass.edu/microbio/rasmol/nonengli.htm I hope that volunteers will come forth to provide German translations, as they have for French and Spanish translations. At 09:25 PM 11/28/96 -0500, you wrote: >Dear Mr. , >I would like to get a german version of RasMol. If you know any resource >please contact me. > > Sincerely, > > Dr. U. Krueger > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Relative zooms in Chime (-99 limitation) Date: Fri, 29 Nov 1996 18:03:13 -0500 (EST) To: rasmol@noc1.oit.umass.edu In my reply to Andrew Bates, I forgot to warn about a 'catch' in Chime's present (version 0.99) implementation of relative zooms. Negative zooms are presently limited to -99. Larger negative values don't work. Tim Maffett has removed this limitation (in version 1.0 which is not yet available). For example, in my protein secondary structure script, I zoom from 350% to 700% when showing a hydrogen bond, in ALPH1.SPT: set zoom center off #see explanation below move 0 0 0 350 -35 45 0 0 2 10 Later, I want to zoom back down to 350%. At present I can't use move with a zoom parameter of -350, so I work around this with the following sequence (which produces a rather bumpy result): #unzoom #move 0 0 0 -350 35 -45 0 0 1 10 but -99 is largest negative zoom move 0 0 0 -99 10 -13 0 0 1 5 move 0 0 0 -99 10 -13 0 0 1 5 move 0 0 0 -99 10 -13 0 0 1 5 move 0 0 0 -53 4.5 -7 0 0 1 5 I elected not to use Chime's new feature which automatically keeps a specified 'center' location centered during zooms, because I wanted to change the center of the image smoothly during the zoom. That is why, in addition to the relative zoom value of 350, -99, or -53, I am also specifying some X and Y translation values. I reduced the target frames per second from the default of 30 to 5 in order not to have the total movement take too long on my (slow) 486DX/66MHz. As explained in my 'Guide to script creation for RasMol and Chime' (http://www.umass.edu/microbio/rasmol/makescrp.htm) you can find out the desired values (zoom to 700%, translate X 35 and Y -45) by approximating the desired starting and ending images with the mouse, and then reporting the positions of each with RasMol's 'save script '. Then you examine the contents of the automatically-generated RasMol script file and find the rotation, translation, and zoom commands which occur early in that file. If you are developing directly in Chime, this is now quite convenient, using Chime's new 'view show user' command (try it in http://www.umass.edu/microbio/chime/authtool/fs_au1.htm). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: German version of RasMol Date: Mon, 2 Dec 1996 10:20:37 -0500 (EST) To: steipe@lmb.uni-muenchen.de Cc: rasmol@noc1.oit.umass.edu Dear Boris: There is quite a bit which could be translated: RasMol scripts, Chime scripts, the RasMol Manual, web pages, possibly even RasMol itself, etc. There are two concerns, however. First, some of the resources are under rapid development and may be revised frequently. Second is the issue of whether the main German audience for the resources really needs the translation. I have no information on the second issue. It would be simplest if the translator can provide the translated resources on his/her own web server. That way, I can simply put a link to your server rather than having to maintain copies on my server. (I am already too far behind in maintaining such copies provided by others.) Also, that way the translator can monitor the access or downloading frequencies to find out whether more effort is justified. If you wish to give this a try, I suggest that you pick a RasMol script or Chime resource which you think would be most useful, contact the author to see whether a revision is planned in the near future, provide the translation, and watch the access rates. The RasMol Home Page has been visited by about 2,000 people per month for the past several months. 1,500 people downloaded RasMol scripts from this site during the first nine months of 1996. I am copying this message to the RasMol list in case others (perhaps in other languages) wish to join this discussion. Also perhaps Naoum Salame (French Ministry of Education) or Jose Miguel Fernandez-Fernandez (Granada, Spain) can add some comments based on their ongoing translation efforts. At 08:53 AM 12/2/96 +0000, you wrote: >Eric Martz wrote: > >> I hope that volunteers will come forth to provide German translations, as >> they have for French and Spanish translations. > >I could contribute. *What* needs to be translated ? And would someone >(you ?) be willing to coordinate the effort ? > >Best wishes, >Boris > >-- > +---Dr. Boris Steipe---------------+ > | Genzentrum | > | Feodor-Lynen Str. 25 Tel +49 (0)89 74017-417 | > | 81377 Muenchen, Germany Fax - 448 | > +------+ > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Sun-Charset: US-ASCII ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: bugs Date: Tue, 3 Dec 1996 12:55:45 GMT To: rasmol@noc1.oit.umass.edu Hi, I've found a minor bug in RasMol 2.6b2: If you load a mol2 file, Dummy atoms are interpretted as Deuteriums. I was wondering how I went about logging this for the future?? Jason ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Fw: RE: bugs Date: Tue, 3 Dec 1996 10:39:25 -0500 (EST) To: Cc: cole@chemcrys.cam.ac.uk I forward this reply from Jason Cole as it may be of interest to others. -Eric ------------------------------ Tue, 3 Dec 1996 15:25:23 GMT From: cole@chemcrys.cam.ac.uk Subject: RE: bugs To: emartz@microbio.umass.edu > [Martz reply to Jason Cole:] > By mentioning the bug on this list you have 'logged' it (Roger Sayle > reads the list). However, I for one don't know what you mean > by dummy atoms. Perhaps you need to provide a simple example > mol2 file to illustrate the problem? > Hi, The TRIPOS mol2 format has defined an atom-type "Du" which represents anything which they dont have a set type defined for. (Some metals for example fall into this category). The SYBYL program assigns this atom type for such cases. It is also useful for representing disordered atoms in small molecule compounds, centroids of molecules or coordinates in space that may have some use (e.g. the origin). We use rasmol to view "structure-averaged" distributions of weak interactions from the cambridge structural database (I like the new "noconnect" feature in rasmol by the way, it saves me using a patched version). An example follows: isoxazole...any polar X-H group. In it there are 3 of these Dummy atom types (which TRIPOS specify with the atom type Du). In this case they represent average positions of substituents on the ring, not always H atoms. Jason P.S. If you load that mol2 file into RasMol make sure you use the -noconnect switch, otherwise you'll get a mess! @MOLECULE csd-080-isoxazole_1_csd-c02-NOSH_any.cor 156 82 SMALL NO_CHARGES @ATOM 1 Du -1.368 -2.079 0.000 Du 2 Du 1.638 -1.270 0.000 Du 3 Du 1.619 1.877 0.000 Du 4 C 0.531 0.987 0.000 C.ar 5 C 0.560 -0.439 0.000 C.ar 6 C -0.741 -0.805 0.000 C.ar 7 N -0.701 1.440 0.000 N.ar 8 O -1.537 0.290 0.000 O.2 9 O10 -1.586 3.982 0.130 O.3 10 H27 -1.309 3.040 0.179 H 11 O2 -1.599 3.990 0.032 O.3 12 H1 -1.395 3.029 -0.008 H 13 O14 -1.612 3.994 0.223 O.3 14 H40 -1.349 3.057 0.082 H 15 O6 -1.574 4.001 0.025 O.3 16 H14 -1.441 3.028 -0.021 H 17 O6 -1.603 4.021 0.075 O.3 18 H6 -1.424 3.054 0.089 H 19 O3 -2.321 3.672 0.130 O.3 20 H5 -1.701 2.911 0.076 H 21 N1 -2.092 3.787 0.761 N.3 22 H11 -1.562 2.950 0.568 H 23 O10 -2.217 3.704 0.560 O.3 24 H2 -1.574 2.964 0.493 H 25 O10 -1.714 3.820 1.127 O.3 26 H14 -1.363 2.959 0.806 H 27 O3 -2.071 3.871 0.509 O.3 28 H81 -1.561 3.092 0.193 H 29 O3 -2.910 3.171 0.481 O.3 30 H31 -2.196 2.519 0.308 H 31 N1 -1.897 4.011 0.422 N.3 32 H7 -1.480 3.113 0.228 H 33 O2 -2.862 3.279 0.219 O.3 34 H1 -2.035 2.748 0.208 H 35 O5 -3.122 2.979 0.568 O.3 36 H8 -2.294 2.496 0.352 H 37 N2 -1.840 3.842 1.219 N.3 38 H2 -1.488 3.017 0.757 H 39 N1 -2.029 4.021 0.515 N.3 40 H1 -1.540 3.169 0.283 H 41 N2 -1.775 4.170 0.256 N.3 42 H7 -1.514 3.201 0.158 H 43 O2 -2.879 3.235 0.326 O.3 44 H2 -1.993 2.909 0.053 H 45 N2 -2.026 4.105 0.160 N.3 46 H2 -1.655 3.167 0.135 H 47 N1 -2.863 3.246 0.873 N.3 48 H711 -1.981 2.767 0.774 H 49 N2 -2.649 3.666 0.288 N.3 50 H2 -1.914 2.985 0.408 H 51 N1 -2.030 3.197 1.866 N.3 52 H12 -1.371 2.946 1.144 H 53 N2 -1.693 4.207 0.437 N.3 54 H2 -1.539 3.213 0.368 H 55 N7 -1.061 4.436 0.003 N.3 56 H72 -1.021 3.428 0.045 H 57 N2 -1.977 4.152 0.214 N.3 58 H12 -1.665 3.210 0.030 H 59 N2 -1.826 4.075 0.971 N.3 60 H1 -1.690 3.189 0.507 H 61 N1 -2.124 4.070 0.469 N.3 62 H1 -1.830 3.170 0.120 H 63 O8 -0.587 3.925 1.885 O.3 64 H19 -0.646 3.240 1.182 H 65 N6 -4.455 -0.174 1.647 N.3 66 H61 -3.568 -0.197 1.165 H 67 N3 -3.563 1.726 2.224 N.3 68 H9 -2.769 1.240 1.833 H 69 O10 -2.217 3.704 0.560 O.3 70 H1 -2.833 3.539 1.308 H 71 N1 -2.092 3.787 0.761 N.3 72 H12 -1.494 4.583 0.929 H 73 O10 -1.714 3.820 1.127 O.3 74 H15 -2.335 4.071 0.408 H 75 O3 -2.071 3.871 0.509 O.3 76 H82 -1.680 4.667 0.086 H 77 O2 -2.896 -2.699 1.500 O.3 78 H2 -3.782 -2.372 1.774 H 79 O3 -2.910 3.171 0.481 O.3 80 H32 -3.427 2.797 1.228 H 81 N1 -2.030 3.197 1.866 N.3 82 H11 -1.938 2.483 2.573 H 83 O10 2.140 0.771 2.587 O.3 84 H1 2.970 0.311 2.330 H 85 N8 1.566 -0.157 3.264 N.3 86 H82 1.086 -0.792 2.644 H 87 O2 -2.962 -2.528 1.602 O.3 88 H1 -3.789 -1.997 1.612 H 89 N1 1.107 0.679 3.260 N.3 90 H11 1.170 -0.108 2.631 H 91 N1 -2.863 3.246 0.873 N.3 92 H712 -2.688 4.190 1.183 H 93 O5 -3.122 2.979 0.568 O.3 94 H9 -2.944 3.461 1.407 H 95 N2 -2.649 3.666 -0.288 N.3 96 H1 -3.322 3.319 0.379 H 97 N2 -2.026 4.105 0.160 N.3 98 H1 -2.980 4.226 -0.145 H 99 O11 1.274 0.131 2.951 O.3 100 H23 0.306 0.290 2.897 H 101 N7 -1.061 4.436 -0.003 N.3 102 H71 -1.884 4.874 0.382 H 103 N1 -2.124 4.070 0.469 N.3 104 H2 -2.938 4.477 0.034 H 105 O5 0.027 -0.177 3.127 O.3 106 H8 -0.938 -0.025 3.014 H 107 O8 -0.587 3.925 1.885 O.3 108 H20 -0.786 4.882 1.783 H 109 N1 1.107 0.679 3.260 N.3 110 H12 0.267 1.233 3.194 H 111 O3 1.033 0.681 3.285 O.3 112 H14 0.054 0.762 3.265 H 113 O11 -1.726 0.056 3.273 O.3 114 H23 -0.812 -0.156 2.978 H 115 N2 -0.857 -0.344 3.366 N.3 116 H1 -0.242 -1.139 3.285 H 117 N1 2.084 -2.096 2.864 N.3 118 H13 2.666 -1.847 2.078 H 119 N8 1.566 -0.157 3.264 N.3 120 H81 2.316 0.323 2.789 H 121 N3 1.946 -0.208 3.126 N.3 122 H9 2.740 -0.693 2.736 H 123 O3 -2.664 1.850 2.596 O.3 124 H5 -3.284 2.611 2.542 H 125 O10 -3.439 3.642 -0.158 O.3 126 H200 -3.094 3.071 0.563 H 127 N3 -3.563 1.726 2.224 N.3 128 H10 -3.567 2.733 2.282 H 129 O3 2.464 -2.246 2.570 O.3 130 H81 2.945 -2.986 3.003 H 131 O3 0.068 -1.753 3.280 O.3 132 H3 -0.794 -1.280 3.296 H 133 N5 -2.349 2.413 2.870 N.3 134 H5 -1.722 1.622 2.862 H 135 N6 -4.455 -0.174 1.647 N.3 136 H65 -4.705 -1.140 1.793 H 137 O6 -3.739 0.231 2.594 O.3 138 H14 -3.869 1.202 2.513 H 139 N1 4.014 -2.164 1.422 N.3 140 H73 4.062 -1.591 0.593 H 141 O14 -3.636 0.145 2.712 O.3 142 H40 -3.902 1.085 2.608 H 143 N1 2.084 -2.096 2.864 N.3 144 H11 1.554 -1.259 3.057 H 145 N1 -4.869 0.530 0.940 N.3 146 H5 -4.496 1.365 0.514 H 147 N1 4.014 -2.164 1.422 N.3 148 H71 3.267 -2.833 1.311 H 149 N2 -1.473 1.584 3.629 N.3 150 H3 -0.615 1.795 3.143 H 151 N2 -1.857 1.436 3.334 N.3 152 H1 -2.577 2.143 3.356 H 153 O10 -3.439 3.642 0.158 O.3 154 H100 -3.092 3.375 1.038 H 155 O2 -2.826 -0.631 3.155 O.3 156 H821 -2.749 -1.609 3.216 H @BOND 1 7 4 ar 2 4 5 ar 3 5 6 ar 4 6 8 ar 5 7 8 ar 6 6 1 ar 7 5 2 ar 8 4 3 ar 9 9 10 1 10 11 12 1 11 13 14 1 12 15 16 1 13 17 18 1 14 19 20 1 15 21 22 1 16 23 24 1 17 25 26 1 18 27 28 1 19 29 30 1 20 31 32 1 21 33 34 1 22 35 36 1 23 37 38 1 24 39 40 1 25 41 42 1 26 43 44 1 27 45 46 1 28 47 48 1 29 49 50 1 30 51 52 1 31 53 54 1 32 55 56 1 33 57 58 1 34 59 60 1 35 61 62 1 36 63 64 1 37 65 66 1 38 67 68 1 39 69 70 1 40 71 72 1 41 73 74 1 42 75 76 1 43 77 78 1 44 79 80 1 45 81 82 1 46 83 84 1 47 85 86 1 48 87 88 1 49 89 90 1 50 91 92 1 51 93 94 1 52 95 96 1 53 97 98 1 54 99 100 1 55 101 102 1 56 103 104 1 57 105 106 1 58 107 108 1 59 109 110 1 60 111 112 1 61 113 114 1 62 115 116 1 63 117 118 1 64 119 120 1 65 121 122 1 66 123 124 1 67 125 126 1 68 127 128 1 69 129 130 1 70 131 132 1 71 133 134 1 72 135 136 1 73 137 138 1 74 139 140 1 75 141 142 1 76 143 144 1 77 145 146 1 78 147 148 1 79 149 150 1 80 151 152 1 81 153 154 1 82 155 156 1 @SET CENTRAL STATIC ATOMS **** central group 9 1 2 3 4 5 6 7 8 156 Set1 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,1.80)} Set2 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,2.10)} Set3 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,2.40)} Set4 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,2.70)} Set5 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,3.00)} Set6 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,3.30)} Set7 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,3.60)} Set8 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,3.90)} Set9 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,4.20)} Set10 DYNAMIC ATOMS **** Distance based atom shell {subst_sphere(1+2+3+4+5+6+7+8+156,4.50)} /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: new -noconnect switch? Date: Tue, 3 Dec 1996 12:09:48 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: cole@chemcrys.cam.ac.uk, ras32425@ggr.co.uk Will someone please explain the "new -noconnect switch" for RasMol mentioned by Jason Cole? I was unaware of this. Must it be used at startup, e.g. "raswin.exe -noconnect"? (It is not mentioned in the "up to date" 2.6b2 manual http://www.umass.edu/microbio/rasmol/distrib/rasman.htm nor in the documents provided by Roger with beta-1 or beta-2.) X-Sun-Charset: US-ASCII ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: Re: new -noconnect switch? Date: Tue, 3 Dec 1996 17:16:49 GMT To: rasmol@noc1.oit.umass.edu Dear Eric, In the latest rasmol 2.6 beta_2 you can start up Rasmol as rasmol -noconnect or in my case rasmol -noconnect -mol2 What this does (in the case of mol2 files) is to force rasmol not to recalculate the connectivity. It uses the connectivity given in the mol2 file instead. In the past this was not the case (in fact try loading that mol2 file into rasmol with and without -noconnect and you will see what I mean) Jason X-Sun-Charset: US-ASCII ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: Re: new -noconnect switch? Date: Tue, 3 Dec 1996 17:22:10 GMT To: rasmol@noc1.oit.umass.edu on th -noconnect switch... : I'm not using the windows version, I use the Unix version. Jason "RASMOL use in General Chemistry" (Nov 21, 10:55am) References: <3.0b36.32.19961121105543.006abec4@unccvm.uncc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: RASMOL use in General Chemistry Date: Tue, 3 Dec 1996 19:10:43 -0500 To: rasmol@noc1.oit.umass.edu Please look at the October 1996 Protein Data Bank Newsletter for 2 excellent articles on using PDB for educational purposes. THE PDB IN UNDERGRADUATE EDUCATION Virginia B. Pett, The College of Wooster, Wooster, OH, USA and NEW RESOURCES FOR EDUCATION USING RASMOL AND CHIME Eric Martz, University of Massachusetts, Amherst, MA, USA The Newsletter is released quarterly, and is available from the PDB home page at: http://www.pdb.bnl.gov/ Regards, Nancy Manning On Nov 21, 10:55am, Dewey Williams wrote: > Subject: RASMOL use in General Chemistry > I know many of you use RASMOL in advanced chemistry, biochemistry and > research but we are looking for ways to use it for our first semester > chemistry majors. > > If anyone has ideas, scripts, web pages or other information on how we can > utilize RASMOL in general chemistry, please let me know. > > Thanks in advance. > > Dewey Williams - Lab Manager williams@unccvm.uncc.edu > UNC-Charlotte Chemistry Dept. http://www.chem.uncc.edu > "These are my ideas and no one else will claim them." > "If you are not part of the solution, you are part of the precipitate" >-- End of excerpt from Dewey Williams -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Head User Support Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Typo in PDB Newsletter Date: Wed, 04 Dec 1996 16:55:27 -0500 To: rasmol@noc1.oit.umass.edu I would like to bring to this group's attention a typographical error in my article in the most recent PDB Newsletter. The article states that 1,600 lines of RasMol's source code were incorporated into Chime. The correct value is 16,000. The other figures in the article are correct (e.g. that over 90,000 lines of Chime's source code are original with MDLI). I apologize for any confusion. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Greg Flack Subject: attn:chime script writers, a bug? Date: Thu, 05 Dec 1996 05:18:22 -0700 To: rasmol@noc1.oit.umass.edu I have been working on an embedded html document and have come across what may be a bug, or is at least a strange inconsistency with Chime. I want to keep the size of my html file small, and so have been using .spt files within the html, rather than writing the scripts themselves into the document. I've noticed that if the script is short (four lines or so) Chime seems to ignore it. Because such scripts are short there is little hassle in writing them in, but all the same I had intended to reuse some for other molecules. I'm curious to know if this is a problem only on my system, or has anyone else experieced the same? Aside: my project is an undergraduate independent study and much of what my professor knows about Rasmol and Chime I have shown him. If anyone would care to send me comment or make suggestions on this latest document it would be much appreciated, as much of my work receives little scrutiny. The url is http://holly.colostate.edu/~gsflack/5hvp/chime/alln1.htm -- Gregory Flack gsflack@holly.colostate.edu Undergraduate - Department of Microbiology Colorado State University Fort Collins, Colorado ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: attn:chime script writers, a bug? Date: Thu, 05 Dec 1996 10:13:27 -0500 (EST) To: rasmol@noc1.oit.umass.edu Dear Greg Flack: (who reported that short script files (<= 4 lines) fail to execute in Chime) What operating system are you using? I am using 16-bit Chime 0.99 for Windows 3.1. I do not find the bug you describe in this version. However you would need to provide the exact syntax/sample files if you cannot solve this (preferably by ftp). Exactly how are you calling the scripts? I have several short script files called with strings sent to an button using immediate=1. For example, one has only two lines and works fine. However, I have found working with html/javascript very slow and frustrating. Almost everything I do fails the first 2 or 5 tries, but eventually I figure out some syntactical issue or pecularity and get it to work. In one case I had to ask for help, and Tim Maffett kindly found where I had omitted a critical space character. One bug which I haven't been able to solve occurs when two script files (whatever.spt) are called in series in the same command-string sent to the button. I have two such instances in which nothing after the first script call is executed (neither a command nor the second script). So far I haven't been able to rule out the possibility that Chime has a bug such that after the return from a script, nothing else gets executed. An easy workaround is to call a single script file which simply in turn calls the other two. This works fine. For example, if I want to call a.spt and b.spt, if I do this script = "select hydrogen and selected; wireframe 0; script a.spt; script b.spt"; scriptToChime(script); // uses immediate button in dummy frame b.spt fails to execute. If I reverse the order, a.spt fails to execute. Therefore I know both scripts are capable of working. Here is the workaround: script = "select hydrogen and selected; wireframe 0; script c.spt;" scriptToChime(script); where file c.spt contains: script a.spt script b.spt /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Command-Line Interface for a Chime HTML Page Date: Thu, 05 Dec 1996 10:36:12 -0500 To: rasmol@noc1.oit.umass.edu As a followup to Greg Flack's question: // This is javascript file CHI2WAY.JS by Eric Martz // Thanks to Tim Maffett of MDLI for showing me how to do this! // For more information (e.g. how to invoke Chime in the first place, // how to use an immediate button in a dummy frame) see // Creating Chime Web Pages at http://www.umass.edu/microbio/chime // Include this file in your chime page with a line in the such as: // // In the body of your html Chime document, calling chime_2way() // // inserts a command-line interface into the document. // This includes a place to type commands, and a box to receive messages // from Chime. // The present code is designed for the case in which the plug-in and // the command-line interface are in the same [frame in the same] document. // The which invokes Chime must include: // MessageCallback="ChimeMsg" // scriptToChime() is defined in chiimmed.js which is required. function ChimeMsg( buttonname, message ) { document.c2w_form.chimemessages.value += message + "\r\n"; } function chime_2way() { with (document) { open(); // Command-line input slot writeln("

"); writeln(""); // Command-line execution button writeln(""); writeln("
"); // Message box writeln(""); writeln("Chime's Messages"); // Clear Msg box writeln(""); writeln(""); close(); } } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Command-Line Interface for a Chime HTML Page Date: Thu, 05 Dec 1996 10:57:56 -0500 To: rasmol@noc1.oit.umass.edu Sorry, I'm still completing my thought following up Greg Flack's question. The point of the javascript file CHI2WAY.JS which I sent in my previous message is as follows. When you are trying to write a Chime page, or debug a problem such as the one Greg reported, it is very helpful to have the command-line interface available. You can call a script directly ('script a.spt') to see if it works. You can issue other commands as needed, such as 'view show user' to report the angles needed in a script to produce the current view, etc. Then, when you have everything working, you can comment out the one line which inserted the command-line interface, and it disappears in the final version. But LEAVE IT THERE so you can uncomment it when the next problem arises! :-) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: <01ICNCW8BOH4000479@pobox.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Thomas Andrew Manderfield Subject: Re: Command-Line Interface for a Chime HTML Page Date: Thu, 5 Dec 1996 11:08:15 -0500 (EST) To: rasmol@noc1.oit.umass.edu Eric, As far as the command line interface in Chime goes, can chime report back the name of the atom the user clicks on (either to the command line or elsewhere). This would be similiar to how rasmol handles clicking on an atom. If this functionallity was built into Chime, it would make it far easier to set up 'quizes' for the view. If the atom number or name was returned by the plugin and the means were available to trap for this information (through javascript etc) then it could be really helpful. I am on a mac, so I am unsure what new features .99 offers. Tom Biological Sciences Carnegie Mellon University manderid+@andrew.cmu.edu Included] ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Command-Line Interface for a Chime HTML Page [Example Date: Thu, 05 Dec 1996 09:59:31 -0800 To: rasmol@noc1.oit.umass.edu At 11:08 AM 12/5/96 -0500, Thomas Andrew Manderfield wrote: >Eric, > >As far as the command line interface in Chime goes, can chime report >back the name of the atom the user clicks on (either to the command line >or elsewhere). This would be similiar to how rasmol handles clicking on >an atom. > >If this functionallity was built into Chime, it would make it far easier >to set up 'quizes' for the view. If the atom number or name was >returned by the plugin and the means were available to trap for this >information (through javascript etc) then it could be really helpful. > >I am on a mac, so I am unsure what new features .99 offers. > >Tom > >Biological Sciences >Carnegie Mellon University >manderid+@andrew.cmu.edu > Chime 0.99 (and soon 1.0 for all platforms) has the following "callback events" which you can register a JavaScript function to have called when that event occurs: PickCallback: This occurs whenever the user clicks (picks) on an atom/bond/residue. The format of the pick info depends on the current pick mode MessageCallback This occurs whenever there is ANY message that Chime needs to output. (This includes pick events, but the 'PickCallback' event can specifically be used to get ONLY pick messages) PauseCallback: Called whenever a 'pause'/'wait' event happens in a script ButtonCallback: Called whenever a button Chime plugin is clicked. AnimFrameCallback: Called whenever a animation frame changes. You 'hook into' these callbacks by specifying a JavaScript function name for any of these callbacks in the Chime HTML tag for each chime structure/button plugin. I have included a "stand alone" HTML example page which illustrates the use of Chime callbacks below. You will need a PDB file called "1crn.pdb" in the same directory as this HTML file if you want to have a structure show up in the Chime structure plugin. Simply save this mail message and then DELETE all of the text above the "=====CUT HERE====" line, then open the file in your Netscape Navigator. NOTE: This page also includes the 'TEXT' of the JavaScript and tags WITHIN the text of the HTML, so you can see the code/working HTML side-by-side. NOTE 2: You need Chime version 0.99 (or 1.0) to view this example. Currently version 0.99 is only available for Windows only. (The full 1.0 Chime release for Win/Mac/SGI will be available very soon). -tim ps. If there are other 'callback events' which you think would be useful within Chime please let us know! Send email to 'chime-feedback@mdli.com' or post a message here (to the rasmol mailing list). ========CUT HERE======= Test Events in Chime

Example of Callback Events in Chime

JavaScript functions (In Green) on this page that handle the Chime callbacks:
function MyButtonClickCallback( buttonname )
{
  // write 'button callback' message to our MESSAGE textarea...
