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 tw