From d3f012@gator.pnl.gov Tue Dec 29 02:05:17 1992 Date: Tue, 29 Dec 92 10:05:17 PST From: d3f012@gator.pnl.gov Subject: Graphics Packages To: chemistry@ccl.net Message-Id: <9212291805.AA16353@gator.pnl.gov> Does anyone know of any chemistry graphics packages available for PC compatibles? I'm specifically interested in something like an editor for building molecules, etc. More extensive capabilities would be nice, but are not necessary. Source code availability would be great. I'm interested in learning about commerical, academic, homegrown, basically anything that's out there. Also anything written for Unix systems that has a halfway decent chance of being ported to PC's would be interesting as well. It can run under Windows, DOS, OS/2, anything goes. I am already aware of HyperChem. Please respond directly to me. I will post a summary of what I learn. Thanks. Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From hogue@mosquito.den.mmc.com Tue Dec 29 05:44:30 1992 Date: Tue, 29 Dec 92 12:44:30 MST From: hogue@mosquito.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9212291944.AA00276@mosquito.den.mmc.com> To: chemistry@ccl.net Subject: Thesis problems Dear Netters (especially thesis advisors): I need some third party advice. My thesis is turning out to be full of negative results and I'm not sure what to do. The aim of my thesis was to try to explain the reacitivity of perfluoropolyether (PFPE) oil on 440C steel alloy gears. Here it is in a nut shell: I used diethylamine and pyridine as Lewis base probes to measure the strength and amount of Lewis acidity on powders of reagent grade AlN, Al2O3, BN, B4C, Fe, Fe2O3, MgO, Cr, CrO3, Mo, MoO3, Ni, NiO, SiC, Si3N4, TiB2. Lewis acid amount and strength was determined by the temperature and area under the desorption curve using Differential scanning calorimetry. There is not a good correlation between acid strngth or amount and the temperature at which PFPE oil reacted (exothermed). For example B4C reacted but didn't absorb any DEA or pyridine. Next I used AM1 or CNDO to model the variuos molecules, taking the elements as dimers. There is no good correlation between PFPE reactivity and any of the model outputs (e.g., HOMO, HOMO/LUMO gap, dipole moment, polarizability, or interaction with a cavity made of the substrate molecules). The model results compared favorably with handbook values though. Lastly I modelled fully fluorinated versions of dimethyl ether and diethyl ether. Some weak bonds did become apparent. I put the two together to make a dimer and one more diethyl group to make a trimer. At first glance there are weak points in this short PFPE "polymer" that look like candidates for chain cleavage. Any ideas or comments will be greatly appreciated. Pat Hogue From mwd@ferris.cray.com Tue Dec 29 09:07:37 1992 From: mwd@ferris.cray.com (Mark Dalton) Message-Id: <9212292107.AA02993@snoid.cray.com> Subject: RE: Graphics Packages display 3D structure To: chemistry@ccl.net Date: Tue, 29 Dec 92 15:07:37 CST This was posted on Bionet.molbio.proteins Here is a the list: _______________________________________________________________________ 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 -- Mark Dalton Cray Research, inc 655-E Lone Oak Dr. Eagan, MN 55121 Internet: mwd@cray.com Phone: (612) 683-3035