  document.theform.chimemessages.value += 
        "ButtonCallback for Chime plugin named '" + 
        buttonname + 
        "' called.\r\n";
}

function MyMessageCallback( buttonname, message )
{
  // add this message to our message MESSAGE textarea....
  document.theform.chimemessages.value += message + "\r\n";
}

function MyPickCallback( buttonname, message )
{
  // add this message to our message PICK textarea....
  document.theform.chimepicks.value += message + "\r\n";
}
This Chime structure plugin below has a "MessageCallback" and a "PickCallback" set which will cause all messages output by the plugin to call a JavaScript function that will copy the message to the HTML edit box in the lower-right cell of this table. Some Chime buttons which will do various things:
HTML EMBED tag used to embed chime plugin below:
<embed name="themol" 
   type="chemical/x-pdb" src="1crn.pdb" 
   width=300 height=300 
   script="spacefill 120;wireframe 40" 
   MessageCallback="MyMessageCallback"
   PickCallback="MyPickCallback" 
   align=center hspace=20
>
Click on molecule below to cause "Message" and "Pick" events. 		Some Chime buttons which will also cause a JavaScript "ButtonCallback" when clicked:
Wireframe: Spacefill:

Misc Chime Buttons which will cause MessageCallbacks:
Show sequence: Show Molecule Info:

Chime Buttons to Set the Picking Mode:
None: Identify: Label: Distance:
Angle: Torsion: Monitor: Center:

Chime "MessageCallback" JavaScript Output:
Chime "PickCallback" JavaScript function Output:
++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Command-Line Interface for a Chime HTML Page Date: Thu, 05 Dec 1996 14:06:25 -0500 To: rasmol@noc1.oit.umass.edu Tom Manderfield asked what Chime 0.99 can report. Yes, it can report the atom clicked on just like RasMol. Yes, this could be used in a javascript variable to determine whether a question was answered correctly. Version 1.0 of Chime, which MDLI hopes to have out within a couple of weeks, should have all the same reports as RasMol. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: attn:chime script writers, a bug? Date: Thu, 05 Dec 1996 11:30:58 -0800 To: rasmol@noc1.oit.umass.edu At 05:18 AM 12/5/96 -0700, you wrote: >I have been working on an embedded html document and have come across >what may be a bug, or is at least a strange inconsistency with Chime. I >want to keep the size of my html file small, and so have been using .spt >files within the html, rather than writing the scripts themselves into >the document. I've noticed that if the script is short (four lines or >so) Chime seems to ignore it. Because such scripts are short there is >little hassle in writing them in, but all the same I had intended to >reuse some for other molecules. I'm curious to know if this is a >problem only on my system, or has anyone else experieced the same? > >Aside: my project is an undergraduate independent study and much of what >my professor knows about Rasmol and Chime I have shown him. If anyone >would care to send me comment or make suggestions on this latest >document it would be much appreciated, as much of my work receives >little scrutiny. The url is >http://holly.colostate.edu/~gsflack/5hvp/chime/alln1.htm You page appears to work correctly for me (the "Top View" button correctly loads/executes the 'one.spt' script from your server). The other buttons w/ inline scripts work well also. The 'setup.spt' script is correctly loaded/executed from your molecule's embed tag script) Note, it takes an additional 10-20 seconds, or more, for each of the *separate* script files to retrieved from your host machine. One thing to consider when using scripts in separate files on the host is that both your host machine and the user 'pay the price'. - For your host machine the price is having to dole out very small files (which although small can/do have as much impact on your server's performance as very large files). - For your users the Chime buttons can be fairly slow to "work", taking several seconds (or more!) to retrieve the script file from your host machine. The time required can have to do with many factors: 1) load on your machine 2) load on the internet 3) users connection to the internet An important thing to remember is that it is often not the SIZE of the transaction, but the transaction itself that can be slow with the HTTP protocol. For development purposes it can be very useful to keep the files separate, but for sites accessible to others/the public I think the 'pain' of moving the rasmol scripts 'into' the HTML Chime embed tags is small compared to the benefits to your server machine and your users... The above is of course just my opinion, and I would love to open discussion on this topic. -tim >-- >Gregory Flack >gsflack@holly.colostate.edu >Undergraduate - Department of Microbiology >Colorado State University >Fort Collins, Colorado > > "Re: attn:chime script writers, a bug?" (Dec 5, 11:30am) References: <3.0.32.19961205113041.00fa19b4@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: "Christoph Weber" Subject: Re: attn:chime script writers, a bug? Date: Thu, 5 Dec 1996 12:45:13 -0800 To: rasmol@noc1.oit.umass.edu [snip] > For development purposes it can be very useful to keep the files > separate, but for sites accessible to others/the public I think the > 'pain' of moving the rasmol scripts 'into' the HTML Chime embed tags > is small compared to the benefits to your server machine and your > users... > > The above is of course just my opinion, and I would love to open > discussion on this topic. > > -tim How about being able to include a list of all the required scripts, so that they can be fetched from the server in a single HTTP transaction. This would allow us to keep the scripts seperate from the HTML (nice and clean, in my opinion), but reduce server load and bandwidth demand. I seem to recall that java now offers some functionality along these lines. Christoph -- | Dr. Christoph Weber Sen. Research Associate | Dept.of Molecular Biology, MB9 619-784-9869 (phone) | The Scripps Research Institute 619-784-2857 (FAX) | La Jolla CA 92037-1027 weber@scripps.edu | http://www.scripps.edu/~chazin/people/cw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Future development of the Chime plugin. Date: Thu, 5 Dec 96 13:48:19 PST To: rasmol@noc1.oit.umass.edu Dear Chimoleans, Being a long-standing fan of RasMol for the development of computerized intruction, I have also become at great fan of the Chime plugin having widely incorported its features into my instructional web pages. I am also very encouraged by the apparent development trajectory of the plugin as it seems that all efforts are being made to incorporate into it most if not all of the cammand and mouse features that originally made RasMol so popular. Because I have not yet braced myself for the "java jump" -- but I can see now that this is probably inevitable -- it is hard for me to make concrete suggestions for future improvements in the Chime plugin along these lines. However, one detracting feature of the plugin which I have noticed using both the PC and Mac platforms is that the quality of the embedded Chime images seems to be consistently and significantly inferior to the same images rendered with RasMol itself. I don't know whether it is possible to introduce some adjustment of the embedded Chime images to make them as robust as the corresponding RasMol images. I'm not even sure if image parity is possible between the two formats. In any event, I think a significant advance in the Chime plugin would come with much crisper image rendering. I'm curious to know if others have noticed this difference. 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 | | E-mail addresses: | | Faculty: sears@lifesci.lscf.ucsb.edu | | Academic: bioimages@lifesci.lscf.ucsb.edu | | WWW homepages: | | http://mentor.lscf.ucsb.edu/mcdb108a/ | | http://mentor.lscf.ucsb.edu/mcdb133/ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol Quick Start! Date: Thu, 05 Dec 1996 23:15:43 -0500 To: rasmol@noc1.oit.umass.edu I've provided a new document at the RasMol Home Page entitled 'RasMol Quick Start'. Its design was inspired by a science faculty colleague who said 'I downloaded RasMol and ran it and got this black screen. What am I supposed to do next?' This made me realize that I'm not aware of any introduction designed for true beginners, so I tried to write one. I hope it will work for high school students (ages 14-17) as well as other beginners. Comments/feedback welcome. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: attn:chime script writers, a bug? Date: Fri, 06 Dec 1996 00:58:03 -0800 To: rasmol@noc1.oit.umass.edu At 12:45 PM 12/5/96 -0800, Christoph Weber wrote: >[snip] >> For development purposes it can be very useful to keep the files >> separate, but for sites accessible to others/the public I think the >> 'pain' of moving the rasmol scripts 'into' the HTML Chime embed tags >> is small compared to the benefits to your server machine and your >> users... >> >> The above is of course just my opinion, and I would love to open >> discussion on this topic. >> >> -tim > >How about being able to include a list of all the required scripts, so that >they can be fetched from the server in a single HTTP transaction. This would >allow us to keep the scripts seperate from the HTML (nice and clean, in my >opinion), but reduce server load and bandwidth demand. > This is a good idea.. but it will not be straightforward because Chime now uses the URL request mechanism supplied to plugins by Netscape. This mechanism does not have a method for requesting a 'batch' of multiple files in one request (that I am aware of, I will investigate though..) -tim >I seem to recall that java now offers some functionality along these lines. > >Christoph >-- >| Dr. Christoph Weber Sen. Research Associate >| Dept.of Molecular Biology, MB9 619-784-9869 (phone) >| The Scripps Research Institute 619-784-2857 (FAX) >| La Jolla CA 92037-1027 weber@scripps.edu >| http://www.scripps.edu/~chazin/people/cw.html > > ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Future development of the Chime plugin. Date: Fri, 06 Dec 1996 01:08:36 -0800 To: rasmol@noc1.oit.umass.edu At 01:48 PM 12/5/96 PST, Duane Sears wrote: >Dear Chimoleans, > >Being a long-standing fan of RasMol for the development of computerized >intruction, I have also become at great fan of the Chime plugin having >widely incorported its features into my instructional web pages. I am also >very encouraged by the apparent development trajectory of the plugin as it >seems that all efforts are being made to incorporate into it most if not all >of the cammand and mouse features that originally made RasMol so popular. >Because I have not yet braced myself for the "java jump" -- but I can see >now that this is probably inevitable -- it is hard for me to make concrete >suggestions for future improvements in the Chime plugin along these lines. Chime will become a Netscape LiveConnect enabled plugin at some point, which will make it a Java class available for use by Java. My original plans were to complete this for Chime 1.0, but I have delayed this for now. Chime 1.0 does have a cross-platform mechanism for 2 way communication with JavaScript, which I think is much more versatile for the time being. This solution was needed because LiveConnect requires Java (even for JavaScript only interfaces), which would exclude Windows 3.1 and Mac68k. The Chime 1.0 JavsScript communication mechanism will work all mac, windows and SGI versions of Netscape. >However, one detracting feature of the plugin which I have noticed using >both the PC and Mac platforms is that the quality of the embedded Chime >images seems to be consistently and significantly inferior to the same >images rendered with RasMol itself. I don't know whether it is possible to >introduce some adjustment of the embedded Chime images to make them as >robust as the corresponding RasMol images. I'm not even sure if image >parity is possible between the two formats. In any event, I think a >significant advance in the Chime plugin would come with much crisper image >rendering. I'm curious to know if others have noticed this difference. > I suspect that you are using a windows platform. On the windows platform (especially Windows 3.1) there are color palette issues which dictate that Chime should request a "background" palette by default. This "background" palette has a lower priority for getting colors than a stand alone applications (i.e. Rasmol) than a 'foreground' palette (there can only be ONE window with a 'foreground' palette at any one time). (The Mac and SGI platform do a much, much nicer job of palette management) The good news is that you CAN enable Chime to get virtually the same quality of images as a stand alone Rasmol image, and this is possible via the Chime menu, or using an embed tag option. via the Chime Menu: One the 'Color' menu you will find that the Windows platform has one additional item 'Force Palette'. If you select this menu item then the Chime plugin will ask windows for a 'foreground' palette which should result in more colors and a better image. via the HTML tag used to invoke Chime: ^^^^^^^^^^^^^^^^^^ simply add THIS to your embed tag Note you can only have a ONE chime plugin on a page which uses the 'palette=foreground' command. (others will be ignored). This option will be ignored on NON windows platforms. For an example of it's use see: http://www.mdli.com/chemscape/chime/example/tablef/table-f.html If I were developing Chime web pages I would certainly use this option in most cases, as it presents a *much* nicer image to the user. Be aware that using a foreground palette in Chime can effect the colors available to Netscape, this is especially true on the Windows 3.1 platform. If you have any questions please ask. -tim >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 | >| E-mail addresses: | >| Faculty: sears@lifesci.lscf.ucsb.edu | >| Academic: bioimages@lifesci.lscf.ucsb.edu | >| WWW homepages: | >| http://mentor.lscf.ucsb.edu/mcdb108a/ | >| http://mentor.lscf.ucsb.edu/mcdb133/ | >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > References: <3.0.32.19961206004921.00eadda4@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: attn:chime script writers, a bug? Date: Fri, 6 Dec 1996 08:33:00 -0500 (EST) To: rasmol@noc1.oit.umass.edu, rasmol@noc1.oit.umass.edu Excerpts from mail: 6-Dec-96 Re: attn:chime script write.. by Tim Maffett@mdli.com > This is a good idea.. but it will not be straightforward because Chime > now uses the URL request mechanism supplied to plugins by Netscape. > This mechanism does not have a method for requesting a 'batch' > of multiple files in one request (that I am aware of, I will investigate > though..) > I don't know whether it's applicable to batch serving of script files, but GIFs can be "preloaded" onto a page as a, "WIDTH=1 HEIGHT=1", dot. This trick is used in JavaScript when a call is made to alter an image quickly, eg. an "onMouseOver" or "onClick" feature for a button. The GIF required is already in cache and is displayed (full size) without going back to the server. By analogy (only), if JavaScript could cause downloading of all linked scripts on a page into cache with "onOpen", they could be called without server intervention. Are there any JScript mavens out there that know whether this is possible? -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Quality of images Date: Fri, 6 Dec 1996 10:47:24 -0500 (EST) To: sears@lifesci.ucsb.edu Cc: Duane, my impression is that Chime's images are of identical quality to those of RasMol. This requires, of course, that the same number of pixels be involved in each image (images same size at same screen resolution), and in some cases that the palette be 'forced' as Tim described. Once I set up a Chime window next to a RasMol window side by side, same size, same image. I had noticed the choppiness of the color boundary on stick bonds in Chime, but it was identical in RasMol. However, I certainly can't speak for all situations. Can you provide an example of a particular molecule and rendering where Chime's image differs from RasMol's? /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: timp@vt.edu (Timothy L. Pickering) Subject: Question re Expiration of Chime Date: Mon, 9 Dec 1996 09:39:15 -0500 To: rasmol@noc1.oit.umass.edu The current software license for use of the Chime plug-in for Netscape states: THIS SOFTWARE CONTAINS CODE THAT DISABLES FEATURES AFTER DECEMBER 31st, 1996. I know that work is underway to deliver Chime version 1.0 before the expiration date. My question is, what happens if MDL is not able to release the new version for all platforms by the target date? My assumption is that the plug-in will simply cease working, and web pages that depend on Chime will lose the functionality that depends on the plug-in, but will still be available in a more limited form - akin to viewing web pages in text only mode. However, there is always a lurking fear that there will be unexpected/unanticipated consequences that will affect the operation of browsers in some fashion. Will we need to go in and reconfigure all our options so that the browser can read .pdb files and do all the other things that were done with helper applications before Chime absorbed all those functions? I would like to hear some discussion on these questions and perhaps some suggestions on strategies for how to cope if all does not go as planned for the release of Chime 1.0 and we suddenly lose the Chime plug-in capability. =*=*=*=*=*=*=*=*=*=*=*=*=*=*= Dr. Timothy L. Pickering, Assistant Director NSF Center for Polymeric Adhesives and Composites Virginia Tech 201A Hancock Hall Blacksburg, VA 24061-0257 Tel. (540) 231-4443, FAX: (540) 231-9452 E-Mail: timp@vt.edu URL http://www.vt.edu:10021/research/stc/STC.Home.Page.html =*=*=*=*=*=*=*=*=*=*=*=*=*=*= ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Question re Expiration of Chime Date: Mon, 09 Dec 1996 12:44:28 -0800 To: rasmol@noc1.oit.umass.edu At 09:39 AM 12/9/96 -0500, Timothy L. Pickering wrote: >The current software license for use of the Chime plug-in for Netscape states: > >THIS SOFTWARE CONTAINS CODE THAT DISABLES FEATURES AFTER DECEMBER 31st, 1996. > >I know that work is underway to deliver Chime version 1.0 before the >expiration date. My question is, what happens if MDL is not able to >release the new version for all platforms by the target date? My >assumption is that the plug-in will simply cease working, and web pages >that depend on Chime will lose the functionality that depends on the >plug-in, but will still be available in a more limited form - akin to >viewing web pages in text only mode. However, there is always a lurking >fear that there will be unexpected/unanticipated consequences that will >affect the operation of browsers in some fashion. Will we need to go in >and reconfigure all our options so that the browser can read .pdb files and >do all the other things that were done with helper applications before >Chime absorbed all those functions? > >I would like to hear some discussion on these questions and perhaps some >suggestions on strategies for how to cope if all does not go as planned for >the release of Chime 1.0 and we suddenly lose the Chime plug-in capability. > > Chime 1.0 will be released very soon, most likely within A WEEK barring something major (like my death). (and if it isn't done I will wish I was dead ;) Seriously though, if for some reason we do NOT have a Chime 1.0 ready for release within a week we will release new versions of the Chime plugin (0.99??) for all platforms with an extended expiration date. MDL would not let the current version expire without another version being available. The behavior of Chime when it does expire is to just put up a dialog which states that it has expired, and then has a button you can press to go to the MDL Chime web page to download a new version. Any web pages containing Chime structures will continue to 'work' (but Chime will not display structures). I also want to reiterate that the Chime 1.0 version has NO EXPIRATION DATE. Anyone wanting to mirror the Chime 1.0 distribution will be able to do so by downloading a Adobe Acrobat license agreement from our web site. Once you have filled out the license agreement you send it back to mdl, and mdl will send you back a signed copy. Once you have the copy returned to you from MDL you will be able to mirror the Chime distribution on your servers. For our UK (and european) users we now have our UK mirror site up and running at: http://www-uk.mdli.com/ (it will also be available soon using the more conventional "http://www.mdli.co.uk" URL.) I apologize for the delay in getting Chime 1.0 done, but I hope you will all find it worth the wait. The Chemscape team has been working furiously to get Chime 1.0 ready to go. -tim Tim Maffett tim@mdli.com Principal Architect, Internet Technologies MDL Information Systems, Inc. >=*=*=*=*=*=*=*=*=*=*=*=*=*=*= >Dr. Timothy L. Pickering, Assistant Director >NSF Center for Polymeric Adhesives and Composites >Virginia Tech >201A Hancock Hall >Blacksburg, VA 24061-0257 >Tel. (540) 231-4443, FAX: (540) 231-9452 >E-Mail: timp@vt.edu >URL http://www.vt.edu:10021/research/stc/STC.Home.Page.html >=*=*=*=*=*=*=*=*=*=*=*=*=*=*= ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Improved Chime command-line example Date: Tue, 10 Dec 1996 14:12:26 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: bryan@mttam.com, bryan@mdli.com, tim@mind.net, tim@mdli.com A much-improved example of Chime's command-line interface (via html/javascript) is now available at the UMass Chime Resources page http://www.umass.edu/microbio/chime This supercedes the example I mailed to this list recently. Among other improvements, all the relevant javascript is now in a single file, and you can press Enter to execute the command (instead of the former Execute button). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: ++++------+------+------+------+------+------+------+------+------+------+ From: Thomas Atkins Subject: Re: Question re Expiration of Chime Date: Wed, 11 Dec 1996 05:53:36 +0000 To: rasmol@noc1.oit.umass.edu When is Chime going to be ready for the Mac Platform? Hurry..... Hurry!!! Thanks Thomas Atkins ++++------+------+------+------+------+------+------+------+------+------+ From: timp@vt.edu (Timothy L. Pickering) Subject: Chime and Memory Date: Thu, 12 Dec 1996 10:23:11 -0500 To: rasmol@noc1.oit.umass.edu When viewing multi-page sites using Netscape with Chime, e.g. tutorial sites such as David Woodcock's on nomenclature, after a number of pages have been viewed I begin to get messages that memory is full. What does one do to alleviate the distress of the browser? I have no other applications running, and don't know what to do other than shut down Netscape and re-start. This seems a rather inelegant solution. =*=*=*=*=*=*=*=*=*=*=*=*=*=*= Dr. Timothy L. Pickering, Assistant Director NSF Center for Polymeric Adhesives and Composites Virginia Tech 201A Hancock Hall Blacksburg, VA 24061-0257 Tel. (540) 231-4443, FAX: (540) 231-9452 E-Mail: timp@vt.edu URL http://www.vt.edu:10021/research/stc/STC.Home.Page.html =*=*=*=*=*=*=*=*=*=*=*=*=*=*= ++++------+------+------+------+------+------+------+------+------+------+ From: skg Subject: Re: Chime and Memory Date: Thu, 12 Dec 1996 08:53:57 -0800 To: rasmol@noc1.oit.umass.edu At 10:23 AM 12/12/96 -0500, you wrote: >When viewing multi-page sites using Netscape with Chime, e.g. tutorial >sites such as David Woodcock's on nomenclature, after a number of pages >have been viewed I begin to get messages that memory is full. What does >one do to alleviate the distress of the browser? I have no other >applications running, and don't know what to do other than shut down >Netscape and re-start. This seems a rather inelegant solution. > > > >=*=*=*=*=*=*=*=*=*=*=*=*=*=*= >Dr. Timothy L. Pickering, Assistant Director >NSF Center for Polymeric Adhesives and Composites >Virginia Tech >201A Hancock Hall >Blacksburg, VA 24061-0257 >Tel. (540) 231-4443, FAX: (540) 231-9452 >E-Mail: timp@vt.edu >URL http://www.vt.edu:10021/research/stc/STC.Home.Page.html >=*=*=*=*=*=*=*=*=*=*=*=*=*=*= > > >Try increasing the size of your cache.....go to options/network, and under cache, increase the size to whatever works for you......... > References: <1.5.4.32.19961212165357.0066a54c@asis.com> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Chime and Memory Date: Fri, 13 Dec 1996 12:23:13 -0500 (EST) To: rasmol@noc1.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: skg Subject: Re: Chime and Memory Date: Thu, 12 Dec 1996 08:53:57 -0800 To: rasmol@noc1.oit.umass.edu At 10:23 AM 12/12/96 -0500, Dr. Timothy L. Pickering wrote: >>When viewing multi-page sites using Netscape with Chime, e.g. tutorial >>sites such as David Woodcock's on nomenclature, after a number of pages >>have been viewed I begin to get messages that memory is full. What does >>one do to alleviate the distress of the browser? I have no other >>applications running, and don't know what to do other than shut down >>Netscape and re-start. This seems a rather inelegant solution. skg wrote: >Try increasing the size of your cache.....go to options/network, and >under cache, increase the size to whatever works for you......... > My experience (on a Mac) is that 2M of cache suffices and that at most sites, Netscape will simply clear cache automatically if more is required. However, at a few sites, it is RAM that gets filled up causing dire prompts first, and then quitting altogether, eventually. For those cases, I think the only remedy is to increase the memory allocation for Netscape: 7M is the minimum; 9M is recommended for 3.0; and 12M works routinely with Ram Doubler installed. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Klaus Frommer Subject: Program helping in 3D-graphical calculations Date: Tue, 17 Dec 1996 13:29:01 +0100 (MEZ) To: rasmol@noc1.oit.umass.edu Many Molecular Modelling Programs require that the locations of the centers of the atoms forming the molecule are given in cartesian coordinates. But often I only have the distances between the centers of the atoms and the angles between the covalent bonds. With these data and by means of analytical geometry it is possible to calculate coordinate locations but it is quite fussy. Now my question: Is there a program that can do such calculations, i.e. transform the distance-data and the angular data into cartesian coordinate data? Klaus Frommer, Eberhard-Karls-University of Tuebingen ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Re: Program helping in 3D-graphical calculations Date: Tue, 17 Dec 1996 14:51:44 -0500 (EST) To: (forwarded by E Martz due to technical difficulties) From: Boris Steipe Klaus Frommer wrote: > often I only have the distances between the centers of > the atoms and the angles between the covalent bonds. Often ? When ? > With these data and > by means of analytical geometry it is possible to calculate coordinate > locations but it is quite fussy. Actually, if distances and angles are known *exactly*, the problem is easy, save for chirality. It becomes difficult only if your information is approximate. Then this so called embedding problem becomes difficult, because in essence you have to solve a high-dimensional minimization problem: how to find the set of coordinates that will best represent your data. > Now my question: Is there a program that > can do such calculations, i.e. transform the distance-data and the > angular data into cartesian coordinate data? As far as macromolecules are concerned, this is the daily bread of any macromolecular NMR spectroscopist - programs like DIANA and X-PLOR exemplify two alternate approaches to the problem Diana and FANTOM X-PLOR All these are not trivial to work with. But maybe your problem is simpler or more limited ? Could you be more specific (What kind of input do you have, what kind of output do you want...) Greetings Boris /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Program helping in 3D-graphical calculations Date: Tue, 17 Dec 1996 13:17:58 -0800 To: rasmol@noc1.oit.umass.edu At 04:29 AM 12/17/96 -0800, you wrote: > >Many Molecular Modelling Programs require that the locations of the >centers of the atoms forming the molecule are given in cartesian >coordinates. But often I only have the distances between the centers of >the atoms and the angles between the covalent bonds. With these data and >by means of analytical geometry it is possible to calculate coordinate >locations but it is quite fussy. Now my question: Is there a program that >can do such calculations, i.e. transform the distance-data and the >angular data into cartesian coordinate data? > Rasmol supports the MOPAC file format, which can contain coordinates in Z Matrix format (distance/angle/dihedral angle). In addition to MOPAC files Chime also supports Gaussian Z-Matrix files. You may be able to put your angle/distance data into one of these two file formats. You can find documentation of these two formats by searching altavista. -tim >Klaus Frommer, Eberhard-Karls-University of Tuebingen > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord <100412.1707@compuserve.com> Subject: Re: Program helping in 3D-graphical calculations Date: Wed, 18 Dec 1996 12:07:09 -0500 To: Rasmol List On Tue, 17 Dec 1996, Klaus Frommer wrote: > [...] Is there a program that can do such calculations, i.e. transform the distance-data and the angular data into cartesian coordinate data? There is a free program called BABEL which can perform such calculations. Versions for DOS, Unix and Mac are available at: ftp://joplin.biosci.arizona.edu/pub/Babel/ Also of interest is MolEdit, a DOS program to edit chemical data files: http://pctc.chemie.uni-erlangen.de/~gedeck/moledit.html Sincerely Jean Debord Faculte de Medecine, Limoges, France http://ourworld.compuserve.com/homepages/JDebord ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Hello world! Date: Thu, 02 Jan 1997 19:35:54 +0100 To: rasmol@noc1.oit.umass.edu Hi All! I´m new to the RASMOL discussion-list and want to intoduce myself (and test the connection at the same time :-): My name is Marc Saric, I am 25 years old and live in Essen, Germany. I study Biology at the Ruhr-University of Bochum. http://www.ruhr-uni-bochum.de I´m interested in molecular dynamics simulation and bochemical computer graphics (although I don´t know much about the physic´s underlying things like "Potential Energy Surfaces" and "Forcefields" or about programming and computer sciences). I have started to use RASMOL aprox. 