>From usenet.ucs.indiana.edu!news.cs.indiana.edu!mips!sdd.hp.com!wupost!bcserv!eric Wed Aug 5 07:46:05 EST 1992 Article: 367 of bionet.software Path: usenet.ucs.indiana.edu!news.cs.indiana.edu!mips!sdd.hp.com!wupost!bcserv!eric >From: eric@bcserv.wustl.edu (Hugo (Eric R.)) Newsgroups: bionet.software Subject: PDB file viewers for MSDOS machines (SUMMARY-long) Date: 5 Aug 92 12:05:05 GMT Organization: Washington University in Saint Louis, MO USA Lines: 124 Message-ID: NNTP-Posting-Host: bcserv.wustl.edu Summary: Information on protein data bank file viewers Keywords: pdb, molecular modeling, protein structure A week ago I posted a request for programs (MSDOS and or Windows 3.x) that would allow one to view and manipulate Brookhaven Natl. Lab. Protein Data Bank files (.pdb files). The following text is a summary of the responses. Of the answers I received one set of programs was mentioned that is available by anonymous ftp. These are shareware programs written at the University of Illinois and distributed by Dr. A.R Croft. These programs (pdViewer and PSAAM) are written in Visual Basic and run under Windows 3.x. I've just downloaded them and am in the process of evaluating them. The two programs can be obtained from nemo.life.uiuc.edu (128.174.183.6) in the pub/pdvwin and the pub/psaam subdirectories by anonymous ftp. Thanks to all of the individuals that responded to my query, the information was greatly appreciated. Eric ;-) SUMMARY INFORMATION: Tom Branham writes: I do know of a commercial program called HyperChem from Autodesk for which the educational price is $600, but they do have a full free to researchers program (if you keep them updated on your work, etc.) The program is not only a visual interface, but performs molecular orbital calculations and molecular dynamics. I have been very tempted to take them up on the research program, but the one thing worrying me is that it comes with a hardware key and I have serial ports that are not well behaved. If anyone else comes up with any other sugestions I would appreciate hearing about them, as I am running Quanta at the lab, on our SGI's, and then I am working with my own programs, lotus123 and Mathcad at home on the pdb files, but can not view them at home, a minor irritation. I also purchase the programs on my own rather than with lab moneys. I like to feel that I do not "live off " the lab grants, perhaps a sense of hubris I REally can not afford this month :) ........Tom Branham P. S. Dr. Pochapsky brought back the PDB and Atlas of sequences from the same meeting. Wasn't that a Nice suprise.....? Watson Ko writes: Alchemy III will do the job you want, but it will be very slow if you try to rotate(or whatever) since the program has to redraw the whole molecule. What I did was just showing the active site of the specific enzyme(or protein) and manipulated the molecule. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Watson Ko v999r36x@ubvms.cc.buffalo.edu Space, the final ... parking place! =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Jim Cassatt writes: I have been using a shareware version of PCMODEL. Check previous messages regarding availability. Included are two sample files for chymotrypsin and B-DNA obtained from the PDB. They can be viewed quite effectively with a 486, less so with a 386SX and poorly with an 8088. What I have not been able to find out is whether a program to convert PDB format to PCMODEL format is available. The main difficulty is generating a connect table. There are also two versions of PCMODET, one a shareware version and the other distributed by Gilbert at Indiana. His version does not have a conversion program. I awaiting a response from the author of the shareware program. Jim Cassatt Dr. Ferenc Czegledy writes: There are several ways that I know of to visualize PDB files in the MS-DOS environment: >>>1. Using pdViewer which one can obtained by anonymous ftp from >>>nemo.life.uiuc.edu >>>The package must be transferred using the binary protocol and runs >>>under Windows 3.1/3.0. 2. Using a package called Alchemy III (for Windows) which is available from Tripos Assoc. Inc. ,St. Louis, MO. Phone: 314-647-1099. 3. Using Chem-X from Chemical Design Inc., 200 Route 17 South, Suite 120, Mahwah, NJ 07430. phone: 201-529-3323. I have only seen the brochure for this package but it looks very impressive. The only problem is that it is very expensive: ~ $ 2,500.00/year. The software will self-destruct after 1 year but if you pay for an additional year the software is upgraded for you. Anyway, good luck and tell me if you hear of any additional approaches to visualization and modeling on the PC. -- Ferenc Czegledy Dept. Of Cardiology Columbia University 630 W 168th Street New York, NY 10032 email: ferenc@cucrd0.med.columbia.edu Rhee Hwan-Seok writes concerning the program MOBY The following is the snail-mail address of MOBY manufacturer. In my address file they have no e-mail address known. ---------------------------- Springer-Verlag Heidelberger Platz 3 W-1000 Berlin 33 F.R.G ( Germany ) Telex : 461723 Telefax : (06221)413982 ---------------------------- They will send you a demo disk FREE of charge. And the disk could be 3" or 5" on your request. e-mail : hyunerho@krsnucc1.BITNET -- Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu Dept. of Biochemistry and Molecular Biophysics| Washington University School of Medicine | Box 8231, St. Louis, MO 63110_________________| (314) 362-3342