1 1/2 year ago (after I got my Internet-account and found the program on the net), and have some minor experiences with InsightII and GROMOS, which I used during a course at the university (Lehrstuhl fuer Biophysik, Univerity of Bochum). That´s all for now! Happy New Year to everyone! -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/index.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: ProtSecS & linear presentation structure for Chime 1.0 Date: Fri, 3 Jan 1997 11:43:25 -0500 (EST) To: rasmol@noc1.oit.umass.edu A new version of my short elementary Chime tutorial on protein secondary structure is now available at http://www.umass.edu/microbio/chime It has been thoroughly tested for Windows 3.1 and Windows 95 but may require some fine-tuning for Macintosh or SGI. I will soon be able to do Macintosh tests myself. However, I won't do SGI tests myself. If you find problems (particularly with the layout of the debug screen) a GIF snapshot of the screen would be a significant help to me (ftp to marlin.bio.umass.edu/incoming; please do not attach to email). Chime 1.0 was released for all platforms on December 31, 1996. Tim Maffett, principal architect of Chime, was kind enough to share pre-release versions with me which allowed me to work on a new html/javascript control structure for linear presentations in Chime, using my short elementary tutorial on protein secondary structure for content. For those interested in developing linear presentations with Chime, I have provided detailed instructions on how to put your own content into what I call 'linear control structure version 2' (LCS2) for Chime presentations. Existing RasMol scripts or linear Chime scripts can of course be inserted into LCS2. The web site provides mechanisms for downloading the 60-some files which comprise LCS2 with the protein secondary structure Chime-scripts. Once you have downloaded a private copy, you can play the tutorial, examine its construction, and insert your own content, all using Netscape 3.01 to display local files without an Internet connection. Version 1, available since November 6, already provided the ability to enter the Chime-script at any desired section, to replay a section (backing up), and to cancel play at any point. These features have been retained and improved. LCS2 and Chime have abolished the 'press any key' mechanism of releasing a pause in a RasMol/Chime-script. Pauses are now released by clicking on a button. LCS2 provides a continuous-play mode. This means that a paused Chime-script can also be played continuously from start to finish without needing any button clicking to continue. Chime has a new command 'javascript'. This means that the contents of the legend frame can now be changed directly by the Chime-script itself using javascript calls. LCS2 also provides a development/debugging mode which displays each Chime-script command line as it is executed, monitors which script or subscript file is executing, and provides several trace modes (new script files, single-step tracing, or tracing of any desired command). When a traced event occurs, you have the options of continuing the Chime-script with tracing on, continuing with tracing off, or interrupting the script. After an interrupt, the command-line interface allows you to type commands manually to test possible modifications to the script command sequence. LCS2 consists of about 1,000 lines of javascript plus over 800 lines of html (excluding the design/methods document and blank lines). The protein secondary structure Chime-script itself is 440-some commands in length, and runs about 5 minutes if played continuously without pausing. However, a script of any length can be presented with LCS2. Happy new year! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ X-Nextstep-Mailer: Mail 3.3 (Enhance 1.3) ++++------+------+------+------+------+------+------+------+------+------+ From: Vicki Bragin Subject: Need help from NEXTSTEP Rasmol users ! Date: Fri, 3 Jan 97 10:55:23 -0800 To: rasmol@noc1.oit.umass.edu Cc: vbragin@ix.netcom.com --NeXT-Mail-1821844478-1 Are there any NEXTSTEP Rasmol users out there who might be willing = to help recompile the NEXTSTEP version so as to add the picking = functionality, and perhpas other capabilities as well which I may = not even be aware of and which have not been updated on the = NEXTSTEP version. For starters, I thought I would first try to = compile the code as is. I downloaded the source code, compiled it = on my Pentium Intel running NEXTSTEP 3.3, then loaded a pdb file, = but no graphics appears in the graphics window at all. =20 Some detail: In response to the error message, rasmol.c: In function `ras_init': rasmol.c:1047: warning: braces around scalar initializer I replaced the braces with (). The app compiled fine but, still, = no graphics on the window. rasmol.h: I changed the user-defined options from #define TWOBIT to #define SIXTEENBIT=20 Anything that I may have missed? Thanks. ********************************************************** Victoria M. Bragin Physical Sciences Division, Pasadena City College 1570 E. Colorado Blvd., Pasadena, CA 91106-2003 Phone: (818) 585-7147 Fax: (818) 585-7919 E-mail: (NeXTmail and MIME mail welcome) vbragin@nextlab.calstatela.edu vbragin@ix.netcom.com vbragin@paccd.cc.ca.us vbragin@pslc.ucla.edu ********************************************************** --NeXT-Mail-1821844478-1 Are there any NEXTSTEP Rasmol users out there who might be willing = to help recompile the NEXTSTEP version so as to add the picking = functionality, and perhpas other capabilities as well which I may = not even be aware of and which have not been updated on the = NEXTSTEP version. For starters, I thought I would first try to = compile the code as is. I downloaded the source code, compiled it = on my Pentium Intel running NEXTSTEP 3.3, then loaded a pdb file, = but no graphics appears in the graphics window at all. =20 Some detail: In response to the error message, =09 rasmol.c: In function `ras_init': rasmol.c:1047: warning: braces around scalar initializer I replaced the braces with (). The app compiled fine but, still, = no graphics on the window. rasmol.h: I changed the user-defined options from #define TWOBIT to #define SIXTEENBIT=20 Anything that I may have missed? Thanks. ********************************************************** Victoria M. Bragin Physical Sciences Division, Pasadena City College 1570 E. Colorado Blvd., Pasadena, CA 91106-2003 Phone: (818) 585-7147 Fax: (818) 585-7919 E-mail: (NeXTmail and MIME mail welcome) vbragin@nextlab.calstatela.edu vbragin@ix.netcom.com vbragin@paccd.cc.ca.us vbragin@pslc.ucla.edu ********************************************************** --NeXT-Mail-1821844478-1-- X-Nextstep-Mailer: Mail 3.3 (Enhance 1.3) ++++------+------+------+------+------+------+------+------+------+------+ From: Vicki Bragin Subject: RasMol for NEXTSTEP able to run as many molecules as desired Date: Sun, 5 Jan 97 22:59:35 -0800 To: rasmol@noc1.oit.umass.edu Cc: vbragin@ix.netcom.com For NEXTSTEP users of RasMol, one can load as many molecules as = desired in as many windows and move them independently - no = additional code is needed. One is limited only by the = impracticality of having too many windows running RasMol = simultaneously! Simply create as many links to the original = application as desired and run the applications independently. = For example, to enable simultaneous display of 3 different = molecules and be able to move them independently, create 2 links = to the original application, locate these links in different = directories, and position the graphics viewer any where on the = screen such that all 3 windows are simultaneously visible. I use = this method to have my students run a script on one window, have = them load two different sample molecules on the other windows = while the script is paused (or even while it is running), = manipulate them independenty, ... and thus be able to make beter = comparisons of structures. I imagine this must be true for all = UNIX versions of RasMol due to UNIX multitasking capability. =20 Vicki Bragin ********************************************************** Victoria M. Bragin Physical Sciences Division, Pasadena City College 1570 E. Colorado Blvd., Pasadena, CA 91106-2003 Phone: (818) 585-7147 Fax: (818) 585-7919 E-mail: (NeXTmail and MIME mail welcome) vbragin@nextlab.calstatela.edu vbragin@ix.netcom.com vbragin@paccd.cc.ca.us vbragin@pslc.ucla.edu ********************************************************** desired ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RasMol for NEXTSTEP able to run as many molecules as Date: Mon, 6 Jan 1997 12:02:59 -0500 (EST) To: vbragin@ix.netcom.com Cc: rasmol@noc1.oit.umass.edu On 1/5/97 Vicki Bragin wrote: >For NEXTSTEP users of RasMol, one can load as many molecules as desired in as >many windows and move them independently - no additional code is needed. One could also achieve what Vicki describes with Chime, using multiple Chime invocations on the same web page. You could, for example, run a script up to a pause on one plug-in graphic, while offering a command-line interface on another plug-in graphic side by side. It would be more work (html/javascript programming) than with the NextStep/unix approach, but with the advantage that the layout of the plug-ins ('windows' ) etc. would be defined by the html, and would not have to be manually re-established each time (as with RasMol). Also, you can surround the graphic 'windows' with whatever text/explanation (even in a separately scrolling frame), with content changed to match what is going on in Chime. Remember, now Chime has a javascript command so Chime-scripts can do anything you want to the web page, including change the content of other frames. (See http://www.umass.edu/microbio/chime/protsecs/index.htm for an example of the use of javascript in .spt files to change content of a legend frame.) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: vasil@iabunix.iab.ac.ru Subject: RasMol for Linux Date: Thu, 9 Jan 1997 19:18:15 +0000 To: rasmol@noc1.oit.umass.edu Hi, Do somebody hear about RasMol for Linux Slackware? If you know about such version, please, help me. Sergey Vasil'ev Computer Modeling Group Institute of Agricultural BioTechnology Moscow, Russia ++++------+------+------+------+------+------+------+------+------+------+ From: "Francis M.J. Hsieh" Subject: Re: RasMol for Linux Date: Fri, 10 Jan 1997 01:02:19 +0800 (WST) To: rasmol@noc1.oit.umass.edu > Do somebody hear about RasMol for Linux Slackware? > If you know about such version, please, help me. > > Sergey Vasil'ev You can get the unix source code and compile it directly. -- Francis M.J. Hsieh | email: mjhsieh@life.nthu.edu.tw Graduate student at Dept. of Life | Homepage: Science, National TsingHua Univ., | http://life.nthu.edu.tw/~mjhsieh/ Taiwan. | TEL: +886 3 5715131 ext 3482 ++++------+------+------+------+------+------+------+------+------+------+ From: Andrea Bernini Subject: Re: RasMol for Linux Date: Sat, 11 Jan 1997 10:41:20 +0100 (GMT+0100) To: rasmol@noc1.oit.umass.edu On Thu, 9 Jan 1997 vasil@iabunix.iab.ac.ru wrote: > Hi, > > Do somebody hear about RasMol for Linux Slackware? > If you know about such version, please, help me. > > Sergey Vasil'ev > > Computer Modeling Group > Institute of Agricultural BioTechnology > Moscow, Russia > Hi Sergey, to install RasMol 2.6 beta2 on linux you have to get the source package RasMol26b2.tar.gz placed in ftp://marlin.bio.umass.edu/pub/shareware/rasmol/distrib/ then you have to compile it. Andrea Bernini, Dep. Molecular Biology, University of Siena, Italy References: <199701091623.LAA03476@noc1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: RasMol for Linux Date: Sun, 12 Jan 1997 15:33:09 +0100 To: rasmol@noc1.oit.umass.edu vasil@iabunix.iab.ac.ru wrote: > Do somebody hear about RasMol for Linux Slackware? > If you know about such version, please, help me. You have to get the source-code (as you allready should know from the other mails), but it only works with monochrome, 8 or 24bit X-Window-Displays, no other (unfortunately). Maybe this will change in future versions. -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/index.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasMol for Linux Date: Sun, 12 Jan 1997 16:45:42 +0000 (GMT) To: Marc Saric Cc: rasmol@noc1.oit.umass.edu Hi Marc, > > Do somebody hear about RasMol for Linux Slackware? > > If you know about such version, please, help me. > You have to get the source-code (as you allready should know from the > other mails), but it only works with monochrome, 8 or 24bit > X-Window-Displays, no other (unfortunately). Maybe this will change in > future versions. You'll be pleased to hear that the currently distributed version of RasMol will also support 16bit per pixel displays as a compile time option. This should help those Linux users that have configured the latest version of the XFree server with "-16bpp". When configuring "rasmol.h" or the Makefile, simply specify "#define SIXTEENBIT" rather than EIGHTBIT or THIRTYTWOBIT. I hope this helps. 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 theurer@student.umass.edu, bev@cs.umass.edu, ehaugsja@cs.umass.edu, dhart@cs.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime DNA Tutorial enhanced Date: Tue, 21 Jan 1997 09:03:21 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: cfinlays@elux3.cs.umass.edu, theurer@student.umass.edu, I have placed an enhanced version of my nonlinear Chime tutorial on DNA structure at http://www.umass.edu/microbio/chime This version shows much more detail on single AT and GC base pairs, including double bonds. You can toggle on and off hydrogen atoms. A development/debugging mode has been implemented. Many of the moves now take full advantage of Chime 1.0's simultaneous XYZ rotation/translation/zoom capability. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Save RasMol's Windows Sizes/Positions! Date: Wed, 22 Jan 1997 22:17:59 -0500 (EST) To: rasmol@noc1.oit.umass.edu I just discovered an amazing shareware program for Windows 3.1 (ONLY, not Win95). It makes RasMol (or most other programs) startup with the same windows sizes and positions (both windows!) as when you last closed it. Get FreezeFrame file FF.ZIP from e.g. http://filepile.com. Use Windows File, New to create an icon for it. Double click the icon and a minimized icon will appear at the bottom of your screen. Startup RasMol, resize/reposition the windows, and close RasMol. Now start it up again and Voila! FF remembers the window settings between sessions. Just start it up before RasMol and you get the same window sizes/positions every time. Oh what a relief it is!! Use Write to view the help file FF.WRI if you wish. Let's each send this guy the $5 he asks for, and maybe he can be persuaded to make a Windows 95 version! Send your check payable to Ronald Crane to: FreezeFrame Registration c/o Ronald Crane 758 Vasona St. Milpitas, California 95035-4316 I could not find this gentleman nor his product by searching AltaVista. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol; other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Gryko Subject: displaying crystals Date: Mon, 3 Feb 1997 15:30:31 -0700 To: "'rasmol1'" Hello: I need to display unit cell of a crystal. Any hints how to do this in Rasmol? Of course, I can put dummy atoms at cell vertices and draw all conncting lines but maybe there is a better way to do this. Thanks, Jan Gryko College of Eastern Utah ++++------+------+------+------+------+------+------+------+------+------+ From: Hidehiro UEKUSA Subject: Re: displaying crystals Date: Tue, 04 Feb 1997 11:49:21 +0900 To: rasmol@noc1.oit.umass.edu Hi Jan, In message you write: > > Hello: > > I need to display unit cell of a crystal. Any hints how to do this in >Rasmol? I usually do that by inserting 'CRYST1' line in a PDB format data file and use 'set unitcell on' command in rasmol. In my experience in ver. 2.6, angles alpha and beta angle in 'CRYST1' line should be 'inverted', i.e., subtracted from 180 degree when composing 'CRYST1' line (if beta is 100 degree, enter 80 in the line. But this might be my misunderstanding). I hope this would help you. ---------------------------------------------------------------- Hidehiro UEKUSA (uekusa@chem.titech.ac.jp) Department of Chemistry, Tokyo Institute of Technology, JAPAN ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: 2 Chime questions Date: Tue, 4 Feb 1997 17:27:32 +0000 To: rasmol@noc1.oit.umass.edu Now that Chime rotates so fast, is there a simple command to control the speed of rotation? Also, sorry I forgot, but to ensure lack of palette problems with Windows browsers and Chime, is the command I should include "palette=foreground" or vice a versa? TIA _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: "Mike Fearn" Subject: rasmol default display mode Date: Tue, 4 Feb 1997 17:58:40 +0000 To: rasmol@noc1.oit.umass.edu On the Unix version of rasmol, can I insert a command in my .rasmolrc which will ensure the initial display mode is set to 'Ball & Stick' ? Regards, Mike Fearn. -- ------------------------------------------------------------------- | Mike Fearn, Tel : UK (01684) 896536 | | Room PA101, Fax : UK (01684) 896150 | | D.R.A, Malvern, | | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | ------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RE: 2 Chime questions Date: Tue, 4 Feb 1997 12:57:32 -0500 (EST) To: rasmol@noc1.oit.umass.edu In message Tue, 4 Feb 1997 17:27:32 +0000, Fergus Doherty writes: > Now that Chime rotates so fast, is there a simple command to control the > speed of rotation? Yes. See the draft Chime manual on the 'move' command. http://www.umass.edu/microbio/chime/manual/chimeman.htm > Also, sorry I forgot, but to ensure lack of palette problems with Windows > browsers and Chime, is the command I should include "palette=foreground" > or vice a versa? I don't use this. In my tutorials, I need colors in the legend frame color key to remain true. On a 256-color Windows platform, forcing the Chime palette sometimes causes colors in another frame to be incorrect. I haven't had time to find out whether this problem can be avoided if I use legend colors which are exactly the same rgb value as the nominal color in the Chime frame. For this purpose, it would be helpful if Roger Sayle or Tim Maffett could post on this list the starting RGB values used for the CPK color scheme and secondary structure color schemes. Presumably they could be found in the source code to RasMol (ported to Chime), but I haven't managed to look for them there yet. -Eric /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Mitchell Miller Subject: Re: 2 Chime questions Date: Tue, 4 Feb 1997 12:15:34 -0800 To: rasmol@noc1.oit.umass.edu Cc: Chime-feedback@mdli.com Hello Fergus, You can control the speed of continuous rotation of a Chime structure by coding spiny= to rotate about the Y axis or spinx= to rotate about the X axis or spinz= to rotate about the Z axis. Combinations are also valid. This goes within the tag and may be simpler than writing a script using 'move.' Nevertheless, move is a far more powerful commmand! Hope this helps! Mitch Miller At 09:27 AM 2/4/97 -0800, Fergus Doherty wrote: >Now that Chime rotates so fast, is there a simple command to control the >speed of rotation? > >Also, sorry I forgot, but to ensure lack of palette problems with Windows >browsers and Chime, is the command I should include "palette=foreground" or >vice a versa? > >TIA > > >_____________________________________________________________________ >Fergus Doherty PhD >Dept. Biochemistry, >University Medical School, >Queen's Medical Centre, >Nottingham NG7 2UH > >e-mail: Fergus.Doherty@nottingham.ac.uk >Tel: 0115 970 9366 >FAX: 0115 942 2225 >URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > > > Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: RE: 2 Chime questions Date: Tue, 04 Feb 1997 14:16:26 -0800 To: emartz@microbio.umass.edu, rasmol@noc1.oit.umass.edu At 09:57 AM 2/4/97 -0800, Eric Martz wrote: >In message Tue, 4 Feb 1997 17:27:32 +0000, > Fergus Doherty writes: > >> Now that Chime rotates so fast, is there a simple command to control the >> speed of rotation? > >Yes. See the draft Chime manual on the 'move' command. >http://www.umass.edu/microbio/chime/manual/chimeman.htm You can also use tag options to change some the degrees per second for each axis. The default is 360 on the Y axis if nothing is specified, and this is TOO MUCH in the new version of Chime. A much more reasonable value is 120 degrees, and in the next version of Chime I will make that the default if nothing is specified. example: The tag parameters that affect rotation are spinY - Y axis rotation in degrees per second (defaults to 360 (too much) if nothing specified for X,Y & Z) spinX - X axis rotation in degrees per second spinZ - Z axis rotation in degress per second spinFPS - the frames per second that Chime will attempt. (note: because of limitations of Win 3.1/95 the max here that you will be able to achieve is ~15. On an NT machine you should be able to get up to 60. NOTE: The rotation commands described above affect only the Chime rotation menu. The Chime script 'Move' command that Eric mentions is a much more precise method of rotation/translation/zoom/slab changes which can be used from the Chime scripting language. > >> Also, sorry I forgot, but to ensure lack of palette problems with Windows >> browsers and Chime, is the command I should include "palette=foreground" >> or vice a versa? > >I don't use this. In my tutorials, I need colors in the legend >frame color key to remain true. On a 256-color Windows platform, >forcing the Chime palette sometimes causes colors in another frame >to be incorrect. I haven't had time to find out whether this problem >can be avoided if I use legend colors which are exactly the same rgb value >as the nominal color in the Chime frame. For this purpose, it would >be helpful if Roger Sayle or Tim Maffett could post on this list >the starting RGB values used for the CPK color scheme and secondary >structure color schemes. Presumably they could be found in the source >code to RasMol (ported to Chime), but I haven't managed to look for >them there yet. One simple trick that you can use is to make your GIF images in other frames use the 'standard 16 windows colors'. The standard 16 windows colors are always available within Windows because they are reserved for things like the window borders and such. The shareware program LView Pro has an option to reduce a GIF image to use only the 16 standard windows colors. On the 'Retouch' menu you should find 'Color Depth...', in this dialog you can select 'Palette Image' and then choose 'Windows Palette (16 colors)'. You can turn on/off dithering to get different results. This method usually works pretty good for simple button images which do not have a wide variety of colors. As far as the Palette values of Rasmol/Chime for the different color settings I do not have them handy, but you can find them defined at the top of 'transfor.c' file within the Rasmol source. You will find array definitions there for the different color settings, and within each of these arrays is the RGB value, along with a comment about what atom type/residue type the color applies to. -tim > >-Eric >/*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 >Molecular visualization: http://www.umass.edu/microbio/rasmol >Immunology: http://www.bio.umass.edu/immunology/immunology.html >Flow cytometry: http://www.bio.umass.edu/mcbfacs >Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 >- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ > > References: <3.0.32.19970204131532.007531c4@bilbo.mdli.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Slaton Subject: RGB values for Rasmol color schemes Date: Tue, 04 Feb 1997 22:20:58 -0800 To: rasmol@noc1.oit.umass.edu This is taken from the very useful Rasmol v2.5 Quick Reference Card (Roger Sayle) included with RasMol 2.5 and 2.6. The file is called "refcard.doc". Hope it's helpful. Colour Schemes -------------- CPK Atom Colours Carbon light grey [200,200,200] Oxygen red [240,0,0] Nitrogen light blue [143,143,255] Hydrogen white [255,255,255] Sulphur yellow [255,200,50] Phosphorous orange [255,165,0] Chlorine green [0,255,0] Calcium, Metals dark grey [128,128,144] Unknown deep pink [255,20,147] Amino Acid Colours ------------------ ASP, GLU bright red [230,10,10] CYS, MET yellow [230,230,0] LYS, ARG blue [20,90,255] SER, THR orange [250,150,0] PHE, TYR mid blue [50,50,170] ASN, GLN cyan [0,220,220] GLY light grey [235,235,235] LEU, VAL, ILE green [15,130,15] ALA dark grey [200,200,200] TRP pink [180,90,180] HIS pale blue [130,130,210] PRO flesh [220,150,130] Secondary Structure Colours --------------------------- Alpha Helix magenta [240,0,128] Beta Sheet yellow [255,255,0] Turns pale blue [96,128,255] Other white [255,255,255] Hydrogen Bond Type Colours -------------------------- Offset +2 white [255,255,255] Offset +3 magenta [255,0,255] Offset +4 red [255,0,0] Offset +5 orange [255,165,0] Offset -3 cyan [0,255,255] Offset -4 green [0,255,0] default yellow [255,255,0] ----------------------------------- Slaton Lipscomb Cabrillo College Aptos, CA ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Gryko Subject: Colors and bonding of "other atoms" Date: Wed, 5 Feb 1997 07:29:06 -0700 To: "'rasmol@lists.umass.edu'" Hello: Sorry, this is probably silly question, but I would like to know how to force Rasmol to color atoms like transition metals and to draw bonds between these atoms. In standard setting Rasmol draws these atoms as nice pink spheres without distinguishing say beteween iron and tungsten and without bonds. Thanks! Jan Gryko, CEU > ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: rasmol default display mode Date: Wed, 5 Feb 1997 15:22:21 +0000 (GMT) To: hp003@dra.hmg.gb Cc: rasmol@noc1.oit.umass.edu Hi Mike, > On the Unix version of rasmol, can I insert a command in my .rasmolrc > which will ensure the initial display mode is set to 'Ball & Stick' ? The ".rasmolrc" initialization file for RasMol is executed after any molecules specified on the command line but before any scripts specified on the command line. Therefore by adding the following commands to the .rasmolrc file: select all spacefill 120 wireframe 40 you should be able to get RasMol to load any files specified on the command line to appear by default as "Ball & Stick". Note that any file loaded explicitly using a "load" command will still appear in wireframe (or backbone) by default. Hence, this technique is only suitable for molecules specified on the command line, such as those launched from Netscape. I hope this helps. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: MS Explorer 3.0 and Chime? Date: Thu, 6 Feb 1997 09:24:39 +0000 To: rasmol@noc1.oit.umass.edu I know earlier versions of Explorer had problems with Chime, but has anyone tried the full release of MIE 3.0? I have tried it on the Mac (a PowerMac 4400, System 7.5.3). MIE loads Chime OK and displays the image, but when I leave that page it crashes (Type 11 - bad news). This happens with my pages and with others. Has anyone else (MacOS or Windows) had problems? _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: MS Explorer 3.0 and Chime? Date: Thu, 6 Feb 97 09:59:23 PST To: rasmol@noc1.oit.umass.edu RasMol/Chime users. In response to Fergus's query below, I was surprised to discover a couple of days ago, on a PC running Windows 95, that the Chime plugin seems to work effectively with the MIE 3.01 browser. Embedded Chime script commands ran correctly, including the new Chime move command. I had no problem with the system crashing (but I have 32 MB RAM). I have not tested the MIE 3.0 browser on my PowerMac 7100, but I am guessing that the problem Fergus has regarding Type II errors is mainly a reflection of insufficient system RAM for running MS applications on a Mac; I've had problems similar to his when launching MS Excel spreadsheets, for example, from Netscape running on a MacIIsi; these problems tended to go away after I converted to a PowerMac 7100 with more RAM. Nevertheless, my initial enthusiasum for using the MIE 3.01 browser for molecular structure presentation waned after I discovered that the push button feature of Chime is not yet implemented. Chime push buttons simply do not appear where I expect to find them on my web pages and no active links could be detected in areas where buttons should have appeared. Thus, given some of the unique HTML possibilities associated with MIE browser, I'm disappointed that it does not yet fully support all of the neat Chime plugin features for scripting molecular structures on the web. Duane At 09:24 AM 2/6/97 +0000, you wrote: >I know earlier versions of Explorer had problems with Chime, but has anyone >tried the full release of MIE 3.0? I have tried it on the Mac (a PowerMac >4400, System 7.5.3). MIE loads Chime OK and displays the image, but when I >leave that page it crashes (Type 11 - bad news). This happens with my pages >and with others. Has anyone else (MacOS or Windows) had problems? > > >_____________________________________________________________________ >Fergus Doherty PhD >Dept. Biochemistry, >University Medical School, >Queen's Medical Centre, >Nottingham NG7 2UH > >e-mail: Fergus.Doherty@nottingham.ac.uk >Tel: 0115 970 9366 >FAX: 0115 942 2225 >URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | 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 | | E-mail addresses: | | Faculty: sears@lifesci.lscf.ucsb.edu | | Academic: bioimages@lifesci.lscf.ucsb.edu | | WWW homepages: | | http://mentor.lscf.ucsb.edu/mcdb108a/ | | http://mentor.lscf.ucsb.edu/mcdb133/ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Colors and bonding of "other atoms" Date: Thu, 6 Feb 1997 18:31:47 +0000 (GMT) To: Jan Gryko Cc: rasmol@noc1.oit.umass.edu Hi Jan, > Sorry, this is probably silly question, but I would like to know how > to force Rasmol to color atoms like transition metals and to draw > bonds between these atoms. In standard setting Rasmol draws these > atoms as nice pink spheres without distinguishing say beteween > iron and tungsten and without bonds. Thanks very much for your e-mail. Unfortunately RasMol's CPK colour scheme doesn't ascribe a unique colour to every element in the periodic table and hence most "inorganic" elements tend to be shown in pink. However, it is possible to colour elements individually using commands on the RasMol command line making use of the fact that element names are valid atom expressions. Hence the commands select iron colour green select tungsten colour blue will produce a more colourfull depiction of your molecule. Similarly, RasMol's determination of connectivity is also biased for organic chemistry when displaying large numbers of atoms (i.e. >256). For proteins and nucleic acids, RasMol cheats and uses approximate covalent bonding radii to speed up the calculation. However, more accurate (but often identical) bonds can be found with the connect true command. If this still doesn't improve your heavy atom bonds or your molecule already has less than 250 atoms, the distances between atoms are too large for covalent bonds. Such co-ordination bond are probably best specified by explicitly adding them to the molecular co-ordinate file (i.e. adding CONECT records to a PDB file). I hope this helps. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RasMol cmds in Chime & new cmds missing in draft manual supports) Date: Fri, 7 Feb 1997 13:54:41 -0500 (EST) To: ------------------------------ Fri, 07 Feb 1997 10:09:41 -0800 From: Tim Maffett Subject: Re: Rasmol commands which Chime 1.0 supports To: Multiple recipients of list Chime 1.0 supports all of the Rasmol command except those that write files to the users disk. (These commands are disabled in Rasmol by default, but can be turned on, they can not be turned on in Chime). In addition the Rasmol 2.6Beta3 commands that Chime supports I have a added some new commands for making it easier to do things like 'movies'/tutorials and such. Some of these commands are included in a 'Draft' Rasmol/Chime reference manual that can be found at: http://www.umass.edu/microbio/chime/ (Eric Martz has some excellent tutorials here that demonstrate many of the Chime specific scripting commands.) This manual is currently incomplete, but it does cover some of the commands I have added since Chime 0.99. Some of the commands which are in Chime 1.0 that are missing from the draft manual are: show version - get version name/number of the rasmol script 'container' (Chime in this case) javascript - sends everything after the 'Javascript' command to be executed by Javascript. examples: javascript if(xyz=5){dosomething();} javascript "image.mypic = 'title.gif'" (This is a powerful command, it allows you do any javascript commands from *within* your Chime/Rasmol script!) status - displays the contents of the quoted string in the Netscape Navigator status bar. (animation commands control XYZ animation files) "show animation", or "animation info" - show anim info "animation" | "anim" - either can be used for command "" can be: "on" - starts animation playing "off" - stops animation "mode" - sets animation mode while playing "loop" - loop from start to end, over and over "once" - loop from start to end ONCE "palindrome" - loop start to end, then end to start over and over "direction" - sets current play direction: "+1" - forward "-1" - backward "fps" "#" of frames per second "info" - prints anim info (see above, you can also use 'show animation" examples: animation mode palindrome animation fps 10 animation direction +1 animation on (Forwarded by ... /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey A. Vasil'ev" Subject: Chime and MS IE 3.01 under Win95 Date: Mon, 10 Feb 1997 19:14:52 +0000 To: rasmol@noc1.oit.umass.edu Hi, I try to install Chime 1.0 on my computer (Windows95 and IE 3.01) but it says that Chime doesn't work without Netscape Navigator. What can I do? Sergey Vasil'ev,M.Sc. Computer Modeling Group, Institute of Agricultural BioTechnology, 42 Timiryazevskaya st., Moscow, 127550, Russia tel. 7(095)211-0509 fax. 7(095)216-4777 e.mail vasil@iabunix.iab.ac.ru vasil@agrobio.msk.su References: <199702101618.LAA02419@noc1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Milne Subject: get Netscape Date: Tue, 11 Feb 1997 00:36:46 -0500 To: rasmol@noc1.oit.umass.edu If you can run I.E. 3.0 you can run Netscape so just download it from www.netscape.com then install the plugin. Other possibility is to just load the file you'd like to view into Rasmol or Web Lab Viewer (if you've got them). Chris Milne Carleton University cmilne@chat.carleton.ca ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 13:50:26 +0000 To: rasmol@noc1.oit.umass.edu I know Chime can display .mol files as 2D representations of molecules, and as "3D". But if I create a 2D mol file with ISIDraw this doesn't contain 3D information and the file in "3D" viewed with Chime is flat. A PDB file viewed in Chime on the other hand can only be viewed in 3D. What I want to be able to do is use Chime to load one file (of a small molecule, say cAMP) and view this in 2D, and switch to "real" 3D with the Chime menu. Is this possible, and if so how would I generate the necessary file? If not, is there another way to do it (load mol or pdb files with an embedded script and button)? Finally, how can I generate pdb files from 2D representations of simple molecules - would I need something lke Chem3D to do this? TIA Fergus _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: tbender@ccs.carleton.ca (timothy bender) Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 97 18:10:50 EST To: rasmol@noc1.oit.umass.edu ---------------------------------------------------------------------- Tim Bender, B.Sc | To know chemistry, Student, Department of Chemistry | is to know a little Carleton University, Ottawa, Ont, Canada | piece of nature ... Email address: tbender@ccs.carleton.ca | ---------------------------------------------------------------------- Hello ... the newest version of a program called Babel will convert ISISdraw files (.skc) to .pdb files, it is available free of charge from ftp.joplin.biosci.arizona.edu Tim :-) ---------------------------------------------------------------------- "Make something idiot proof and somebody will find a better idiot ..." ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Milne Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 97 18:17:38 EST To: rasmol@noc1.oit.umass.edu You'll need a molecular modelling program like Hyperchem or Chem3d to generate the proper (well maybe not proper, but most likely anyways) 3D coordinates for the structure. These programs will actually minimize the structure using energy calculations (not necessarily all that reliable a calculation). OR : your other option is Web friendly. There's a site hooked to a system called Corina that does molecular modelling for you. You can either enter the molecule into a form on the page (in SMILES format) and submit it, or e-mail them the mol file as text in the message. The site address eludes me now, but it can be found by searching Yahoo's Altavista for 'Corina'. Good luck, ----------------------------------------------------------------------- Chris Milne Carleton University "But then came the day I climbed out of these safe limbs Ventured away Walking tall, head high up, and singing I went to the city Car horns, corners and the gritty Now I am the proudest monkey you've ever seen" - Dave Matthews Band ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne R Fiori Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 15:31:21 -0800 (PST) To: rasmol@noc1.oit.umass.edu On a tangent of this 2D/3D discussion. Is there a program out there that will take a pdb (or other common) format file and 'grow' hydrogens onto the structure?? -- ======================================================================== | Wayne R Fiori | e-mail: fiori@cmgm.stanford.edu | | Biochemistry Dept. | Phone: (415)723-6902 [Lab] | | Beckman Center, Stanford | (415)723-6161 [message] | | Stanford, CA 94305-5307 _________|_________ (415)723-6783 [fax] | ======================================================================== "Re: 2D and 3D images with Chime" (Feb 12, 3:31pm) References: <199702122331.PAA18329@cmgm.Stanford.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: "Andrew Dalke" Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 17:51:52 -0600 To: rasmol@noc1.oit.umass.edu Wayne R. Fiori asked: > On a tangent of this 2D/3D discussion. Is there a program out there that > will take a pdb (or other common) format file and 'grow' hydrogens onto the > structure?? Babel, mentioned in Tim Bender's email can do this. As he said, Babel is at ftp.joplin.biosci.arizona.edu, and it is free. XPLOR can also do this, but it costs money. xplor.csb.yale.edu, if I recall. Andrew Dalke dalke@ks.uiuc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: b_duke@lacebark.ntu.edu.au Subject: Re: 2D and 3D images with Chime Date: Thu, 13 Feb 1997 09:42:14 +1000 (EET) To: rasmol@noc1.oit.umass.edu > > Wayne R. Fiori asked: > > On a tangent of this 2D/3D discussion. Is there a program out there that > > will take a pdb (or other common) format file and 'grow' hydrogens onto the > > structure?? > > Babel, mentioned in Tim Bender's email can do this. As he said, > Babel is at ftp.joplin.biosci.arizona.edu, and it is free. This did not work for me. I found it at joplin.biosci.arizona.edu in /pub/Babel. For unix it looks as if 1.6 is the latest version. There are older unix versions there and PC and Mac versions. Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89410460 e-mail: b_duke@lacebark.ntu.edu.au WWW http://lacebark.ntu.edu.au/chemistry References: <9702122342.AA14252@lacebark.ntu.edu.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: 2D and 3D images with Chime Date: Wed, 12 Feb 1997 16:32:14 -0800 To: rasmol@noc1.oit.umass.edu > > This did not work for me. I found it at joplin.biosci.arizona.edu > in /pub/Babel. For unix it looks as if 1.6 is the latest version. > There are older unix versions there and PC and Mac versions. Now that you mention it, I seem to remember having some problems there - If I recall correctly, the way I solved it was to not use the babel command line, but use the menu (babel -m). If this still doesn't work, try converting the pdb file into an xyz and then convert that into a mol file. Keep trying....babel really does work......... References: ; from "Fergus Doherty" at Feb 12, 97 1:50 pm ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Dearie Subject: Babel - trouble finding it Date: Thu, 13 Feb 97 20:42 EST To: rasmol@noc1.oit.umass.edu Cc: tbender@ccs.carleton.ca Tim- What program did you use to access ftp.joplin.biosci.arizona.edu? I tried netscape and fetch, but was told by both that there was no host by that name. Thanks in advance. TGD References: <199702122310.XAA21556@rideau> ; from "Fergus Doherty" at Feb 12, 97 1:50 pm ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Re: Babel - trouble finding it Date: Fri, 14 Feb 1997 09:41:14 +0000 To: rasmol@noc1.oit.umass.edu >Tim- >What program did you use to access ftp.joplin.biosci.arizona.edu? >I tried netscape and fetch, but was told by both that there was no host by >that name. > >Thanks in advance. > >TGD Leave out the ftp., just joplin.biosci.arizona.edu worked for me 9same problem as you to start with). Fergus _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html ++++------+------+------+------+------+------+------+------+------+------+ From: Mr AJ Pemberton Subject: Re: Babel - trouble finding it Date: Fri, 14 Feb 1997 11:10:47 +0000 (GMT) To: rasmol@noc1.oit.umass.edu On Thu, 13 Feb 1997, Tom Dearie wrote: > Tim- > What program did you use to access ftp.joplin.biosci.arizona.edu? > I tried netscape and fetch, but was told by both that there was no host by > that name. > > Thanks in advance. > > TGD > > > The babel ftp site is: joplin.biosci.arizona.edu not ftp.joplin.biosci.arizona.edu Tony P. ********************************************************************** Mr. A.J.Pemberton c/o Dept. Rheumatology, Tel: +121-414-3388 Medical School, Fax: +121-414-6794 The University of Birmingham, Email: A.J.Pemberton@bham.ac.uk Birmingham B15 2TT. www: http://sgisw.bham.ac.uk/~pemberaj/ U.K. ********************************************************************** References: ++++------+------+------+------+------+------+------+------+------+------+ From: Bernhard Vogler Subject: Re: Babel - trouble finding it Date: Fri, 14 Feb 1997 16:16:20 +0100 To: rasmol@noc1.oit.umass.edu At 11:10 14.02.97 +0000, you wrote: >On Thu, 13 Feb 1997, Tom Dearie wrote: > >> Tim- >> What program did you use to access ftp.joplin.biosci.arizona.edu? >> I tried netscape and fetch, but was told by both that there was no host by >> that name. >> >> Thanks in advance. >> >> TGD >> >> >> > >The babel ftp site is: > >joplin.biosci.arizona.edu > >not > >ftp.joplin.biosci.arizona.edu > >Tony P. > >********************************************************************** >Mr. A.J.Pemberton >c/o Dept. Rheumatology, Tel: +121-414-3388 >Medical School, Fax: +121-414-6794 >The University of Birmingham, Email: A.J.Pemberton@bham.ac.uk >Birmingham B15 2TT. www: http://sgisw.bham.ac.uk/~pemberaj/ >U.K. >********************************************************************** > > > Use Netscape : adress ftp://joplin.biosci.arizona.edu or an ftp-client: ftp to joplin.biosci.arizona.edu than anonymous ( login) and mailadress (passwd) Regards B. V. ------------------------------------------------ Bernhard Vogler Institut fuer Chemie Universitaet Hohenheim Garbenstrasse 30 70599 Stuttgart Tel.: (49)711 - 459 - 2944 - 2963 (NMR) - 3908 (Computer Raum) FAX:(49)711 - 459 - 2951 e-mail: chemvogl@uni-hohenheim.de ------------------------------------------------ ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Gryko Subject: Colors and bonds in rasmol Date: Fri, 14 Feb 1997 08:56:07 -0700 To: "'rasmol@lists.umass.edu'" Several days ago I asked how to select color for atoms like iron, zinc, and other metals and how to force rasmol to draw bonds between metals. Any suggestions? Thanks, J. Gryko College of Eastern Utah > ++++------+------+------+------+------+------+------+------+------+------+ From: Gregory Flack Subject: Re: Colors and bonds in rasmol Date: Fri, 14 Feb 1997 10:05:02 -0700 (MST) To: rasmol@noc1.oit.umass.edu One can color specific elements by using the select and color commands. For example: select iron color red Don't forget to use the 'spacefill' command to see the atoms afterwards because metals are typically a point in space and if they are not connected a wireframe or similar symbology won't display them. I am unaware of a command for drawing a line between atoms when there is no instruction in the molecule file for this. Although I haven't taken the time to explore the architecture of the file, there is bonding information at the end of a PDB file and that can be edited to give a bond you desire. I expect that other file types can be edited in this way also. I have forgotten the exact nature of your inquiry days back, but I hope this helps. -Greg ------------------------------------------- Gregory Flack gsflack@holly.colostate.edu undergraduate - Department of Microbiology Colorado State University, Fort Collins, CO ------------------------------------------- On Fri, 14 Feb 1997, Jan Gryko wrote: > > Several days ago I asked how to select color for atoms like iron, zinc, > and other metals and how to force rasmol to draw bonds between metals. > Any suggestions? Thanks, > > J. Gryko > College of Eastern Utah > > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Chris Milne Subject: Re: Colors and bonds in rasmol Date: Fri, 14 Feb 97 12:12:26 EST To: rasmol@noc1.oit.umass.edu under colour there's a user defined choice (for windows system). there's another option under the command-line interface. just use the help file to figure it out ! as for forcing bonds, you can try converting it to a mol file then opening it in chem draw/web and drawing the bonds in then re-opening it in RasMol. ----------------------------------------------------------------------- Chris Milne Carleton University "But then came the day I climbed out of these safe limbs Ventured away Walking tall, head high up, and singing I went to the city Car horns, corners and the gritty Now I am the proudest monkey you've ever seen" - Dave Matthews Band References: <199702122310.XAA21556@rideau> ; from "Fergus Doherty" at Feb 12, 97 1:50 pm ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Dearie Subject: Re: Babel - trouble finding it Date: Sun, 16 Feb 97 14:20 EST To: rasmol@noc1.oit.umass.edu Thanks to all for help in getting Babel. One question: I downloaded version 1.03 for Mac, posted in 1994. Does anyone know if there's a more recent version? Tom Dearie BioLogic Scientific Communications, Toronto, Canada. ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: chime web pages Date: Mon, 24 Feb 1997 10:08:10 -0800 To: rasmol@noc1.oit.umass.edu Hi-sorry if this already asked...uploaded new chime-capable web page to my server. When I try to access it, it trys to open rasmol instead of chime. My browser (netscape) works normally on chime sites on other servers - is this a mime problem at my server or something at my end? Thank you kindly.............. ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: mime types Date: Mon, 24 Feb 1997 10:37:33 -0800 To: rasmol@noc1.oit.umass.edu Sorry to bother everyone - clear case of RTFM. Answered my own question at http://www.mdli.com/chemscape/chime/chimehelp.html#Install5. Thank you for your patience. types] ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: chime web pages [Configuring web server for Chemical MIME Date: Mon, 24 Feb 1997 10:30:28 -0800 To: skg@asis.com, rasmol@noc1.oit.umass.edu At 10:08 AM 2/24/97 -0800, you wrote: >Hi-sorry if this already asked...uploaded new chime-capable web page >to my server. When I try to access it, it trys to open rasmol instead of >chime. My browser (netscape) works normally on chime sites on other >servers - is this a mime problem at my server or something at my end? >Thank you kindly.............. > You must configure your web server to serve the MIME types of the chemical files. There is information in the Chime FAQ that tells how to do this for several web servers: http://www.mdli.com/chemscape/chime/chimehelp.html#Install5 -tim ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: 2D and 3D images with Chime Date: Mon, 24 Feb 1997 17:26:33 -0800 To: rasmol@noc1.oit.umass.edu At 05:50 AM 2/12/97 -0800, Fergus Doherty wrote: >I know Chime can display .mol files as 2D representations of molecules, and >as "3D". But if I create a 2D mol file with ISIDraw this doesn't contain >3D information and the file in "3D" viewed with Chime is flat. A PDB file >viewed in Chime on the other hand can only be viewed in 3D. > >What I want to be able to do is use Chime to load one file (of a small >molecule, say cAMP) and view this in 2D, and switch to "real" 3D with the >Chime menu. We hope to have 3D 'automatic' coordinate generation for 2D structures in a future version of Chime. The Chemscape/Chime team at MDL is extremely fortunate that Michael Hartshorn has joined our team. He will be working with Roger Sayle at GlaxoWellcome on exciting new extensions to the Rasmol/Chime 'platform'. Among these *possible* features is a very fast 3D coordinate generator Michael has developed (Michael's algorithm also sprouts hydrogens) BTW, there is a bug in the Chime 1.0 release which prevents you from entering 2D mode from 3D mode. This will be fixed in an upcoming release. -tim >Is this possible, and if so how would I generate the necessary file? > >If not, is there another way to do it (load mol or pdb files with an >embedded script and button)? > >Finally, how can I generate pdb files from 2D representations of simple >molecules - would I need something lke Chem3D to do this? > >TIA > >Fergus > > >_____________________________________________________________________ >Fergus Doherty PhD >Dept. Biochemistry, >University Medical School, >Queen's Medical Centre, >Nottingham NG7 2UH > >e-mail: Fergus.Doherty@nottingham.ac.uk >Tel: 0115 970 9366 >FAX: 0115 942 2225 >URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > > > > References: <3.0.32.19970224172251.00c00d98@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: 2D and 3D images with Chime Date: Mon, 24 Feb 1997 21:04:54 -0800 To: rasmol@noc1.oit.umass.edu . He will be working with Roger Sayle > at GlaxoWellcome on exciting new extensions to the Rasmol/Chime 'platform'. > Among these *possible* features is a very fast 3D coordinate generator > Michael has developed (Michael's algorithm also sprouts hydrogens) > > BTW, there is a bug in the Chime 1.0 release which prevents you > from entering 2D mode from 3D mode. This will be fixed in an > upcoming release. > > -tim > Awesome! Thanks again....I see what you mean about 2D from 3D - but all you have to do is use a mol file & you can have both, so it's really no problem.....Cheers... , , , ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: RE: Chime and MS IE 3.01 under Win95 Date: Tue, 25 Feb 1997 20:38:48 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: , , Download Netscape Navigator 3.01 from www.netscape.com. It is free for academic users. -Eric In message Mon, 10 Feb 1997 19:14:52 +0000, "Sergey A. Vasil'ev" writes: > Hi, > > I try to install Chime 1.0 on my computer (Windows95 and IE 3.01) but > it says that Chime doesn't work without Netscape Navigator. > > What can I do? > > > Sergey Vasil'ev,M.Sc. > > Computer Modeling Group, > Institute of Agricultural BioTechnology, > 42 Timiryazevskaya st., > Moscow, 127550, Russia > > tel. 7(095)211-0509 > fax. 7(095)216-4777 > e.mail vasil@iabunix.iab.ac.ru > vasil@agrobio.msk.su > /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Babel: history, websites, hydrogens. Date: Wed, 26 Feb 1997 14:37:52 -0500 (EST) To: Cc: rick_hallick@tikal.biosci.arizona.edu Rick's message below was rejected by listproc for technical reasons and then delayed due to my being out of town. Here it is at last. ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Hallick Subject: Re: 2D and 3D images with C Date: Fri, 14 Feb 1997 To: rasmol@noc1.oit.umass.edu Babel was written by Pat Walters and Matt Stahl, doctoral students at the University of Arizona Department of Chemistry in the lab of Dan Dolata. We have hosted the archives on one of our servers at joplin.biosci.arizona.edu for many years. Pat, Matt, and Don have all left the University of Arizona. However there is still a legacy web site for Babel at: http://mercury.aichem.arizona.edu/babel.html We continue to mirror the archives at joplin.biosci.arizona.edu, but we may transfer the mirror site to http://www.blc.arizona.edu. Meanwhile, Matt and Pat are now in the private sector, Dan has moved to Ohio, and the current archives have moved with him to the following address: ftp://ccl.osc.edu/pub/chemistry/software/MAC/babel/ Babel is a useful program for adding hydrogens to PDB format files, but it does make mistakes in some situations, such as modified bases in tRNAs. Another disadvantage is that all of the information except atom number and x, y, z coordinates are lost when Babel writes new files. RasMol users might also be interested in learning more about MacMolecule2 and PCMolecule2 molecular graphics programs: http://www.blc.arizona.edu/linus/linus.html Richard Hallick Professor of Biochemsitry University of Arizona hallick@arizona.edu http://www.blc.arizona.edu/rick/ [Forwarded by: /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: GRIFFITHSJ@rsc.org Subject: Chime help Date: Thu, 27 Feb 1997 17:42 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Dear all As part of the CLIC Consortium (see URL below), I receive various structure files from authors who wish these included with the enhanced web version of their ChemComm publication. For viewing purposes, we rely on the Chime plugin for Netscape Generally, these structure files are either PDB files or XYZ files. If the author wishes a specific "initial" view, then I've achieved this by using either using in-line script files or CSML files (I've not ventured into blending JavaScript with Rasmol script files yet). Often, I receive structure files of inorganic compounds where the organometallic bonds don't appear (I believe this is due to bond lengths exceeding those expected by Chime). So far, I've only had to show spacefilling models and by setting the radii of the spacefill atoms I can make reasonable representations. However, to force Chime to draw bonds in (say) wireframe mode, I believe I'm correct in saying that the structure file needs some connecting information (CONECT ...). However, there are various points I'm not sure about here, such as whether this is only available for PDB files and not XYZ files etc, what is the correct syntax etc. Also, I often get given so-called PDB and XYZ files that don't parse correctly with Chime (or generic programs) and I have to hack these manually to get them to display. I guess I could answer these problems myself if I knew the specifications for both file formats - could anybody point me to where I could find these (and other ?) specifications? My second question also involves inorganic compounds. Is there any way to show a crystal structure in the polyhedra format? Any help would be much appreciated .. regards Griff ---------- Dr Jonathan Griffiths 1) The CLIC Consortium - http://chemcomm.clic.ac.uk/ 2) NewMedia, The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, United Kingdom Tel/Fax: +44 (0)1223 432136/420247, http://chemistry.rsc.org/rsc/ ---------- ++++------+------+------+------+------+------+------+------+------+------+ From: LEVY SAM Subject: Rasmol to Molscript Problems Date: Thu, 27 Feb 1997 14:26:15 -0700 (MST) To: rasmol@noc1.oit.umass.edu Cc: levy@spot.colorado.edu I have been using Rasmol(2.6) to orientate molecules on a Unix workstation employing stereo mode and then output the viewing transformation into a Molscript file using the Rasmol command write molscript (output_filename) When I execute Molscript using the file outputted by Rasmol as Molscript input, the resulting postscript image depicts a 'mirror' image of the original Rasmol view. As far as I can tell, the z-coordinate is somehow interpretted as -z. Has anyone experienced this behavior and (most importantly) found a fix. Any help would be appreciated. ------------------------------------------------------------------------------- Samuel Levy, Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, 80309-0347, USA Tel:+1 303 492 8893 Fax:+1 303 492 7744 Email: levy@spot.colorado.edu ------------------------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Mr AJ Pemberton Subject: Re: Chime help Date: Fri, 28 Feb 1997 09:24:29 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu On Thu, 27 Feb 1997 GRIFFITHSJ@rsc.org wrote: > > Dear all > > As part of the CLIC Consortium (see URL below), I receive various > structure files from authors who wish these included with the enhanced > web version of their ChemComm publication. For viewing purposes, we > rely on the Chime plugin for Netscape > > Generally, these structure files are either PDB files or XYZ files. > If the author wishes a specific "initial" view, then I've achieved > this by using either using in-line script files or CSML files (I've > not ventured into blending JavaScript with Rasmol script files yet). > > Often, I receive structure files of inorganic compounds where the > organometallic bonds don't appear (I believe this is due to bond > lengths exceeding those expected by Chime). So far, I've only had to > show spacefilling models and by setting the radii of the spacefill > atoms I can make reasonable representations. However, to force Chime > to draw bonds in (say) wireframe mode, I believe I'm correct in saying > that the structure file needs some connecting information (CONECT > ...). However, there are various points I'm not sure about here, such > as whether this is only available for PDB files and not XYZ files etc, > what is the correct syntax etc. Also, I often get given so-called PDB > and XYZ files that don't parse correctly with Chime (or generic > programs) and I have to hack these manually to get them to display. I > guess I could answer these problems myself if I knew the > specifications for both file formats - could anybody point me to where > I could find these (and other ?) specifications? see http://www2.ebi.ac.uk/pdb/Format.doc/Contents_Guide_21.html for PDB format I am not sure about XYZ! Tony P. ********************************************************************** Mr. A.J.Pemberton c/o Dept. Rheumatology, Tel: +121-414-3388 Medical School, Fax: +121-414-6794 The University of Birmingham, Email: A.J.Pemberton@bham.ac.uk Birmingham B15 2TT. www: http://sgisw.bham.ac.uk/~pemberaj/ U.K. ********************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: GRIFFITHSJ@rsc.org Subject: PDB file and groups Date: Fri, 28 Feb 1997 17:11 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Dear All I have a PDB file ( > 900 atoms) that I wish to display with the colour scheme specified by group. Unfortunately, when the file was generated, no group information was added. Using Chem3D I can add the group information, but I can't save this group information in any file format other than the native Chem3D file; does anyone know of any software (preferably freeware that runs on Windows 3.11) that would allow me to achieve my aim? (I do have limited access to a PC running 95 and NT 4.0) Many thanks in advance Griff ---------- Dr Jonathan Griffiths 1) The CLIC Consortium - http://chemcomm.clic.ac.uk/ 2) NewMedia, The Royal Society of Chemistry, Thomas Graham House, Science Park, Milton Road, Cambridge, United Kingdom Tel/Fax: +44 (0)1223 432136/420247, http://chemistry.rsc.org/rsc/ ---------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Pre-arrange RasMol windows in Win95 Date: Fri, 28 Feb 1997 19:47:47 -0500 (EST) To: Not long ago, I mentioned here the shareware Freezeframe which makes RasMol's windows start up in the same positions and sizes as when it was last closed. But Freezeframe works only for Windows 3.1. Rod Levine (NIH) pointed out to me a solution for Windows 95, Deskey from Softarts, www.spiresoft.com. The shareware version runs for 1 hr at a time for 30 days. Registration is $15. When you run Deskey's SETUP.EXE, nothing seems to happen. However, at the right end of the Taskbar (the bar with Start on it), you will now see a gold key. Click on this for Deskey's menu. Start RasMol and arrange the graphics window as you want it. Now select Window Placements on Deskey's menu, Add, Capture from window, and OK the Add Window Placement Dialog (no further changes are necessary; be sure to leave the Auto-apply option checked). Now arrange the RasMol Command Line window and do the same sequence to add a window placement in Deskey. Close RasMol, restart it, and voila! Your window arrangement is automatically restored for both windows. If you have multiple icons for multiple RasMol scripts, you do not have to add window placements for each icon. Deskey recognizes RasMol as such regardless of which icon you use to start it. Enjoy! /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Andrea Bernini Subject: Hbonds in pdb. Date: Mon, 3 Mar 1997 14:30:41 +0100 (MET) To: Rasmol mailing list I know Rasmol calculates H-bonds, but does exist a way to put hbonds directly in pdb records? Thanks in advance. ++++------+------+------+------+------+------+------+------+------+------+ From: "Francis M.J. Hsieh" Subject: Re: Hbonds in pdb. Date: Tue, 4 Mar 1997 02:49:45 +0800 (WST) To: rasmol@noc1.oit.umass.edu In the article, Andrea Bernini wrote: > I know Rasmol calculates H-bonds, but does exist a way to put > hbonds directly in pdb records? I think the standard pdb format doesn't content hbond information. And the pdb format is not only for RasMol. :p -- Francis M.J. Hsieh | email: mjhsieh@life.nthu.edu.tw Graduate student at Dept. of Life | Homepage: Science, National TsingHua Univ., | http://life.nthu.edu.tw/~mjhsieh/ Taiwan. | TEL: +886 3 5715131 ext 3482 ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: Hbonds in the PDB Date: Mon, 3 Mar 1997 14:52:23 -0500 To: rasmol@noc1.oit.umass.edu Just to set the record straigt, PDB's Contents Guide (http://www.pdb.bnl.gov/Format.doc/Format_Home.html) specifies the format for hydrogen bonds. The HYDBND record is optional, but sometimes is supplied in the submission to PDB. I believe that these records are handmade by the authors, but perhaps someone knows of a program which writes them out. Regards, Nancy Excerpt from the PDB Content Guide: HYDBND Overview The HYDBND records specify hydrogen bonds in the entry. Record Format COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "HYDBND" 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1 Residue name. 22 Character Chain1 Chain identifier. 23 - 27 Integer resSeq1 Residue sequence number. 28 AChar ICode1 Insertion code. 30 - 33 Atom nameH Hydrogen atom name. 34 Character altLocH Alternate location indicator. 36 Character ChainH Chain identifier. 37 - 41 Integer resSeqH Residue sequence number. 42 AChar iCodeH Insertion code. 44 - 47 Atom name2 Atom name. 48 Character altLoc2 Alternate location indicator. 49 - 51 Residue name resName2 Residue name. 53 Character chainID2 Chain identifier. 54 - 58 Integer resSeq2 Residue sequence number. 59 AChar iCode2 Insertion code. 60 - 65 SymOP sym1 Symmetry operator for 1st non-hydrogen atom. 67 - 72 SymOP sym2 Symmetry operator for 2nd non-hydrogen atom. Details * The hydrogen bonds listed normally are those supplied by the depositor. * The atoms forming the hydrogen bond are listed on the HYDBND record. * Each record has place for three atom specifications. * Columns 13 - 28 and 44 - 59 are for the atoms associated with the hydrogen atom of the hydrogen bond. * If the coordinates of the hydrogen atom itself are presented in the entry, that atom is specified in columns 30 - 42. * For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional. * sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the atom. For hydrogen atoms use the symmetry operator of the heavy atom to which it is bonded. Verification/Validation/Value Authority Control The distance between the atoms listed must be consistent with the bonding. Relationships to Other Record Types CONECT records are generated consistent with the bond type. If symmetry operators are given to generate one of the residues involved in the hydrogen bond, REMARK200 defines the symmetry transformation. Example 1 2 3 4 5 6 7 123456789012345678901234567890123456789012345678901234567890123456789012 HYDBND N LEU 10 AO3* NDP 501 HYDBND NH2 ARG 111 OD1 ASP 149 1555 -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Head User Support Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne R Fiori Subject: Re: Hbonds in pdb. Date: Mon, 3 Mar 1997 11:59:55 -0800 (PST) To: rasmol@noc1.oit.umass.edu > > In the article, Andrea Bernini wrote: > > I know Rasmol calculates H-bonds, but does exist a way to put > > hbonds directly in pdb records? > > I think the standard pdb format doesn't content hbond information. > And the pdb format is not only for RasMol. :p > The CONECT record can specify hydrogen bonding. Unfortunately, I don't remember the exact manner (columns and numbers) needed to do this. Take a look at Brookhaven's on line docs. It should be there. =Wayne ++++------+------+------+------+------+------+------+------+------+------+ From: tpthoms Subject: Rasmol: Limitations and compilation Date: Mon, 03 Mar 1997 18:18:52 -0500 To: rasmol@noc1.oit.umass.edu Hi! I'm a student at U.C. Irvine, and while using your wonderful software, I ran into an error while trying to display a molecule we are attempting to synthesize: Database error:Too many new atom types! This error occurs in both the windows and macintosh version of your software. What does it mean? Secondly, I am trying to compile Rasmol for XFree86/OS2 and I received the following message: [D:\tar\rasmol2]make gcc -m486 -O2 -fno-strength-reduce -D__ST_MT_ERRNO -Zmtd -Zsysv-signals -Id:/ XFree86/include -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/XFree86/lib/rasm ol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o rasmol.c: In function `InitTerminal': rasmol.c:264: sizeof applied to an incomplete type rasmol.c: In function `FetchCharacter': rasmol.c:337: invalid use of undefined type `struct fd_set' rasmol.c:338: invalid use of undefined type `struct fd_set' rasmol.c:350: invalid use of undefined type `struct fd_set' rasmol.c: At top level: rasmol.c:110: storage size of `WaitSet' isn't known X11MAKE.EXE: *** [rasmol.o] Error 1 Is their some compiler switch that I missed? Any help you can give would be greatly appreciated. Thanks Travis Thoms tpthoms@mail.fia.net ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Rasmol: Limitations and compilation Date: Wed, 5 Mar 1997 15:22:25 +0000 (GMT) To: tpthoms Cc: rasmol@noc1.oit.umass.edu Hi Travis, > I ran into an error while trying to display a molecule we are > attempting to synthesize: > "Database error:Too many new atom types!" > This error occurs in both the windows and macintosh version of your > software. What does it mean? Thanks very much for your e-mail. This problem is caused when RasMol attempts to define new indices for the atom names defined in the input co-ordinate file. Normally in a PDB or similar file atoms are given unique names within a residue such as " CA " or " O1P". RasMol uses indices into an array rather than a string for each of these to reduce the overhead in storing and comparing them. The above error is caused when RasMol discovers too many new names in a file. The current limit is 256 which is considered sufficient as Brookhaven only needs 67 for all standard protein and nucleic acid atoms. The probable cause of this error is either that the column formating in your co-ordinate file is wrong or you are attempting to name atoms as "C1", "C2", "C3", etc... > Secondly, I am trying to compile Rasmol for XFree86/OS2 and I received > the following message: > > [D:\tar\rasmol2]make > gcc -m486 -O2 -fno-strength-reduce -D__ST_MT_ERRNO -Zmtd > -Zsysv-signals -Id:/ > XFree86/include -DFUNCPROTO=15 -DNARROWPROTO > -DRASMOLDIR=\"/XFree86/lib/rasm > ol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o > rasmol.c: In function `InitTerminal': > rasmol.c:264: sizeof applied to an incomplete type > rasmol.c: In function `FetchCharacter': > rasmol.c:337: invalid use of undefined type `struct fd_set' > rasmol.c:338: invalid use of undefined type `struct fd_set' > rasmol.c:350: invalid use of undefined type `struct fd_set' > rasmol.c: At top level: > rasmol.c:110: storage size of `WaitSet' isn't known > X11MAKE.EXE: *** [rasmol.o] Error 1 It sounds as though the UNIX structure "struct fd_set" is not being defined by any of the OS2 header files. This is used by RasMol as an argument to the UNIX select(2) system call to multiplex stdin and X Windows events. Fortunately, this dependency can be removed from RasMol by commenting out the line "#define TERMIOS" in the "rasmol.h" header file. This will instruct RasMol not to use "select" or "struct fd_set" but will mean that you can no longer type commands into the controlling "xterm" window. However, you can still type into the main RasMol graphics window (when it has input focus). 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 ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: BABEL Home Page Date: Wed, 5 Mar 1997 13:34:40 -0500 (EST) To: ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord Subject: BABEL Home Page Date: Tue, 4 Mar 1997 13:03:07 -0500 To: Rasmol List [This got rejected by listproc over a technicality so I'm forwarding it. -Eric] Dear All, A home page is now available for BABEL, a program to convert between different chemical file formats. Its URL is: http://mercury.aichem.arizona.edu/babel.html It is possible to download BABEL and to register it on-line. I hope you will find this information useful. Sincerely, Jean Debord Faculte de Medecine, Limoges, France /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Hbonds in the PDB Date: Tue, 11 Mar 1997 19:34:02 +0000 (GMT) To: rasmol@noc1.oit.umass.edu Dear RasMolians, > Just to set the record straigt, PDB's Contents Guide > (http://www.pdb.bnl.gov/Format.doc/Format_Home.html) specifies the > format for for hydrogen bonds. The HYDBND record is optional, but > sometimes is supplied in the submission to PDB. I believe that these > records are handmade by the authors, but perhaps someone knows of a > program which writes them out. Unfortunately RasMol currently does not support specification of hydrogen bonds by either CONECT or HYDBND records. HYDBND and many other version 2.x features will hopefully be supported in the next release of RasMol. Alas Wavefunction's Spartan software places covalent bonding information in the hydrogen bond fields of the CONECT record (v1.0). As there seem to be more PDB files generated by Spartan and MacSpartan than PDB files containing explicit hydrogen bonds it was decided to support the former. Luckily, the new HYDBND record has helped resolve the issue. It is possible to specify hydrogen bonds to RasMol in Alchemy file format using the bond type "HYDROGEN". However this conversion will loose all of the macromolecular information that is in a PDB file. 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Group color scheme: RasMol manual revised Date: Sun, 16 Mar 1997 11:59:37 -0500 (EST) To: rasmol@noc1.oit.umass.edu Cc: ras32425@ggr.co.uk, tim@mind.net I have made a minor revision to the on-line (html) RasMol manual (the only version which is up to date, http://www.umass.edu/microbio/rasmol/distrib/rasman.htm). The discussion of the group color scheme omitted mention of the need for a 'set hetero off' command to exclude e.g. water from the spectral range, thereby applying the full range from blue to red to the protein chain. The manual also appeared to me to have the colors reversed for protein, e.g. the N terminus is blue, and the C terminus red, so I corrected that. (Thanks to Roger Sayle for explaining about this effect of 'set hetero off' in an email message to this list, 3/14/96. Sorry that it took me a year and 2 days to integrate this info into the manual!) ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Multiple molecules Date: Mon, 17 Mar 1997 17:36:05 -0500 (EST) To: Dear Rasmolites & Chimeleans: I thought the following ideas from Roger Sayle (in response to my comments on Marcey's illustration of a process) would be of interest. Unlike Marco Molinaro's Berkeley-enhanced RasMol, the ideas below (using Sayle's RasMol without modification) do not allow independent movement of the separate molecules. However, they do facilitate the control of the display or hiding of separate molecules. -Eric Martz ------------------------------ Fri, 14 Mar 1997 From: Sayle Dr R A Hi Eric, [Eric wrote to Roger:] > David Marcey recently put out a chime tutorial on topoisomerase. [www.kenyon.edu/depts/bmb/chime.htm] > He modeled PDB files for 6 different stages in the reaction: a single > stranded DNA is covalently bound to a tyrosine, the molecule cleaves the > SS-DNA, then opens and 'grabs' a double stranded DNA, then closes, > religates the SS-DNA, reopens and releases the DS-DNA. Such a process > would be much easier to comprehend in Molinaro's Berkeley-enhanced rasmol [which would allow moving domains independently of each other] > than with snapshots, but I'm shy of scripting with it in Windows because > when you do a zap from a script file, it hangs (may not do this on the Mac). [Roger Sayle replies:] As I keep insisting RasMol is capable of handling multiple molecules, however all the molecules of interest must be stored in a single file. For example, if you just concatenate Brookhaven PDB files together RasMol will treat the END records in the file to deliniate different molecules. A much better way to organise an animation like this is to use the MODEL and ENDM records in a PDB file, or different chain identifiers. In this way, a RasMol (or Chime) script can be used to turn on or off the displays of chains or models independently. Locally, short scripts are used to cycle through a number of protein inhibitors displayed within the active site. One chain contains all of the protein atoms that don't move and a series of other chains contain the active site side chains and inhibitors. These are then turned on and off with the single click of a button in Netscape or with a single RasMol script without containing a "zap". 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 /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: StartSpin As A Script Command Date: Tue, 18 Mar 1997 09:55:31 -0800 To: rasmol@noc1.oit.umass.edu I was attempting to place a startspin button on a web page with an embeded chime model and could not find a Rasmol script command to start rotation of a model. The Chime menu has a "Rotation" command which leads me to believe that there must be some kind of command to start the model spinning, but the only command I have found is a property of the model embed tag and it only lets you start the model spinning when it is loaded. I would ultimately like to have a button on the page that would toggle spinning on and off, as well as have a speed control. If there is currently no "spin" script command, I could see it being an important addition to a future version of chime. If anyone knows of a spin script command, or a javascript function that uses "rotation" to spine a molecule, I would greatly appreciate their suggestions or recommendations. Thanks in advance. Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Miller Subject: Re: StartSpin As A Script Command Date: Wed, 19 Mar 1997 10:41:03 -0800 To: baucom@gorby.ucsc.edu Cc: rasmol@noc1.oit.umass.edu, chime-feedback@mdli.com Hello Albion, There are currently two ways to set up buttons that can start/stop rotation of a Chime structure. Both have some advantages/drawbacks. 1) Put the structure in a separate frame and use an HTML button to (re)load the structure frame: This approach does require you to put the structure in a separate frame and when a frame is reloaded, the user will loose any modifications made to the display. You could make the onClick function smarter so it can act as a toggle. 2) Using 'script="move 360000 0 0 0 0 0 0 0 500 15 1"' or something of this nature instead of 'spinx=10 startstpin=yes' in your tag. The move command is actually designed to perform discreet rotations over a finite time span but, when given large input values, will make the structure rotate for a long time. You can create two Chime buttons, one with script move 360000 0 0 0 0 0 0 0 500 15 1 and the other with script interrupt to stop the rotation. This approach will let you keep the structure in the same frame as the rest of the page and will preserve what the user has done to the display (e.g., changing to spacefilling view) but 'move' can consume more system resources than other commands. We're looking at a more efficient approach for the future. Mitch At 09:55 AM 3/18/97 -0800, Albion Baucom wrote: > >I was attempting to place a startspin button on a >web page with an embeded chime model and could not >find a Rasmol script command to start rotation of a >model. The Chime menu has a "Rotation" command which >leads me to believe that there must be some kind of >command to start the model spinning, but the only >command I have found is a property of the model >embed tag and it only lets you start the model spinning >when it is loaded. > I would ultimately like to have a button on the >page that would toggle spinning on and off, as well as >have a speed control. If there is currently no "spin" >script command, I could see it being an important addition >to a future version of chime. > >If anyone knows of a spin script command, or a javascript >function that uses "rotation" to spine a molecule, I would >greatly appreciate their suggestions or recommendations. > >Thanks in advance. > > >Albion E. Baucom > > >UC Santa Cruz >241B Sinsheimer Labs >Santa Cruz, CA 95064 >(408) 920-1616 > Mitchell Miller MDL Information Systems, Inc. (801) 569-1390 VoiceMail (800)955-0051 ext. 2163 mitch@mdli.com ctheurer@bio.umass.edu, rasmol@noc1.oit.umass.edu, ahuja@centaurus.cs.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: RE: Q on Rasmol coloring atoms Date: Wed, 19 Mar 1997 21:04:25 +0000 (GMT) To: Eric Martz Cc: jacobs@pa.msu.edu, bscott@biochem.umass.edu, cfinlays@elux3.cs.umass.edu, Dear Don, > I do not believe you can color atoms differently from bonds, while > retaining half-and-half coloring of bonds. I have CC'd this to > Roger Sayle who can answer authoritatively, and also to the RasMol > Email list as your question and the answer may be of general interest. Eric is quite right that a bond can only be colored half-and-half if the two colours of that bond are the colours of the atoms at either end. I'm not sure if it was clear from the question, but it is possible to colour atoms and bonds completely independently. i.e. select all colour bonds red colour atoms yellow A thought has just struck me... It may be possible to achieve the same effect as you require by adding additional atoms at the end of the bonds with exactly the same co-ordinates. For example, if you wanted to draw a single bond between atoms A and B, you'd add two extra atoms C and D with exactly the same co-ordinates to the molecule file. Now instead of a single bond AB, RasMol will discover six AB,AC,AD,BC,BD and CD. All bonds can be turned off using "select all", "wireframe off", and only the bond CD displayed using "set bondmode and", "select C,D", "wireframe 20". Next all the atoms except A and B can be turned off, "select C,D", "spacefill off". Finally, atoms A, B, C and D may be displayed different colours. This results in a ball and stick like representation where the stick bond is half-and-half coloured but differently from the "spheres" at the ends. I'm sorry if this is hideously confusing. In practice you only need place one of two pseudo-atoms at the boundries of your "mechanical regions". I shall try and think of an way of adding half-and-half bond colouring to RasMol for the next release. A second thought has just struck me (what two in one day!)... The above scheme is simpler by just inserting a single atom E half way between A and B. Now there are three bonds AB,AE,BE. The AB bond can be turned off and AE and BE can be coloured independently using the "color bond" command. One possible advantage of this is that each half of the bond can even have a different cylindrical radius or be displayed as dashes. Sorry for such hacks. The answer is it can be done with a little effort. 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 764918 X-Info: Ross Labs R&D NT-Mail Server ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Schenz Subject: Rasmol and Internet Explorer Date: Wed, 26 Mar 1997 12:55:18 -0500 To: rasmol@noc1.oit.umass.edu We want to distribute molecular structures over our web-intranet using Rasmol as a viewer within a browser. Netscape works fine. But, we have problems using Microsoft Internet Explorer(MIE). After clicking on the .pdb link, Rasmol loads but no molecule is displayed (black screen). We've tried this from the Web with the same results. If we right-click on the link, but save it to disk and then open the pdb file with Rasmol, everything works fine. It seems as though MIE is not passing the file name on to Rasmol. Has anyone else had this problem or know of a solution? Tim _____________________________________________________________________ Timothy W. Schenz, Ph.D. tschenz@sr-server.rossnutrition.com Abbott Labs/Ross Prod. Div. Voice (614)624-7024 Columbus, OH 43215 FAX: (614)624-3070 _____________________________________________________________________ References: <2.2.32.19970326175518.009861fc@sr-server.rossnutrition.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Rasmol and Internet Explorer Date: Thu, 27 Mar 1997 01:46:22 +0100 To: rasmol@noc1.oit.umass.edu > Has anyone else had this problem or know of a solution? Well, not exactly the same but sometimes (depending on the location of the file in my folder-structure) I have similar problems, when I want to start a *.pdb-file by clicking on it (it is registered as Rasmol-datafile). Don=B4t know the reaso though.. -- = Bye, Marc Saric Visit http://www.rat.de/marc_saric/index.htm ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Summer Workshops (Northeastern US) Date: Mon, 31 Mar 1997 12:54:58 -0500 (EST) To: rasmol@noc1.oit.umass.edu ** Free Workshops on Molecular Visualization for Undergraduate Bioscience Teaching ** Amherst MA -- Summer, 1997-8 Understanding the three-dimensional structures of proteins, DNA, RNA, and their interactions is difficult from flat pictures, yet grasping structure is important to understanding function. Free software is now available which displays attention-grabbing 3D animated images of biological molecules in depth-cued spacefilling color. RasMol (http://www.umass.edu/microbio/rasmol), which works on Windows or Macs, encourages self-directed exploration. Chime (http://www.umass.edu/microbio/chime) allows annotated preset views of molecules to be delivered as web tutorials. Free, hands-on workshops will be held this summer at the University of Massachusetts in Amherst to prepare college faculty with no prior experience to use molecular visualization in their classes. Participants will travel to the Amherst campus on three separate days (two this summer, one the following summer), and are responsible for their own travel expenses (and therefore are expected primarily from the Northeastern USA). Overnight accomodations will be provided free to those needing them (based on distance traveled). Participants will be expected to incorporate molecular visualization into their teaching, and to mentor two faculty colleagues at their home institution. The workshops will be led by Eric Martz, a Professor in the Department of Microbiology. Martz has innovated molecular structure tutorials which are in use throughout the USA and in dozens of other countries. The web site he created (see above) was visited by 40,000 people in 1996. 1997 dates are June 17 and 30 (workshop A), or June 19 and July 2 (workshop B). Workshops A and B also meet for one day in late June 1998. To obtain more detailed information and a REGISTRATION FORM, visit http://www.umass.edu/microbio/rasmol/workshop.htm or FAX a request to 413-545-1578, or email a request to emartz@microbio.umass.edu. Supported by the National Science Foundation (Undergraduate Faculty Enhancement, Division of Undergraduate Education) and the University of Massachusetts. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol Other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RHP benefits from snow Date: Tue, 1 Apr 1997 21:35:54 -0500 (EST) To: rasmol@noc1.oit.umass.edu There was a great snow here last night, which closed the U of Mass for the day. That had a beneficial effect on the RasMol Home Page, to wit (copied from "What's New?"): 97/04/01: Henry Brzeski's new RasMol "movie" script on glucocorticoid/zinc finger binding to DNA has been linked. 97/04/01: A list of frequently asked questions, with answers, has been contributed by Roger Sayle. My apologies to Roger for taking far too long to find the time to put this very useful FAQ on the web site. 97/04/01: Babel, a web interface to Babel, MolView, and other links were added to the page on free software other than RasMol, which was also reorganized and better indexed. Now included is an amazing web form which allows you to submit a PDB to RasMol and get back a single image without ever running RasMol! See the Molecule to Image Converter Engine. 97/04/01: The broken downloading link for Win32SOle has been fixed. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: New Index to Chime/RasMol Tutorials Date: Mon, 7 Apr 1997 14:47:12 -0400 (EDT) To: rasmol@noc1.oit.umass.edu I've put my first draft of a World Index (I hope) to BioMolecular Structure Tutorials in Chime and RasMol at www.umass.edu/microbio/rasmol/tutbymol.htm Please tell me about resources I've overlooked. Note that I've limited my index to tutorials on BIOLOGICAL molecules -- unfortunately there are far too many good CHEMISTRY sites for me to index! For the sites I've managed to index, there are a total of 37 tutorials, mostly on different molecules. These comprise 9 RasMol scripts and the remainder Chime scripts. Chime's excellence for educational presentations is clearly making it worth the effort for more people to learn HTML and sometimes some javascript in addition to RasMol chemical script command language (the superset implemented in Chime). I've also reorganized the page formerly entitled 'RasMol in the Classroom', now 'BioMolecules in the Classroom ...." at www.umass.edu/microbio/rasmol/rasclass.htm (As always I've tried hard not to break any existing links to my site.) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology, Univ Massachusetts, Amherst MA US 01003-5720 413-545-2325 FAX:545-1578. RasMol Home Page, http://www.umass.edu/microbio/rasmol Other web projects listed at http://www.umass.edu/microbio/rasmol/em-web.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ ++++------+------+------+------+------+------+------+------+------+------+ From: dwrt@BPHVAX.biophysics.rochester.edu (Steve Dewhurst) Subject: Re: New Index to Chime/RasMol Tutorials Date: Mon, 07 Apr 1997 15:40:14 -0400 (EDT) To: rasmol@noc1.oit.umass.edu >I've put my first draft of a World Index (I hope) to BioMolecular Structure >Tutorials in Chime and RasMol at > >www.umass.edu/microbio/rasmol/tutbymol.htm > >Please tell me about resources I've overlooked. >Note that I've limited my index to tutorials on BIOLOGICAL molecules -- >unfortunately there are far too many good CHEMISTRY sites for me to index! Dear Eric I have a couple of CHIME presentations online, which appear to now be glitch-free. They include CD4 and RANTES as well as HIV protease (already on your list): http://www.urmc.rochester.edu/smd/mbi/grad/cd4frame.html http://www.urmc.rochester.edu/smd/mbi/grad/ranframe.html Best regards Steve Dewhurst ************************************************************************* Steve Dewhurst Associate Professor, Department of Microbiology & Immunology University of Rochester Medical Center 575 Elmwood Avenue, Room 5-8106, Box 672. Rochester, NY 14642 Tel.:(716)275-3216; FAX:(716)473-2361 OR 473-9573 http://www.urmc.rochester.edu/smd/mbi/steved.html ************************************************************************* ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: New Index to Chime/RasMol Tutorials Date: Tue, 8 Apr 1997 07:53:16 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Thanks very much for pointing them out. I ran the CD4 one and it looked great! They are now in the 'World Index'. I'll also add your class page to my 'immunology classes on the web' site www.umass.edu/microbio/immclass At 03:47 PM 4/7/97 -0500, you wrote: >>I've put my first draft of a World Index (I hope) to BioMolecular Structure >>Tutorials in Chime and RasMol at >> >>www.umass.edu/microbio/rasmol/tutbymol.htm >> >>Please tell me about resources I've overlooked. >>Note that I've limited my index to tutorials on BIOLOGICAL molecules -- >>unfortunately there are far too many good CHEMISTRY sites for me to index! > > >Dear Eric > >I have a couple of CHIME presentations online, which appear to now be >glitch-free. They include CD4 and RANTES as well as HIV protease (already >on your list): > >http://www.urmc.rochester.edu/smd/mbi/grad/cd4frame.html >http://www.urmc.rochester.edu/smd/mbi/grad/ranframe.html > >Best regards > >Steve Dewhurst > >************************************************************************* >Steve Dewhurst >Associate Professor, Department of Microbiology & Immunology >University of Rochester Medical Center >575 Elmwood Avenue, Room 5-8106, Box 672. Rochester, NY 14642 >Tel.:(716)275-3216; FAX:(716)473-2361 OR 473-9573 >http://www.urmc.rochester.edu/smd/mbi/steved.html >************************************************************************* > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Eric Martz" Subject: Chime and Internet Explorer Date: Thu, 10 Apr 1997 14:04:27 -0500 (EST) To: [The following information comes from Bryan Van Vliet of MDLI and is forwarded to the RasMol list with his permission. -Eric Martz] Chime works with Internet Explorer today as a 2D and 3D renderer. However, the scripting capabilities of Chime are still not available from IE 3.0. We need 3 features in Internet Explorer: * Support for the EMBED tag option TYPE= in order that our plug-in can be instantiated without having to place a separate structure file on the host. For example, we use to instantiate a button which runs a RasMol Script and changes the display of Chime in another window. * Support for javascript: URL references. In Netscape you can reference a JavaScript method or command via the URL "javascript:{command}" from both a plug-in or even the Open command. We make use of this capability from our plug-in to make it possible to create some of the tutorials you see with Chime. * Full support for JavaScript (Microsoft's JScript is JavaScript 1.0 compatible and Navigator 3.0 supports JavaScript 1.1). We have been talking to Microsoft about the need for these features. We expect IE 4.0 to completely support JavaScript. We have been told by a Microsoft engineer that the first 2 problems have been addressed in IE 4.0, but we haven't had a chance to verify this. If we do get support for the above 3 items all of the tutorials using Chime should be able to run from either Navigator 3.0 and above or Internet Explorer 4.0. If plug-in support is not fixed in Internet Explorer 4.0 our backup plan is to provide "Chime Pro for ActiveX". We already have a version of Chime Pro as an ActiveX component which we will ship to customers in the next few months. We would rather not release an Internet version (it is targeted at corporate Intranets) of this plug-in for the simple reason that every tutorial creator would have to modify their tutorials so that one version supported ActiveX and one supported plug-ins. Here is an example of embedding a plug-in: Here is an example of embedding an ActiveX component: In lieu of full plug-in support in Internet Explorer, Eric Martz would have to provide some mechanism for writing the proper plug-in or ActiveX object tag in his tutorials depending on which browser was being used. Furthermore, if there was a problem with using ActiveX in JavaScript in IE 4.0, or some JavaScript feature he was depending on didn't work, he might have to rewrite his tutorials in VBScript and serve completely distinct pages depending on which browser was being used. And since the Macintosh is usually behind on features in Internet Explorer (one of the reasons IE 3.0 is so small compared to Navigator on the Mac is because Microsoft left out their JScript support and ActiveX isn't included by default) Eric might be left with some difficult choices on the Macintosh as far as IE is concerned. And, although Microsoft has hinted at UNIX support for IE, I have not seen a version nor am I confident that it would include ActiveX even if it was available, so he could never just write ActiveX/VBScript pages or ActiveX/JavaScript pages to serve to the Internet community. MDL would really like to be able to support IE fully today. Should we put out an ActiveX version of our plug-in and make people like Eric have to create 2 sets of tutorials, one for Internet Explorer and one for Navigator? IE is a nice web browser which almost supports plug-ins completely. If only Microsoft would finish its plug-in support the Internet community would be better served. I'd like to hear opinions on this subject. MDL wants to support the scientific community with our rendering technology, but in a rational way. Thanks, Bryan ------------------------------------------------------------------------ | Bryan Van Vliet bryan@mdli.com | | Project Manager, Internet Technologies 510.895.1313 x1160 (Voice) | | MDL Information Systems, Inc. 510.352.2870 (Fax) | | 14600 Catalina Street, San Leandro, CA 94577 http://www.mdli.com | ------------------------------------------------------------------------ /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Dept Microbiology, Voice: 413-545-2325, FAX: 413-545-1578 Molecular visualization: http://www.umass.edu/microbio/rasmol Immunology: http://www.bio.umass.edu/immunology/immunology.html Flow cytometry: http://www.bio.umass.edu/mcbfacs Morrill IVN 203, 639 N Pleasant St, Univ. Mass., Amherst MA 01003-5720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/ References: <50668.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Chime and Internet Explorer Date: Fri, 11 Apr 1997 08:16:50 -0400 (EDT) To: rasmol@noc1.oit.umass.edu, emartz@microbio.umass.edu Excerpts from mail: 10-Apr-97 Chime and Internet Explorer by "Eric Martz"@microbio.um >[The following information comes from Bryan Van Vliet of MDLI and is >forwarded to the RasMol list with his permission. -Eric Martz] > > > MDL would really like to be able to support IE fully today. Should we > put out an ActiveX version of our plug-in and make people like Eric > have to create 2 sets of tutorials, one for Internet Explorer and one > for Navigator? I won't speak for Eric or whether he would "have to create 2 sets of tutorials", but no way will I ever be induced to go that route. Aside from the colossal hassle of actually implementing such nonsense, it would be retrograde progression in terms of what the WWW is all about. The problem is clearly with IE 3.0. When the geniuses in Redmond get around to implementing EMBED tag options and JavaScript comparable to Netscape 3.01, I would be happy to make small changes so that both browsers could be used on the same page. -Will McClure References: <50668.emartz@microbio.umass.edu> <50668.emartz@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Re: Chime and Internet Explorer Date: Fri, 11 Apr 1997 12:42:36 +0000 To: rasmol@noc1.oit.umass.edu I absolutely agree with the sentiments below. Internet "standards" are shaky enough as it is, we don't want them to break down even more so that all our stuff has to be produced in Navigator and MIE versions. >Excerpts from mail: 10-Apr-97 Chime and Internet Explorer by "Eric >Martz"@microbio.um >>[The following information comes from Bryan Van Vliet of MDLI and is >>forwarded to the RasMol list with his permission. -Eric Martz] >> >> >> MDL would really like to be able to support IE fully today. Should we >> put out an ActiveX version of our plug-in and make people like Eric >> have to create 2 sets of tutorials, one for Internet Explorer and one >> for Navigator? > > I won't speak for Eric or whether he would "have to create 2 sets of >tutorials", but no way will I ever be induced to go that route. Aside >from the colossal hassle of actually implementing such nonsense, it >would be retrograde progression in terms of what the WWW is all about. >The problem is clearly with IE 3.0. When the geniuses in Redmond get >around to implementing EMBED tag options and JavaScript comparable to >Netscape 3.01, I would be happy to make small changes so that both >browsers could be used on the same page. > >-Will McClure _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.ccc.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html References: <199703161659.LAA07690@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: tpthoms Subject: Rasmol 2.5 for XfreeOS/2 Date: Tue, 22 Apr 1997 00:25:44 -0400 To: rasmol@noc1.oit.umass.edu Hi! I finally finished the port of Rasmol 2.5 to Xfree86 for OS/2. It can be found at hobbes.nmsu.edu /incoming. Thanks to everyone that contributed. Travis Thoms ++++------+------+------+------+------+------+------+------+------+------+ From: "Orjan Hansson" Subject: Biomolecular Structures, a Chime Course Date: Tue, 22 Apr 1997 18:33:17 GMT+0100 To: rasmol@noc1.oit.umass.edu Dear Chime Users, I have developed a course on "Biomolecular Structures" which is described in more detail below. Any comments are highly appreciated! With best regards, Orjan Hansson Announcement ------------ "Biomolecular Structures" is an Internet course intended to be used as a computer-based laboratory exercise for undergraduate students in basic biochemistry. It was designed to accompany the textbook "Biochemistry (2nd ed.)", by C.K. Mathews and K.E. van Holde (Benjamin/Cummings, 1996), but can be used together with any introductory course on biochemistry and biophysics. The following topics are covered: 1. Amino acids 1.1 Movement, atom coloring and molecular representation 1.2 Chemical groups 1.3 Stereoisomers 1.4 Atom labelling 1.5 Side chain properties 2. Peptides 2.1 Primary sequence 2.2 Molecular dynamics 3. Proteins 3.1 BPTI 3.2 Hemoglobin 3.3 Plastocyanin 3.4 Alcohol dehydrogenase 4. Nucleotides 4.1 Chemical groups 4.2 AMP and dAMP 4.3 Purines 4.4 Pyrimidines in DNA 4.5 Pyrimidines in RNA 4.6 Nucleotide coenzymes 5. Nucleic acids 5.1 B-DNA 5.2 A-DNA 5.3 Z-DNA 5.4 Transfer RNA 5.5 A protein/DNA complex The course makes use of the Chemscape Chime plug-in and JavaScript 1.1. Thus, Netscape Navigator 3.0 is required. Particular attention has been paid to the design of the user interface so that students which are not so experienced with computers can navigate easily through the course. A form with simple questions is included and when the student has completed it, he/she can send it via Email to a teacher for marking. Extensive help is available to guide the user. During December 1996, some 200 biochemistry students ran the course as a 2.5 hour laboratory exercise in our computer lab. Their response was very positive. A link to the course can be found at the following URL: http://www.lundberg.gu.se/bcbp/edu/ Orjan Hansson E-mail: Orjan.Hansson@bcbp.gu.se Orjan Hansson, Ph.D. | E-mail: Orjan.Hansson@bcbp.gu.se Dept. of Biochemistry & Biophysics | or: bcbpoh@lundberg.gu.se Lundberg Institute | Tel: +46 31 773 39 29 Goteborg University and | Fax: +46 31 773 39 10 Chalmers University of Technology | WWW: http://www.lundberg.gu.se Medicinaregatan 9C, S-413 90 Goteborg (Sweden) ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: User File Upload CGI Program And Chime Date: Wed, 23 Apr 1997 20:47:08 -0700 To: rasmol@noc1.oit.umass.edu I was wondering if a CGI program existed that could be used to direct files set from a client to chime, that is a CGI program that would allow a user to specify a local file to view in Chime on a server. I am asking because I am in the process of developing a web site for protein sequence alignment assessment and would like the user to be able to upload their own file to the server for assessment (specifically a protein homolog used for threading). Thanks in advance. Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Klaus Frommer Subject: Books about Molecular Modeling and Visualization Date: Thu, 24 Apr 1997 14:58:37 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu I am an undergraduate student of biochemistry and that is why I have the following question: Can anyone recommend one or more introducing books about Molecular Modeling and Visualization for beginners? The literature I have found was either only for specialists in this field or was rather a collection of essays than an overall tutorial. Thanks for your advice in advance Klaus Frommer _________________________________________________________________________ Eberhard-Karls-University of Tuebingen, GERMANY _________________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Lora Burgess Subject: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 09:33:05 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Hello, I am updating a review chapter for Bioinorganic Catalysis. We would like to incorporate nice black and white ribbon and string type pictures of metalloproteins into the chapter. I know that we can write a Molscript file from RasMol, and port it over to an SGI, but we produce everything on Macs in our lab. Is there a similar program for a Mac that we can use to get good postscript results for black and white printing? I am starting a new job next week, and will have limited time to get back up here to use an SGI. Id like to be able to work from home on my Mac. Lora *************************** Lora Burgess Dept. of Chemistry Johns Hopkins University 34th & Charles Sts. Baltimore, MD 21218 410-516-7937 *************************** ++++------+------+------+------+------+------+------+------+------+------+ From: pujadas@argo.urv.es (Gerard Pujadas) Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 18:18:45 +0200 To: rasmol@noc1.oit.umass.edu Hi, RasMac is the Mac version of RasMol. I have installed it in a SGI and in a PowerMac and it runs with exactly the same commands and syntax. > Hello, > I am updating a review chapter for Bioinorganic Catalysis. We >would like to incorporate nice black and white ribbon and string type >pictures of metalloproteins into the chapter. I know that we can write a >Molscript file from RasMol, and port it over to an SGI, but we produce >everything on Macs in our lab. Is there a similar program for a Mac that >we can use to get good postscript results for black and white printing? >I am starting a new job next week, and will have limited time to get back >up here to use an SGI. Id like to be able to work from home on my Mac. > Lora > Hope this helps. Regards from our little Mediterranean country !!! Gerard. *************************************************************************** * Gerard Pujadas * * Biotecnologia Computacional * * Dept. Bioquimica i Biotecnologia e-mail: pujadas@quimica.urv.es * * Univ. Rovira i Virgili phone: 34 77 559565 * * Pla=E7a Imperial Tarraco 1 fax: 34 77 559597 = * * 43005 Tarragona (CATALONIA) * * State: Spain (European Union) * *************************************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: User File Upload CGI Program And Chime Date: Thu, 24 Apr 1997 10:54:08 -0700 To: rasmol@noc1.oit.umass.edu At 08:47 PM 4/23/97 -0700, Albion Baucom wrote: > >I was wondering if a CGI program existed that could be >used to direct files set from a client to chime, that is >a CGI program that would allow a user to specify a local >file to view in Chime on a server. > I am asking because I am in the process of >developing a web site for protein sequence alignment >assessment and would like the user to be able to upload >their own file to the server for assessment (specifically >a protein homolog used for threading). > >Thanks in advance. > You should be able to upload any file (pdb/etc.) to the server using the HTML 'file upload' form element. (This allows the user to pick a file to be uploaded when the user clicks submit..) >From there you need a CGI program to write the file out from the submission, and then trigger your special programs, and then presumably the CGI program would output a HTML page which points to the results of the processing. I suspect that if you search on "CGI and file and upload" you should be able to find some example CGI programs which accept a uploaded file. MDL's Chemscape system, which works with Chime Pro and Netscape LiveWire, allow for pasting structures directly into Chime Pro and then having the structure uploaded to the server automatically when the form is submitted. (Because of performance reasons we do not use CGI, so I have no direct experience with the CGI solution for what you are asking for...)). -tim >Albion E. Baucom >baucom@gorby.ucsc.edu > >UC Santa Cruz >241B Sinsheimer Labs >Santa Cruz, CA 95064 >(408) 920-1616 > > ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne R Fiori Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 11:42:06 -0700 To: rasmol@noc1.oit.umass.edu >Hi, RasMac is the Mac version of RasMol. I have installed it in a SGI and >in a PowerMac and it runs with exactly the same commands and syntax. > Yes RasMol runs on the Mac, but there isn't a version of MolScript for the Mac. If you have network access to your SGI running MolScript, you can still work from home. Generate the MolScript input files using RasMac, upload them to the SGI, generate the postscript (or eps) file, drag that file back to your Mac, and preview it with GhostScript. It's a little slower than sitting on the SGI, but fast enough. You can get GhostScript from any Macintosh archive. > >> Hello, >> I am updating a review chapter for Bioinorganic Catalysis. We >>would like to incorporate nice black and white ribbon and string type >>pictures of metalloproteins into the chapter. I know that we can write a >>Molscript file from RasMol, and port it over to an SGI, but we produce >>everything on Macs in our lab. Is there a similar program for a Mac that >>we can use to get good postscript results for black and white printing? >>I am starting a new job next week, and will have limited time to get back >>up here to use an SGI. Id like to be able to work from home on my Mac. >> ++++------+------+------+------+------+------+------+------+------+------+ From: Ramiro Tellez Sanz Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 20:42:28 +0200 (DFT) To: rasmol@noc1.oit.umass.edu On Thu, 24 Apr 1997, Lora Burgess wrote: > > Hello, > I am updating a review chapter for Bioinorganic Catalysis. We > would like to incorporate nice black and white ribbon and string type > pictures of metalloproteins into the chapter. I know that we can write a > Molscript file from RasMol, and port it over to an SGI, but we produce > everything on Macs in our lab. Is there a similar program for a Mac that > we can use to get good postscript results for black and white printing? > I am starting a new job next week, and will have limited time to get back > up here to use an SGI. Id like to be able to work from home on my Mac. > Lora > > *************************** > Lora Burgess > Dept. of Chemistry > Johns Hopkins University > 34th & Charles Sts. > Baltimore, MD 21218 > 410-516-7937 > *************************** > > > Hi! I use RasMac 2.6, the Rasmol version for the Mac OS. It prints OK also in Postcript, but has a minor bugs regarding the Spacefill structures when printing under Postcript. Just try it. BTW, its faster and nicer than on the PC, of course! Regards from SPAIN Ramiro Tellez Sanz Dpto. Physical Chemistry University of Almeria SPAIN ingen.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Books about Molecular Modeling and Visualization Date: Thu, 24 Apr 1997 17:44:58 -0400 To: rasmol@noc1.oit.umass.edu Have you seen Branden and Tooze's excellent intro? It is very readable and full of great pictures. A new edition is due out this fall. Introduction to Protein Structure by Carl Branden and John Tooze At 02:58 PM 4/24/97 +0200, you wrote: > >I am an undergraduate student of biochemistry and that is why I have the >following question: > >Can anyone recommend one or more introducing books about Molecular >Modeling and Visualization for beginners? > >The literature I have found was either only for specialists in this field >or was rather a collection of essays than an overall tutorial. > >Thanks for your advice in advance > >Klaus Frommer > >_________________________________________________________________________ > >Eberhard-Karls-University of Tuebingen, GERMANY >_________________________________________________________________________ > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu www.umass.edu/microbio/rasmol/emartz.htm - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Lora Burgess Subject: Re: molscript equivalent for a Mac? Date: Thu, 24 Apr 1997 23:01:45 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Many thanks to the replies about my question about a molscript equivalent. I didnt make it clear that I am using RasMac now, but want to print black and white representations of proteins such as Molscript can generate, for example 3D arrows to represent beta-sheets, etc. Wayne Fiori's suggestion may be the most workable- thanks for the tip about Ghostscript- I wasnt aware of that program. Lora *************************** Lora Burgess Dept. of Chemistry Johns Hopkins University 34th & Charles Sts. Baltimore, MD 21218 410-516-7937 *************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: Books about Molecular Modeling and Visualization Date: Fri, 25 Apr 1997 12:04:10 +0100 (BST) To: rasmol@noc1.oit.umass.edu > >Can anyone recommend one or more introducing books about Molecular > >Modeling and Visualization for beginners? I'd also strongly recommend Eric Martz's recommendation of Brandon & Tooze as an excellent introduction to Protein Structure. Here are some of my other recommendations. Please note that these are my personal opinions and not those of my employer and I hope pretty much impartial. Molecular Modelling & Visualization: "Molecular Modelling: Principles and Applications", Andrew Leach, Longman, 595 pages, 1996. "Computer Aided Molecular Design", Jean-Pierre Douchet and Jacques Weber, Academic Press, 487 pages, 1996. "Protein Architecture: A Practical Approach", A.M. Lesk, IRL Press, 287 pages, 1991. Protein Structure: "Introduction to Protein Structure", Carl Branden & John Tooze, Garland Press, 302 pages, 1991 "Principles of Protein Structure", G.E. Schulz and R.H. Schirmir, Springer Verlag, 314 pages, 1979. Computer Graphics: "Computer Graphics: Principles and Practice", Foley, van Dam, Feiner and Hughes, 2nd Edition, Addison Wesley, 1174 pages, 1990 Biochemistry: "Biochemistry", Lubert Stryer, 4th Edition, Freeman, 1089? pages, 1995?. My apologies to anyone that I've missed out. I'd be very interested in hearing other peoples recommendations. 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 764918 ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: Re: Books about Molecular Modeling and Visualization Date: Fri, 25 Apr 1997 07:47:00 -0700 To: rasmol@noc1.oit.umass.edu This is an interesting book I have come across which is specific to Molecular visualization: Data Visualization in Molecular Science: Tools for Insight and Innovation Jack E. Bowie, Ed. ISBN 0-201-58157-4 It may be a bit technical for a beginner, but is specific to just this type of work. Hope this helps. Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Books about Molecular Modeling and Visualization Date: Fri, 25 Apr 1997 16:13:06 +0200 (MESZ) To: rasmol@noc1.oit.umass.edu > > > > >Can anyone recommend one or more introducing books about Molecular > > >Modeling and Visualization for beginners? > > I'd also strongly recommend Eric Martz's recommendation of Brandon & > Tooze as an excellent introduction to Protein Structure. Here are some > of my other recommendations. Please note that these are my personal > opinions and not those of my employer and I hope pretty much impartial. > > ... > My apologies to anyone that I've missed out. I'd be very interested in > hearing other peoples recommendations. Hello All, I'm also very interested in souch books. My personal tip is Molecular Modeling Basic Principles and Applications by H.-D Holtje and G. Folkers VHC, ISBN 3-527-29384-1 It seems to be a comprehensive book which explains "all" recent methods in modeling, Thanks, Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Aguinaldo Robinson de Souza Subject: Re: Books about Molecular Modeling and Visualization Date: Sat, 26 Apr 1997 09:36:34 -0200 (GRNLNDDT) To: rasmol@noc1.oit.umass.edu Cc: rasmol@noc1.oit.umass.edu Hi All, I recommend the book: Proteins. A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. by C.L. Brooks III, M. Karplus, B. M. Pettitt John Wiley & Sons ISBN 0-471-62801-8 (cloth) ISBN 0-471-52977-X (paper) That's a nice book about computer simulation of proteins. Dr. Aguinaldo Robinson Departamento de Quimica Universidade Estadual Paulista Bauru, Sao Paulo, Brazil 17033-360 Phone:(014) 230-2111 (ext. 134) FAX: (014) 230-4470 e-mail: arobinso@azul.bauru.unesp.br arobinso@rhodes.cenapad.unicamp.br ++++------+------+------+------+------+------+------+------+------+------+ From: Randy Bumgardner Subject: path length limitation in Netscape Date: Tue, 29 Apr 1997 14:27:01 -0700 To: rasmol@noc1.oit.umass.edu Cc: chime-feedback@mdli.com Eric Martz requested that I post this to the list to answer any questions, or potential questions, concerning problems with opening image files on the Mac. Apparently, if the path length to the html doc is longer than 256 characters, Netscape will give an error that it could not find the file. However, if the path length to the html doc it not longer than 256 characters, but the absolute path to an embedded image or structure is, Netscape will display the page without the image or structure. The reason for this is the way that the Mac OS handles filenames. However, one workaround I can suggest is not to nest documents too deeply in the directory structure, unless its absolutely necessary. Additional information from Roger Sayle: The reason for this is that in theory filenames on Apple Macintoshes can never be longer than 255 characters. All of the Macintosh operating system API calls pass their filename parameters as Str255, using the pascal convention that the first byte holds the string length. (In RasMol): The ConvertFilename routine is a port of the InsideMacintosh routine that used to return a Str255. Indeed in a similar routine "SetFileInfo" I convert a filename into a Str255 in order to set the file's icon. If current versions of the Mac OS can have FSS structures whose absolute filepath is longer than 256 characters, not only would bounds checks be needed (and the "buffer" and "Filename" arrays extended) but many of the file manipulation routines would have to parse the filename and traverse the directory tree until the remaining filepath was less than 255 characters in order call the MacOS API. Randy Bumgardner **************************************************** Randy Bumgardner MDL Information Systems (510) 895-1313, ext. 1172 Voice:(510) 357-2222, x1172 randyb@mdli.com **************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Rasmol Date: Tue, 29 Apr 1997 18:41:21 -0400 To: mriehl@wp.bsu.edu Cc: rasmol@noc1.oit.umass.edu At 04:56 PM 4/29/97 -0500, you wrote: >Hello -- > >I am a professor of chemistry at Ball State University in Muncie, IN, >and I have been using Chime to enhance my course web pages for the last >year. > >My question is this: I use PowerPoint in my lectures and I would like >to incorporate Rasmol into the presentations. PowerPoint 7.0 (Windows >95) has interactive settings which allows me to start Rasmol (with a >blank screen) by clicking on an icon, or to open a .PDB file in Rasmol >in the same manner. However, I do not know how to open Rasmol with a >specific .MOL file, display, background, etc. from PowerPoint. Is there >a way to do this? If not, is this a limitation of Rasmol or PowerPoint? > >Thanks for your help and suggestions. > >Matthew Riehl, Professor >Department of Chemistry >Ball State University >Muncie, IN 47306 >(765) 285-8074 > > It would help to know whether you are using Windows or Mac. If Windows, then each RasMol icon will have a working directory/folder. If this folder contains a file named RASMOL.INI, when RasMol starts up, it will do whatever commands are in the INI file. So it can contain a script with a load command and other commands which set up an initial view, or it can call another script. I've copied this to the RasMol email list in case others have more to add. I don't know any way to do this on a Mac but I don't know much about Macs. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: Re: Rasmol Date: Wed, 30 Apr 1997 09:13:06 +0100 To: rasmol@noc1.oit.umass.edu >>My question is this: I use PowerPoint in my lectures and I would like >>to incorporate Rasmol into the presentations. PowerPoint 7.0 (Windows >>95) has interactive settings which allows me to start Rasmol (with a >>blank screen) by clicking on an icon, or to open a .PDB file in Rasmol >>in the same manner. However, I do not know how to open Rasmol with a >>specific .MOL file, display, background, etc. from PowerPoint. Is there >>a way to do this? If not, is this a limitation of Rasmol or PowerPoint? An alternative suggestion Use Netscape as a presentation manager as in my lacrep presentation on Eric's tutorial page. I use it for presentation during lectures. Its not as glitzy as Powerpoint (but that is just to impress people) but it is far more useful (it can incorporate any movie, sound or chime plug-in) and allows you to use two frames (one for graphics and one for text). h Henry Brzeski Dept of Bioscience and Biotechnology The Todd Centre University of Strathclyde 31 Taylor Street GLASGOW G4 0NR Tel 0141-548 3727 Fax 0141 553 4115 ++++------+------+------+------+------+------+------+------+------+------+ From: "Martin Glancy" Subject: Producing .xyz animations Date: Wed, 30 Apr 1997 10:09:10 0000 To: rasmol@noc1.oit.umass.edu I work at the Exploratory Hands-on Science Centre in Bristol, UK - we may be using Chime to provide an explanatory display on molecules. Do you know of a reference to making XYZ animations? I specifically want to show atoms and small molecules joining to form larger molecules (up to ethanol). I have been able to make some simple files by manually altering and adding coordinates in a .xyz text file. (These are for intranet use - I do not intend to 'infect' reliable sources with these simulations.) Ideally I would like a simple method of producing these, or suggestions of sources of files. Martin Glancy, The Exploratory Science Centre Bristol Old Station, Temple Meads, Bristol BS1 6QU. UK Tel 0117 907 9000 Fax 0117 907 8000 email martin@exploratory.org.uk ++++------+------+------+------+------+------+------+------+------+------+ From: skg Subject: Re: Producing .xyz animations Date: Wed, 30 Apr 1997 11:48:42 -0700 To: rasmol@noc1.oit.umass.edu At 10:09 AM 4/30/97, you wrote: >I work at the Exploratory Hands-on Science Centre in Bristol, UK - we >may be using Chime to provide an explanatory display on molecules. > >Do you know of a reference to making XYZ animations? I specifically >want to show atoms and small molecules joining to form larger >molecules (up to ethanol). > A good place to start would be with re_view, a program that facilitates animation of xyz files. The problem is if you want to animate a reaction, you have to learn a little quantum chem & a program like mopac that generates reaction coordinates....it's really easy doing thermal vibrations, but in reactions you have to guesstimate the transition states, etc. There's lots of higher end programs that do this (eg gaussian) but they are very expensive. Re-view is cheap (there might even be a shareware version), and it has some ancillary programs that help generate reaction files, as well as some example reaction files that you can animate easily to see what they look like. My personal interest with re_view has been it's ability to port xyz files to povray so you can not only do interesting still graphics but high quality animation using povray, dta and a .flc file player (AAPlayer). I've had alot of fun creating "molecular movies" - you can add sound files if you like. Of course the povray image files are large - I've got about 100 megs of animation at this point! I'd really like to be competent at this myself - if you run accross other programs that generate reaction state animations, or if you become well versed in generating transition states, let me know, please! I'm learning slowly, but mopac isn't the most user friendly program (It is free, however!). In the meantime, check out re_view at: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/ Have fun! "It would now be technically possible to unify the world, abolish war and poverty altogether, if men desired their own happiness more than the misery of their enemies" Bertrand Russel ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: RasWin question Date: Mon, 5 May 1997 11:50:45 +0100 To: rasmol@noc1.oit.umass.edu Dear All, I currently run rasmol on a machine running unix. I use Rasmol in tandem with a controller tcl script that communicates directly with Rasmol via a unix file pipe. In the tcl/tk language, file pipes have been ported to PCs running windows, however the behaviour of Raswin seems to be different: when I try to open rasmol on a file pipe, raswin automatically starts a controller window: is there a way of forcing raswin not to spawn this control window but accept its commnds directly from the file pipe? Jason ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Feedback from Chime Resources Date: Mon, 05 May 1997 10:29:44 -0400 To: dmix@kodak.com Cc: rasmol@noc1.oit.umass.edu, molinaro@cchem.berkeley.edu At 07:51 AM 5/5/97 -0400, you wrote: >First, thanks for providing your source code and examples. They >have been very helpful in understanding how to use Chime and the >scripting tools. > >Question for you... >Is it possible to have Chime separate a molecule (pdb file) into >separate pieces and have those pieces "come together" via a set >of move commands. I have found the define, select, and restrict >commands for operating on separate parts of the file, but I have >not been able to dissect a molecule and operate on separate pieces >simulaneously within the same Chime window. > >I would like to simulate synthesis of DNA from a template and >fragments. I considered using xyz files and an animation but >have not found a reasonable way to generate the xyz files. > >Thanks, >Dave Mix >dmix@kodak.com You are trying to move two sets of atomic coordinates independently (e.g. to dock two molecules). Unfortunately, neither RasMol nor Chime supports this, though I believe both plan to do so in the future. Marco Molinaro created a version of RasMol which does exactly this. It is very nice as far as it goes but has an unfortunate bug which limits its ability to support scripts under Windows ('zap' in a script causes a crash). You can find Molinaro's UCB RasMol at http://mc2.cchem.berkeley.edu/Rasmol/v2.6/ As for XYZ files, this has been discussed recently on the rasmol email list http://www.umass.edu/microbio/rasmol/raslist.htm to which I am copying this message. If you search the recent history, you will find links to methods for creating XYZ files. However, in order to do docking from an XYZ file in Chime, it seems to me that you would need software to save the atomic coordinates for the two molecules in a sequence of different distances. I don't believe you could do this with Molinaro's RasMol. Even for a single molecule, RasMol does not have an option to save the selected atoms as a PDB in a user-specified orientation (or even for the original origin). I hope this will be added in the future (please note Roger Sayle and Mike Hartshorn :-) ). WebLab (free, just released in version 2) does allow saving a selected atoms from a single molecule in a user-specified orientation. http://www.msi.com/ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Dalke Date: Mon, 5 May 1997 11:01:36 -0500 To: rasmol@noc1.oit.umass.edu Re: Feedback from Chime Resources Eric Martz said: > You are trying to move two sets of atomic coordinates independently (e.g. > to dock two molecules). Unfortunately, neither RasMol nor Chime supports > this, though I believe both plan to do so in the future. As a way around the problem, I was wondering if there would be any way for the Java interface to Chime to be able to transfer a new coordinate set. Thus, Java would do the work of computing the paths for the different coordinate sets, and Chime would display the results. Andrew dalke@ks.uiuc.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: RasWin question Date: Tue, 6 May 1997 12:27:00 +0100 (BST) To: cole@chemcrys.cam.ac.uk Cc: rasmol@noc1.oit.umass.edu Hi Jason, > I currently run rasmol on a machine running unix. I use Rasmol in tandem > with a controller tcl script that communicates directly with Rasmol via a > unix file pipe. In the tcl/tk language, file pipes have been ported to PCs > running windows, however the behaviour of Raswin seems to be different: when > I try to open rasmol on a file pipe, raswin automatically starts a controller > window: is there a way of forcing raswin not to spawn this control window > but accept its commands directly from the file pipe? Unfortunately the problem is one of operating system philosophy rather than programming. Unlike UNIX, programs running on the Macintosh or under Microsoft Windows do not have a "default" controlling window, i.e. there is no equivalent of an "xterm" to type commands in from. Such programs have neither an input or output pipe (indeed C programs for Microsoft Windows can't call "printf"). Unfortunately the situation is confused by "MSDOS" which does have input and output pipes. However MSDOS programs aren't allowed to create their own windows etc... There is a possible solution. It is possible to communicate directly to RasWin using Microsoft DDE to both send commands and receive information about which atoms have been clicked. Hence most programs that attempt the things you are doing use Visual Basic, Word, Excel or similar package to send commands to RasWin. In addition there are a number of potential solutions on the horizon. On UNIX, RasMol supports Tcl/Tk's "send" mechanism for sending commands between Tcl/Tk program. In theory, RasWin should support Windows Tcl/Tk's "send" mechanism. Unfortunately Windows Tcl/Tk doesn't currently implement the send command. One solution is for me to contribute the necessary patches to SUN Microsystem to implement Tcl/Tk "send" using Microsoft DDE and make any changes necessary to RasWin to support it. Another possible course of action is to finish the support for WINSOCK sockets in RasWin to behave identically to the socket support in RasMol. This mechanism also allows commands to be passed to RasMol and information on clicked atoms to be passed back. A long term goal is to allow programs to communicate with RasMol on Mac, PC and UNIX from any program (on any host) using the same mechanism. One problem with this is that Windows Tcl/Tk doesn't yet support Sockets either... [One convience of such an approach is that it allows a Java/JavaScript Object/API to be defined that allows communication to either/both Chime and RasMol on all platforms]. To conclude, Windows Tcl/Tk does a very poor job of covering up the differences between UNIX and Windows with most useful functionality not implemented. Unless this changes its best to use a Windows supported languages on PCs and UNIX supported languages under UNIX. Please let me know which of the above suggestions merits the most attention. If its urgent, I expect we could provide "send" patches for tcl/tk within a month or two. And if anyone knows what SUN's plans to "send" and/or socket support in Windows Tcl/Tk are, or knows of unofficial send/socket patches, I'd be extremely interested in hearing from them. 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 764918 X-Sun-Charset: US-ASCII ++++------+------+------+------+------+------+------+------+------+------+ From: cole@chemcrys.cam.ac.uk Subject: Re: RasWin question Date: Tue, 6 May 1997 17:09:46 +0100 To: rasmol@noc1.oit.umass.edu Dear All, Rogers more than encompassing reply to my earlier question has made me spend far to much time today trawlling the web looking for info about windows and Tcl/Tk. I've included any results of this below. If you are more the 'user' type of person of Rasmol, then I'd stop reading now. J. > Hi Jason, > > I currently run rasmol on a machine running unix. I use Rasmol in tandem > > with a controller tcl script that communicates directly with Rasmol via a > > unix file pipe. In the tcl/tk language, file pipes have been ported to PCs > > running windows, however the behaviour of Raswin seems to be different: when > > I try to open rasmol on a file pipe, raswin automatically starts a controller > > window: is there a way of forcing raswin not to spawn this control window > > but accept its commands directly from the file pipe? > > Unfortunately the problem is one of operating system philosophy rather > than programming. Unlike UNIX, programs running on the Macintosh or > under Microsoft Windows do not have a "default" controlling window, > i.e. there is no equivalent of an "xterm" to type commands in from. > > Such programs have neither an input or output pipe (indeed C programs > for Microsoft Windows can't call "printf"). Unfortunately the situation > is confused by "MSDOS" which does have input and output pipes. However > MSDOS programs aren't allowed to create their own windows etc... > I suspected as much. *I just wanted to be sure* > There is a possible solution. It is possible to communicate directly to > RasWin using Microsoft DDE to both send commands and receive information > about which atoms have been clicked. Hence most programs that attempt the > things you are doing use Visual Basic, Word, Excel or similar package to > send commands to RasWin. > > In addition there are a number of potential solutions on the horizon. > On UNIX, RasMol supports Tcl/Tk's "send" mechanism for sending commands > between Tcl/Tk program. In theory, RasWin should support Windows Tcl/Tk's > "send" mechanism. Unfortunately Windows Tcl/Tk doesn't currently > implement the send command. One solution is for me to contribute the > necessary patches to SUN Microsystem to implement Tcl/Tk "send" using > Microsoft DDE and make any changes necessary to RasWin to support it. > As you say, "send" is not directly supported in Windows Tcl/Tk. Current plans on Sun's Tcl/Tk home page seem to have swept it under the carpet, since the send command is very tied up with an X-server. Some ports are allegedly available for it though, although I've never tried them: e.g. here is a link to one: http://www.sunlabs.com/~kcorey/tcldde.html maybe I'll try it out. > Another possible course of action is to finish the support for WINSOCK > sockets in RasWin to behave identically to the socket support in RasMol. > This mechanism also allows commands to be passed to RasMol and information > on clicked atoms to be passed back. A long term goal is to allow programs > to communicate with RasMol on Mac, PC and UNIX from any program (on any > host) using the same mechanism. One problem with this is that Windows > Tcl/Tk doesn't yet support Sockets either... Sockets came into UNIX Tcl/Tk with version Tcl7.5/Tk4.1: I *think* that they have been ported to windows in later releases: I tried Tcl7.6/Tk4.2 and the commands are there (as opposed to send for example), but I've never used them in anger so this doesnt count as a full blown test. Is there somewhere where one can look to get info on UNIX rasmol's socket implementation? > > [One convience of such an approach is that it allows a Java/JavaScript > Object/API to be defined that allows communication to either/both Chime > and RasMol on all platforms]. > > > To conclude, Windows Tcl/Tk does a very poor job of covering up the > differences between UNIX and Windows with most useful functionality > not implemented. Unless this changes its best to use a Windows supported > languages on PCs and UNIX supported languages under UNIX. > Yes, but *wouldn't it be nice* to have just the one set of code: halves the job of maintenance and future development... > > Please let me know which of the above suggestions merits the most > attention. If its urgent, I expect we could provide "send" patches > for tcl/tk within a month or two. And if anyone knows what SUN's > plans to "send" and/or socket support in Windows Tcl/Tk are, or knows of > unofficial send/socket patches, I'd be extremely interested in hearing > from them. > I'm not sure which way we will go to be honest, so I cant say for me which suggestion merits most attention for me. I know that SUN are distributing PC ports of Tcl/Tk, but the home pages on the web dont give a lot away with regards to the directions they are planning to go in. I had more success looking at the WINTCL mailing list. http://www.smli.com/tcl/lists/WINTCL/index.html Best Wishes Jason ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: Hidden Chime Script Buttons Date: Wed, 7 May 1997 21:33:39 -0700 To: rasmol@noc1.oit.umass.edu I am having a lot of problems getting a hidden button (in a hidden frame) to execute. I have had no problem getting an tag to execute in a browser window with a push button, but when I create a hidden frame (no space allocated to it in the frameset) and use the immediate="true" the button will not execute. Is their a standard way to set up these "hidden" buttons that will make them execute (particulary when you are using JavaScript to write a new button to a hidden frame for immediate execution)? Thanks in advance ... Albion E. Baucom baucom@gorby.ucsc.edu UC Santa Cruz 241B Sinsheimer Labs Santa Cruz, CA 95064 (408) 920-1616 ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Hidden Chime Script Buttons Date: Thu, 08 May 1997 01:23:20 -0700 To: rasmol@noc1.oit.umass.edu Cc: chime-feedback@mdli.com At 09:33 PM 5/7/97 -0700, Albion Baucom wrote: > >I am having a lot of problems getting a hidden button (in a hidden frame) >to execute. I have had no problem getting an tag to execute in >a browser window with a push button, but when I create a hidden frame >(no space allocated to it in the frameset) and use the immediate="true" >the button will not execute. Is their a standard way to set up these >"hidden" buttons that will make them execute (particulary when you are >using JavaScript to write a new button to a hidden frame for immediate >execution)? > The only problem I am aware of in this area is in the SGI version of Netscape. If you make the chime plugin 'hidden' (using the hidden argument within the embed tag) the SGI version of Navigator never invokes the plugin, and so the button does not work. Eric has a nice JavaScript routine for sending a script to Chime, which takes care of writing the Chime button embed tag to a hidden frame, and this can be made to work on all Chime platforms by modifying it to *not* put the hidden attribute within the embed tag. (The button will still be hidden because it is within a hidden frame). Please let me know if this is *not* the problem you are seeing. -thanks, tim >Thanks in advance ... > > >Albion E. Baucom >baucom@gorby.ucsc.edu > >UC Santa Cruz >241B Sinsheimer Labs >Santa Cruz, CA 95064 >(408) 920-1616 > > ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Java interface for Chime Date: Thu, 08 May 1997 01:23:32 -0700 To: rasmol@noc1.oit.umass.edu At 11:01 AM 5/5/97 -0500, you wrote: >Re: Feedback from Chime Resources > >Eric Martz said: >> You are trying to move two sets of atomic coordinates independently (e.g. >> to dock two molecules). Unfortunately, neither RasMol nor Chime supports >> this, though I believe both plan to do so in the future. > > As a way around the problem, I was wondering if there would be >any way for the Java interface to Chime to be able to transfer a >new coordinate set. Thus, Java would do the work of computing >the paths for the different coordinate sets, and Chime would display >the results. The upcoming version of Chime does have the ability for atom coordinates to be updated. This is what the Sculpt Explorer uses to change the atom coords as the molecule is manipulated. We should be able to wrap this same mechanism up into the Chime Java interface which is also in development. Once a Java mechanism is available it should be possible to do many things, such as move multiple molecules within a chime window. Some very exciting new features are coming very soon in the upcoming beta of the new Chime. We will keep this list, as well as the Chime mailing list, posted on the developments. -tim > > Andrew > dalke@ks.uiuc.edu > > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Clicking fails to report atom in Mac Chime (bug) Date: Thu, 08 May 1997 19:26:31 -0400 To: rasmol@noc1.oit.umass.edu In case anyone else is wondering, there is a bug in Macintosh Chime 1.0 which prevents it from reporting an atom you have clicked to the messages textarea if you have a command line interface (textarea target for MessageCallBack). This may have been announced here before, but if so I forgot and am announcing it again in case others also forgot. Tim Maffett says the bug is fixed in their development version but it will be awhile before MDL can release an updated Mac version for the rest of us. The default start-up mode of Chime is 'set picking ident'. The extent to which the 'picking ident' bug affects other 'set picking' options is not known to me. There appear to be no bugs for picking ident etc. in Windows 3.1 or Windows 95 versions of Chime. You can test this by going to the demo command line interface http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm pressing the 'heme only' button, and clicking on any atom. (Smooth backbone traces can't report atoms.) A report should appear in the large box below the input box, and also on the Netscape status line (provided you leave the debugscript=on in the embed tag). More specifically, Tim says: " The mac version of Chime has the Y coordinate of the mouse inverted which it uses to identify the atom/residue when picking. If the atom is near the top of the window, and instead you click about the same distance away from the *bottom* of the window, you will get a picking ident report." So, it isn't a bug in YOUR javascript after all! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Clicking fails to report atom in Mac Chime (bug) Date: Thu, 8 May 97 17:59:58 PDT To: rasmol@noc1.oit.umass.edu Eric, I've found the clicking function works with the Mac if you hold down the Control, Option, or Command Key first, although the Mac is very stubborn to respond to the Set Picking commands. I've finally learned how to implement your javascript and find it works much better when embedded in the HTML rather than having it called as a separate *.js file. (See temporary URL: http://mentor.lscf.ucsb.edu/mcdb133-X/chapter04/hel-1.htm). I find that when downloading a web page from the server and calling a *.js file at the same time, there seems to be a critical timing factor or "instability, particularly with the Mac, that very often leads to javascript errors. These are avoided (in my case at least) when the javascript is embedded directly in the HTML. Duane At 07:26 PM 5/8/97 -0400, you wrote: >In case anyone else is wondering, there is a bug in Macintosh Chime 1.0 >which prevents it from reporting an atom you have clicked to the messages >textarea if you have a command line interface (textarea target for >MessageCallBack). This may have been announced here before, but if so I >forgot and am announcing it again in case others also forgot. Tim Maffett >says the bug is fixed in their development version but it will be awhile >before MDL can release an updated Mac version for the rest of us. > >The default start-up mode of Chime is 'set picking ident'. The extent to >which the 'picking ident' bug affects other 'set picking' options is not >known to me. There appear to be no bugs for picking ident etc. in Windows >3.1 or Windows 95 versions of Chime. > >You can test this by going to the demo command line interface > >http://www.umass.edu/microbio/chime/chimehow/fs_cmdln.htm > >pressing the 'heme only' button, and clicking on any atom. (Smooth >backbone traces can't report atoms.) A report should appear in the large >box below the input box, and also on the Netscape status line (provided you >leave the debugscript=on in the embed tag). > >More specifically, Tim says: > >" The mac version of Chime has the Y coordinate of the mouse inverted >which it uses to identify the atom/residue when picking. If the atom is near >the top of the window, and instead you click about the same distance away >from the *bottom* of the window, you will get a picking ident report." > >So, it isn't a bug in YOUR javascript after all! >-Eric >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Eric Martz, Professor (Immunology), Dept Microbiology >Morrill IVN 203, U Mass, Amherst MA US 01003-5720 >413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu >RasMol Home Page http://www.umass.edu/microbio/rasmol >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | 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 | | E-mail addresses: | | Faculty: sears@lifesci.lscf.ucsb.edu | | Academic: bioimages@lifesci.lscf.ucsb.edu | | WWW homepages: | | http://mentor.lscf.ucsb.edu/mcdb108a/ | | http://mentor.lscf.ucsb.edu/mcdb133/ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ References: <9705090059.AA13494@lifesci.lscf.ucsb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Clicking fails to report atom in Mac Chime (bug) Date: Fri, 9 May 1997 10:22:35 -0400 (EDT) To: rasmol@noc1.oit.umass.edu Excerpts from mail: 8-May-97 Re: Clicking fails to repor.. by Duane Sears@lifesci.ucsb > I've found the clicking function works with the Mac if you hold down the > Control, Option, or Command Key first, although the Mac is very stubborn to > respond to the Set Picking commands. I've found the same picking problem described by Duane, but the key commands "work around" are not reliable enough to use on a course page, e.g. for an interactive quiz. It will be great when the next version of Chime includes a fix. Another problem is the AnimFrameCallback. We wanted to show a simulated annealing sequence in connection with the NMR structure portion of a course. Some tests using the Raul E. Cachau helix unfolding sequence did not display correctly on the Mac. It worked fine on a SGI IRIX computer, however. JavaScript is used to provide a frame counter; i.e. a time indicator eventually. I don't know whether Windows will work on this, but if someone wants to try, look at: http://info.bio.cmu.edu/Courses/BiochemMols/XYZAnimJS.html I hope a fix to this problem is also included in the next Chime version. -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol email list is down Date: Tue, 13 May 1997 17:37:08 -0400 To: [270-some subscribers] Due to a hardware failure, the RasMol email list is temporarily out of service. We hope to have it back in action within a week. It is best not to send messages to the list address until the server is repaired. I'll post an announcement to subscribers via the list when it is back in service. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol email list is down Date: Tue, 13 May 1997 17:37:08 -0400 To: rbrzezin@courrier.usherb.ca, cupton@uvic.ca, michnick@BCH.UMontreal.CA, Due to a hardware failure, the RasMol email list is temporarily out of service. We hope to have it back in action within a week. It is best not to send messages to the list address until the server is repaired. I'll post an announcement to subscribers via the list when it is back in service. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: List is up again Date: Tue, 10 Jun 1997 12:33:43 -0400 To: rasmol@lists.umass.edu Cc: john@nic.umass.edu The RasMol email list has been down since May 12, 1997, due to a hardware failure. (Hope you all noticed how much you missed it! :-) It is now operational again, so feel free to send messages to the list. The list of subscribers current at the time of the failure was lost. The most recent backup I had was from February 6, 1997, and contained 276 subscribers. These 276 subscribers have been restored. Unfortunately a couple of dozen people who subscribed between 2/6/97 and the failure on 5/12/97 are no longer subscribed. If you happen to know of someone in this category, please alert them to the need to resubscribe. If you were getting your messages as a weekly digest instead of one at a time, you'll need to send (in the body of the message) set rasmol mail digest again, to listproc@lists.umass.edu As always, full information on the list, how to use it, and the message history, is at http://www.umass.edu/microbio/rasmol/raslist.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Electrostatic Potential Date: Tue, 10 Jun 1997 13:34:26 -0400 To: rasmol@lists.umass.edu >Date: Thu, 5 Jun 1997 18:21:32 +0100 (BST) >From: Sayle Dr R A >To: Steve French >cc: Eric Martz >Subject: Re: Rasmol Elpot > > >Hi Steve, >> >commands recently and I came accross the "colour dots potential command". >> >When I saw this I was overjoyed because I have been trying to map the >> >electrostatic potential of different molecules. However, when I tried >> >using this command on proteins downloaded from Brookhaven they came out all >> >red. I also tried it on some of the carotenoids I have built using >> >Chemoffice 4.0 since I have read that potentials of proteins are not able >> >to be calculated yet. The carotenoids came out as all green. > >Thanks very much for your e-mail. Unfortunately, the problem is that >RasMol cannot determine the atomic partial charges on a molecule but can >make use of them if they are provided. For example, if they are placed >in the b-factor column of a PDB file. For example, the aspirin molecule >provided in Alchemy format with RasMol has charges stored in it which can >be used to colour dot surfaces. > >Without a doubt the best way to get extremely accurate co-ordinates and >charges for small molecules is to use a program such as MOPAC. Luckily >MOPAC is included with ChemOffice 4.0 (a public domain version for MSDOS >and UNIX is also available on the Internet). RasMol's MOPAC file format >reader can automatically extract charges when these are present in a >MOPAC output file. > >I wonder if it is possible to get ChemOffice to output charges in the >B-factor column of a PDB file? > > >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 764918 > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: LAANDERSSON@vassar.edu (LAURA A. ANDERSSON) Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 14:13:20 -0400 (EDT) To: rasmol@lists.umass.edu Hi, I'm a Rasmac user and am studying catalases {tetrameric heme proteins with each of the 4 subunits having a tyrosinate-linked heme moiety}. When I open up a file like 7cat.pdb (or any of the available catalas4e x-ray files) i get only a single subunit displayed, rather than seeing the whole protein. How can I see the tetramer? thanks in advance LAA ***** Laura A. Andersson, Ph.D. Department of Chemistry Vassar College Box 589 Poughkeepsie, NY 12604-0589 (914) 437-5747 FAX: (914) 437-5732 E.mail: LAANDERSSON@vaxsar.vassar.edu ***** ++++------+------+------+------+------+------+------+------+------+------+ From: Aidan Dysart Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 14:26:43 -0400 (EDT) To: rasmol@lists.umass.edu > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalas4e > x-ray files) i get only a single subunit displayed, rather than seeing the > whole protein. > How can I see the tetramer? > thanks in advance My guess is that the file only contains the monomer. I don't know of any way to display multiple copies of the same file (or multiple files for that matter) in the same window. So, I would suggest looking for a pdb file (or other format) that contains the entire tetramer. If one doesn't exist, you could be really sneaky and try to write a program to generate the tetramer from the monomer by processing the file, but that would be alot of work. Anyway, be sure to check the Brrokhaven Protein Data Bank: http://www.pdb.bnl.gov/ +------------------------------------------+ | Aidan Dysart | | The University of Michigan | | adysart@umich.edu | | http://www-personal.umich.edu/~adysart/ | +------------------------------------------+ ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 20:28:43 +0100 (BST) To: "LAURA A. ANDERSSON" Cc: rasmol@lists.umass.edu Dear All, > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalase > x-ray files) i get only a single subunit displayed, rather than seeing the > whole protein. One resource that RasMol and Chime users may find useful is Brookhaven's database of proteins in their biological units. These files can be found at ftp://ftp.pdb.bnl.gov/user_group/biological_units/ Unfortunately, I couldn't see 7cat.pdb included in the list of files and the program I would normally use to scan for "catalase" seems to be hanging mysteriously. However I hope the above URL proves useful. 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 764918 "Re: catalase tetramer" (Jun 10, 8:28pm) References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Christopher Hogue" Subject: Re: catalase tetramer Date: Tue, 10 Jun 1997 17:17:45 -0400 To: "LAURA A. ANDERSSON" , rasmol@lists.umass.edu Cc: bryant@glowworm.nlm.nih.gov, hogue@glowworm.nlm.nih.gov Hi Laura The PDB list of biological units is, as Roger indicates, incomplete, and no effort on Brookhaven's part has been exerted to make it a complete reference or to incorporate it into their database. Instead I would point you to the EBI Mirror of PDB. You will find what you are looking for there! The EBI version of the PDB-3DB browser http://croma.ebi.ac.uk/pdb/cgi-bin/pdbmain (but not the Brookhaven version) can be used with the query 7CAT and the link "Complete MacroMolecule(s) for PDB entry 7cat" will give you the tetramer PDB file, just as you expect! Please visit the Crystal MacroMolecule Files at: http://croma.ebi.ac.uk/pdb/macmol_doc.html For details & credits. This is the most complete source regarding the creation of complete biological units of structure. Many, many thanks to the EBI structure team for this important work, and we look forward to rolling this data into MMDB's database in the future so that Cn3D will always show biological units by default. Christopher Hogue, NCBI On Jun 10, 8:28pm, Sayle Dr R A wrote: > Subject: Re: catalase tetramer > > Dear All, > > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > > When I open up a file like 7cat.pdb (or any of the available catalase > > x-ray files) i get only a single subunit displayed, rather than seeing the > > whole protein. > > One resource that RasMol and Chime users may find useful is Brookhaven's > database of proteins in their biological units. These files can be found > at ftp://ftp.pdb.bnl.gov/user_group/biological_units/ > > Unfortunately, I couldn't see 7cat.pdb included in the list of files and > the program I would normally use to scan for "catalase" seems to be > hanging mysteriously. However I hope the above URL proves useful. > > 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 764918 >-- End of excerpt from Sayle Dr R A -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Christopher Hogue, Ph.D. National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Bldg 38A 8600 Rockville Pike, Bethesda MD 20894 hogue@ncbi.nlm.nih.gov voice (301) 496-2477 x282 fax (301) 435-2433 http://www.ncbi.nlm.nih.gov/Structure ~~~~MOVING ---> July 1 to Toronto See http://www.ncbi.nlm.nih.gov/Structure/alumni.html for details as they become available. ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: catalase tetramer Date: Wed, 11 Jun 97 08:25:04 -0500 To: rasmol@lists.umass.edu 10. June, 1997 Laura, Re: > I'm a Rasmac user and am studying catalases {tetrameric heme proteins >with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalas4e >x-ray files) i get only a single subunit displayed, rather than seeing the >whole protein. > How can I see the tetramer? >thanks in advance In the REMARK section of the 7cat.pdb file, Fita and Rossmann indicate they assumed that all four monomers were indentical during the refinement of the 7cat structure. They discuss how the coordintates for the other three momoners can be generated from the coordinates of the monomer given in 7cat.pdb. They indicate that they also did the refinement without assuming the monomers are identical. The results of this refinement, with all four of the tetramers present, is deposited in the Protein Data Bank as 8cat.pdb. "Re: catalase tetramer" (Jun 10, 2:13pm) References: <01IJWS82L1AA001DO8@VASSAR.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: "Nancy O. Manning" Subject: Re: catalase tetramer Date: Wed, 11 Jun 1997 16:01:15 -0400 To: rasmol@lists.umass.edu Dear Laura, The PDB has a directory of Prepared Biologically Functional Molecules that we have individually generated based on the biological information and symmetry. While not a complete collection yet, we are working on building this up. Any requests for specific molecules will be handled,as well. Please contact the PDB Help Desk, pdbhelp@bnl.govt. While the ftp URL given by Roger Sayle is correct, you will find this index on our Web site more useful: http://www.pdb.bnl.gov/biomol.html >From our Home Page, http://www.pdb.bnl.gov, click on Searching and Browsing the PDB, then on Indexed list of prepared Biological Molecules. The 3DB Browser points to this file if it exists for a selected entry. Also, as Christopher Hogue pointed out, the EBI has prepared a complete collection of macromolecules generated from the symmetry transformations, at http://croma.ebi.ac.uk/pdb/macmol_doc.html. Regards, Nancy On Jun 10, 2:13pm, LAURA A. ANDERSSON wrote: > Subject: Re: catalase tetramer > Hi, > I'm a Rasmac user and am studying catalases {tetrameric heme proteins > with each of the 4 subunits having a tyrosinate-linked heme moiety}. > When I open up a file like 7cat.pdb (or any of the available catalas4e > x-ray files) i get only a single subunit displayed, rather than seeing the > whole protein. > How can I see the tetramer? > thanks in advance > LAA > ***** > Laura A. Andersson, Ph.D. > Department of Chemistry > Vassar College > Box 589 > Poughkeepsie, NY 12604-0589 > (914) 437-5747 > FAX: (914) 437-5732 > E.mail: LAANDERSSON@vaxsar.vassar.edu > ***** >-- End of excerpt from LAURA A. ANDERSSON -- _______________________________________________________________________ Nancy Oeder Manning Protein Data Bank Head User Support Brookhaven National Laboratory oeder@bnl.gov Biology Department, Bldg. 463 (516) 344-5744 phone P.O. Box 5000 (516) 344-5751 FAX Upton, NY 11973-5000 USA _______________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Andrey V Khavryutchenko Subject: write command disabled in scripts Date: Sun, 15 Jun 1997 18:45:39 +0200 (GMT+0200) To: rasmol@lists.umass.edu Hi! Does anyone knows what was the reason of disabling the 'write' and its equivalent 'save' commands in scripts? I'm talking about rasmol 2.6 b1 and b2, don't know about other versions. SY Andrey V Khavryutchenko akhavr@compchem.kiev.ua Std. Disclaimer: My opinions only. Don't take life too seriously, you don't get out of it alive anyway Burt Ward ++++------+------+------+------+------+------+------+------+------+------+ From: Sayle Dr R A Subject: Re: write command disabled in scripts Date: Mon, 16 Jun 1997 15:50:17 +0100 (BST) To: Andrey V Khavryutchenko Cc: rasmol@lists.umass.edu Hi Andrey, > Does anyone knows what was the reason of disabling the > 'write' and its equivalent 'save' commands in scripts? The inability to use the save and write commands in a RasMol script file is a deliberate security feature. There was a concern about the security of using RasMol on the Internet when researchers started e-mailing and FTPing 'untrusted' script files between sites. This was especially true of sites that have configured Netscape to fire up RasMol with a RasMol script file MIME type. Such a script, executed with "rasmol -script " may potentially overwrite system and user files, for example creating a "~/.rhosts" or "/etc/passwd" file on the remote machine. To defend against this threat I decided to disable the save and write commands from within RasMol, unless the command "set write true" had been explicitly typed interactively on the command line. This restriction is very similar to that for Java applets which aren't allowed to create files on a local machine from within a Java applet. This may seem like a UNIX-only feature, but malicious scripts could overwrite system files or startup files on any system. It is still possible for people to create animations using RasMol, writing out an image file for each frame. The secret is that you must interactively type "set write true" to enable writing from scripts. Of course the "set write true" command is also disabled in scripts. Note that unlike RasMol's scripting language, a large number of scripting languages (such as AppleScript, sh, csh, perl, standard Tcl, Tripos SPL, Biosym BCL, Microsoft Word etc...) are potentially unsafe and should be used with extreme caution configured as helper applications under the WWW. Another UNIX security feature is that RasMol is unable to decompress files whose filenames contain special characters. For example, a valid set of compressed co-ordinates may be stored in the file "rm *;.pdb.gz" but RasMol will refuse to read them due to the way it decompresses files. Interestingly, Chime is able to read from such files without violating security due to the way it decompresses files! 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 764918 ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: RasMol Manual Date: Mon, 16 Jun 1997 16:05:16 -0400 (EDT) To: rasmol@lists.umass.edu RasMol Users, I recently divided rasman.htm into 22 files for faster navigation in a frames or linked page format. Except for the additions listed below, very little was changed in the content or format of the original hypertext version of the Manual. The URL for viewing or downloading is: http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/RASMAIN.HTM -Will McClure >From the Introduction: The following pages were added to the frames version. 1. A two-page PDF version of the "RasMol Quick Reference Card". 2. A page illustrating the Pull Down Menu selections. 3. A Summary Table of amino acid classes. 4. Three tables that display Predefined Colors, Amino/Shapely Colors, and CPK Colors. 5. A page on Files and File Formats from the v2.5 Manual and v2.6 update. A PDP file Example page with a glossary of terms is also linked to this page. 6. The Bibliography from the v2.5 Manual with links to some of these references in the text. ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Explorer and Chime/Rasmol Date: Thu, 19 Jun 1997 12:01:30 +0100 To: rasmol@lists.umass.edu Does anyone know if the latest release of Explorer supports Chime scripts (3.0 doesn't)? Also, a user here has problems with Explorer and RasWin as a helper app. Files come across, RasWin (32bit version) opens but doesn't load the file and gives: "can't find C:\winNT\temporary file" and the image window is black. Any clues. _____________________________________________________________________ Fergus Doherty PhD Dept. Biochemistry, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH e-mail: Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 942 2225 URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Compiling Rasmol under Debian Linux 1.2.4 16 bpp Date: Fri, 20 Jun 1997 02:12:08 +0200 To: rasmol@lists.umass.edu Hi all, I tried to compile Rasmol (V2.5 I think) under Debian-Linux 1.2.4 running a 16 bpp X-Server. Everything went fine so far, except, that the program won´t start with 16 bpp color-depth. I can remember, that someone stated, that the actual version of Rasmol can be run on 16 bpp screens. Is there any known workaround, or have I messed up something (or simply forgotten to set some switch or alter something manualy)? Thanks in advance! References: <33A9CAD8.DDF7D924@rz.ruhr-uni-bochum.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Compiling Rasmol under Debian Linux 1.2.4 16 bpp Date: Sat, 21 Jun 1997 18:33:04 +0200 To: rasmol@lists.umass.edu Aww, I made a little mistake: The version is 2.62b2, that´s what the gz-file is named! -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Compiling Rasmol under Debian Linux 1.2.4 16 bpp (fwd) Date: Sun, 22 Jun 1997 13:56:42 +0200 (MESZ) To: rasmol@lists.umass.edu (to all MailingList) Forwarded message: > From owner-rasmol@lists.umass.edu Fri Jun 20 20:32:53 1997 > Delivery-Date: Fri, 20 Jun 1997 20:32:53 +0200 > Message-Id: <33A9CAD8.DDF7D924@rz.ruhr-uni-bochum.de> > Date: Fri, 20 Jun 1997 02:12:08 +0200 > Reply-To: Marc.Saric@rz.ruhr-uni-bochum.de > Sender: owner-rasmol@lists.umass.edu > From: Marc Saric > To: rasmol@lists.umass.edu > Subject: Compiling Rasmol under Debian Linux 1.2.4 16 bpp > MIME-Version: 1.0 > Content-Type: text/plain; charset=iso-8859-1 > X-Mailer: Mozilla 4.0 [en] (Win95; I) > X-Priority: 3 (Normal) > X-Listprocessor-Version: 8.1 -- ListProcessor(tm) by CREN > Content-Transfer-Encoding: quoted-printable > X-MIME-Autoconverted: from 8bit to quoted-printable by dhcp-srv2.oit.umass.edu > id OAA15502 > > Hi all, > > I tried to compile Rasmol (V2.5 I think) under Debian-Linux 1.2.4 > running a 16 bpp X-Server. > Everything went fine so far, except, that the program won=B4t start with > 16 bpp color-depth. > I can remember, that someone stated, that the actual version of Rasmol > can be run on 16 bpp screens. > > Is there any known workaround, or have I messed up something (or simply > forgotten to set some switch or alter something manualy)? > > Thanks in advance! > > Hello all, I built a 16 bit RasMol Version under linux, but rasmol shows me the following message: bash$ ./rasmol RasMol Molecular Renderer Roger Sayle, August 1995 Version 2.6 [24bit version] ... never mind it is a 16 bit version (it runs only on a 16 bit X-Server). Edit rasmol.h: /* rasmol.h * RasMol2 Molecular Graphics * Roger Sayle, August 1995 * Version 2.6 */ /*===========================*/ /* User Definable Options! */ /*===========================*/ /* #define IBMPC */ /* #define APPLEMAC */ /* #define DIALBOX */ #define TERMIOS #define SOCKETS #define MITSHM #define SIXTEENBIT /* #define MMIOLIB */ /* #define OMLCOMMS */ /* #define CEXIOLIB */ /* Use Default Depth! */ /* #define THIRTYTWOBIT */ /* #define EIGHTBIT */ /* use a sexteen bit display! */ #define SIXTEENBIT ... and recompile yout RasMol Arne References: <9706221156.AA58808@gwdu08.gwdg.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Compiling Rasmol under Debian Linux 1.2.4 16 bpp (fwd) Date: Mon, 23 Jun 1997 15:14:18 +0200 To: rasmol@lists.umass.edu Thanks for the answer! Arne Mueller wrote: > > Edit rasmol.h: > /* #define IBMPC */ (..) > #define SIXTEENBIT (..) > /* use a sexteen bit display! */ > #define SIXTEENBIT > > ... > > and recompile yout RasMol Have done that (i.e. like it is stated in the INSTALL-text:[1] xmkmf, [2] edit rasmol.h, [3] make), but it didn´t worked. Then I tried to edit the Imakefile (there is also an #define -DEIGHTBIT (or -DTHIRTYTWOBIT), so I replaced it with -DSIXTEENBIT, compiled it and-- it worked! There are still some problems though: During compilation, I got some error messages stating something about -DSIXTEENBIT (have forgotten the exact reading, if you or someone else need it, I will look it up). Inspite of this, the program starts when typing "rasmol" at the prompt. When I load an *.pdb (tried the famous 1crn.pdb for a start) and try to display it as ribbon with colours set to "temperature" it gives me some weird colormapping (this does not happen with every color option -"cpk" or "structure" works fine most of the time). I use Afterstep as default window-manager, this one is known to take up many colors for its high-color-icons and bitmaps -could this be the reason for the color problems of 16-bit-rasmol?? Another thing is, that the border of the graphics-window is brown -realy ugly :-) Even if this is not of great importance, it would be nice to have another color (grey for example :-). Where can I change this (or is this my fault (i.e. something in my libraries or so))?? -- Bye, Marc Saric Visit http://www.rat.de/marc_saric/ ++++------+------+------+------+------+------+------+------+------+------+ From: Slaton Lipscomb Subject: displaying 2D models and slabbing on Mac Date: Mon, 23 Jun 1997 21:41:11 -0800 To: rasmol@lists.umass.edu I have a couple of questions for the Chime experts out there. First, I have not found in the Chime documentation how to display a molfile in 2D rendering. This is an option in the MDL menu that is only available for molfiles (not for pdb). However there is no option for this in the display3d or options3d attributes for the element. Does anyone know an attribute for to have a molfile Chime model initially displayed in 2D rendering? Second, I have been unable to get the slabbing mouse/keystroke combination to work in Chime for the Macintosh. I have tried this on several different machines. According to the Chime and Rasmol documentation I have seen, ctrl is the key to hold down to engage slabbing with the mouse button held down over a Chime model (on Windows I believe it is ctrl-left click). When I hold down ctrl, mouse-click, and try to rotate the model, the model is frozen and occasionally rotates in sporadic twitches. This is a completely different effect from the engagement of slab plane from the MDL menu (and completely useless). Does anyone know the correct keystroke for slabbing on the Mac? Or does anyone's experience contradict mine? Thanks for your experise. Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://www.cabrillo.cc.ca.us/c4/ ++++------+------+------+------+------+------+------+------+------+------+ From: Randy Bumgardner Subject: Re: displaying 2D models and slabbing on Mac Date: Tue, 24 Jun 1997 15:26:11 -0700 To: rasmol@lists.umass.edu At 10:41 PM 6/23/97 -0700, you wrote: >I have a couple of questions for the Chime experts out there. > >First, I have not found in the Chime documentation how to display a >molfile in 2D rendering. This is an option in the MDL menu that is only >available for molfiles (not for pdb). However there is no option for >this in the display3d or options3d attributes for the element. >Does anyone know an attribute for to have a molfile Chime model >initially displayed in 2D rendering? > Correct, there is no 2D attribute for the embed tag. Chime will display a molfile in two dimensions if the coordinates for the structure are 2D, ie, if the z coordinate is zero. This occurs if the structure is created in a drawing program, ISIS/Draw for example, and exported as a molfile. > >Second, I have been unable to get the slabbing mouse/keystroke >combination to work in Chime for the Macintosh. I have tried this on >several different machines. According to the Chime and Rasmol >documentation I have seen, ctrl is the key to hold down to engage >slabbing with the mouse button held down over a Chime model (on Windows >I believe it is ctrl-left click). When I hold down ctrl, mouse-click, >and try to rotate the model, the model is frozen and occasionally >rotates in sporadic twitches. This is a completely different effect from >the engagement of slab plane from the MDL menu (and completely useless). >Does anyone know the correct keystroke for slabbing on the Mac? Or does >anyone's experience contradict mine? > To move the clipping plane through the structure while in slab mode, the keystroke/mouse combination is '/left mouse button' for Windows, and '/mouse button' for the Mac. Slab mode must be selected from the Chime menu, and both the mouse button and the () key must be held down during the movement. On the Mac, a slight rotation does occur while moving the clipping plane. > >Thanks for your experise. > >Slaton Lipscomb >C4: Computers in Chemistry at Cabrillo College >http://www.cabrillo.cc.ca.us/c4/ > Randy **************************************************** Randy Bumgardner MDL Information Systems (510) 895-1313, ext. 1172 Voice:(510) 357-2222, x1172 randyb@mdli.com **************************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Harry Ungar Subject: New Chime Tutorial Date: Tue, 24 Jun 1997 21:17:04 -0400 (EDT) To: rasmol@lists.umass.edu I invite all members of this list who use Netscape Navigator to take a look at our just completed "Chime Tutorial" at www.cabrillo.cc.ca.us/C4. This self-guided tutorial, created for beginning students, specifically shows how to use Chime molecular models and gives students a few glimpses into the potential power and beauty of molecular modeling. We hope that you will recommend the tutorial to your students, that you will link your web pages to it, and/or that you will download it for use on your own computers. This tutorial is the first product of C4 (Computers in Chemistry at Cabrillo College) and is supported by a grant from the National Science Foundation. All future C4 software will also be distributed over the World Wide Web so that it will immediately be available to everyone interested in using it. All C4 software can be used and reproduced without cost, provided it is for non-commercial purposes only. Harry Ungar C4: Computers in Chemistry at Cabrillo College 6500 Soquel Dr. Aptos, CA 95003 408-479-5059 http://www.cabrillo.cc.ca.us/CWIS/AcademicPrograms/BECHO/Chemistry/organic/i ndex.html. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime problems in 'secure' student computer labs Date: Fri, 27 Jun 1997 17:26:01 -0400 To: rasmol@lists.umass.edu Cc: stolle@cs.umass.edu, bbotch@chem.umass.edu, sbrewer@bio.umass.edu Dear Chimeleons: I'd like to find out how many student computer labs can't run my javascript-laden Chime tutorials, notably http://www.umass.edu/microbio/chime/protsecs (Protein Secondary Structure) and http://www.umass.edu/microbio/chime/dna (the AT or GC base pair buttons are good ones to test here as they use lots of javascript) If you can run these two tutorials on your private computer but not on the computers in your student lab(s), I'd like to know. Also if you have time I'd like to know: in what way does the tutorial fail to work properly or what error message(s) occur? Are you using macs or windows? What kinds of security precautions/software might be responsible? (Ask your lab installation manager.) If you get the same 'cannot open' error message I get, you might try going into the debug mode and seeing what exactly Chime reports it 'cannot open'. I've recently learned that such problems occur in our Chemistry Department's student computer lab. In our case, as I understand it, the security precautions employed are not Netscape Options menu items (such as disabling javascript), but rather some kind of security program is running in the background and intercepting operations deemed dubious. The effect is that when one attempts to run these tutorials, a "Javascript Alert" message occurs frequently reporting a "cannot open" message from Chime. I haven't yet been able to diagnose whether this message is real or a spurious symptom of problems I didn't anticipate when I wrote the code. But it doesn't happen on computers outside the student lab (which don't have the same security measures). My tutorials utilize javascript "cookies" to remember the states of variables between different Netscape windows. Cookies are saved by writing a file to disk. Cookie writing may be what is being intercepted. (A common use of cookies is to remember the contents of a shopping cart at a commercial website.) In any case, I'd like to assess the magnitude of the problem and if large, then work on solutions. For example, if cookies are the problem, I may be able to use global variables instead. (I had trouble figuring out how to do that which is why I resorted to cookies. In particular I could not figure out how to assign a name to the initial/default Netscape window, hence could not reference its variables from other windows.) I'll summarize the replies I get and post the summary to this list. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime problems in 'secure' student computer labs Date: Fri, 27 Jun 1997 18:47:31 -0400 To: rasmol@lists.umass.edu Cc: stolle@cs.umass.edu, bbotch@chem.umass.edu, sbrewer@bio.umass.edu Dear Chimeleons: With regard to my recent request about to finding out how many student computer labs can't run my javascript-laden Chime tutorials, please >>> use Netscape 3.01 ONLY <<< if you run such tests. We already know that some plug-in bugs were fixed since Netscape 3.00, and that Netscape 4 does not yet work as well as 3.01 with Chime, and that Internet Explorer works poorly with Chime. See recent history of this list for more details on these issues. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-1578 emartz@microbio.umass.edu RasMol Home Page http://www.umass.edu/microbio/rasmol - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <3.0.1.32.19970627172601.00685bac@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: William R Mcclure Subject: Re: Chime problems in 'secure' student computer labs Date: Mon, 30 Jun 1997 12:51:53 -0400 (EDT) To: rasmol@lists.umass.edu Excerpts from mail: 27-Jun-97 Chime problems in 'secure' .. by Eric Martz@microbio.umas > I'd like to find out how many student computer labs can't run my > javascript-laden Chime tutorials, notably > > http://www.umass.edu/microbio/chime/protsecs > (Protein Secondary Structure) > > and > > http://www.umass.edu/microbio/chime/dna > (the AT or GC base pair buttons are good ones to test here as they use lots > of javascript) > The .../dna page works fine on our student Macs. The .../protsecs has the same button problems from a few months ago. Is there a problem with allowing "resizing" in this frameset? As I recall, you wanted to keep the preset proportions as a model for lecture display where the image should be the main feature. But if resizing were allowed in the Web version, it would add some desirable flexibility in the viewing. -Will ++++------+------+------+------+------+------+------+------+------+------+ From: "Craig T. Martin" Subject: Several questions Date: Mon, 30 Jun 1997 17:53:05 -0400 To: rasmol@lists.umass.edu I have three questions for the Rasmol group: 1) In CHIME, is it possible from a single HTML embed call (eg., when setting up a window, as in the code below) to load a .pdb file and then run a script from an external file? I can embed the script within the call, but I would prefer to have a separate script file called "Reset.spt" which both initially sets up the view and can be called by a reset button (yes, I know that one could simply reload the structure, but I'm looking for something more elegant). I could load the molecule from within the script, but I have not been able to set up a CHIME window with reference to only a script. 2) I always compress my PDB files with GZIP (on the Mac) and then upload them (binary xfer) to my Unix server. Works great. However, those same "zipped" files are not recognized by CHIME if I load them directly from my local (Mac) disk. Is this a "feature"? 3) In a HTML file which both initializes a JavaScript function (via a call to an external text file) and loads a structure into the same frame, I occasionally get the JavaScript text loading into the CHIME window instead of the structure. The HTML file looks like the following: ----------------- Load Structure