From yama@molbio.ethz.ch Wed Oct 20 11:56:20 1993 From: Bernhard Anton Pabsch Date: Wed, 20 Oct 93 10:56:20 +0100 Message-Id: <9310200956.AA19820@noldi> To: chemistry@ccl.net Subject: GRASP Dear netters, in the last two days on the LATSIS Symposium in Zurich on Horizons in Structural Biology I learnd about the program GRASP from W Hendrickson. Is that program publicly available by ftp? Thanks for listening bap __________________________________________________________________________ Bernhard A. Pabsch yama@molbio.ethz.ch Laboratorium fuer organische Chemie MOM_10@CZHETH5A.bitnet ETH Hoenggerberg (HPM G32) Tel. ++41 1 377 34 89 CH-8093 Zuerich/Switzerland Fax ++41 1 372 00 53 __________________________________________________________________________ From bewilson@Kodak.COM Wed Oct 20 04:15:25 1993 Date: Wed, 20 Oct 93 08:15:25 -0400 Message-Id: <9310201215.AA18545@Kodak.COM> From: bewilson@Kodak.COM (Bruce E. Wilson, Eastman Chemical Company, (bewilson@kodak.com)) To: "chemistry@ccl.net"@Kodak.COM Subject: Gaussian for Windows, followup to Doug Smith's comment > Bottom line -- the product is excellent! Very good, yes. Useful, yes. Excellent, not quite (IMO). Superior value for the money, absolutely. > The windows interface is nice. No molecular graphics, but a nice GUI for > job setup and control. It is pretty intuitive, and really does not require > that you read the manuals. I use either the AVS Chemistry Viewer or > Hyperchem 3.0 for my molecular graphics. On the one hand, what to I expect for $600, but the lack of molecular graphics is a real limitation. Hyperchem and AVS viewer are not cheap (and I say that both as an industrial chemist and as an adjunct professor). This is the biggest problem I've got in terms of helping students use the program, because right now we don't have a good way to get structures in, and analyzing the data out is not much better than 1960's technology. > It does not substantially affect Windows and other applications when running > in the background, so I can use Word, Excell, even HyperChem graphics > without G92 stealing so much time that seconds elapse between my mouse > click and an action. I'll dispute the point. I run it on a 50 MHz 486DX2 with something like 600 Mb of hard drive space. Word and Excel are sort of useable underneath Gaussian, but not if you want to do more than play around with a simple memo. However, the pause feature of Gaussian does work nicely, so what I've done for longer jobs is simply to pause them when I want to do something interactive with the computer, and then resume them when I'm done. That part seems to work like a charm. > If I was limited in money and resources, I would definitely buy and use > G92 for Windows. Now, if someone could provide a cheaper way to get structure in and look at them out, that would be even better. Particularly for understanding the frequency mode calculations. Bruce Wilson (bewilson@kodak.com) Senior Research Chemist, Eastman Chemical Company Adjunct Professor, East Tennessee State University From mike@si.fi.ameslab.gov Wed Oct 20 04:18:14 1993 From: mike@si.fi.ameslab.gov (Mike Schmidt) Message-Id: <9310201418.AA46091@si.fi.ameslab.gov> Subject: sym bug in GAMESS To: chemistry@ccl.net (OSC list) Date: Wed, 20 Oct 93 9:18:14 CDT The symmetry orbital code used in GAMESS from March '92 to Nov '92 contained a mistake in the treatment of the e representations of those groups whose e characters are complex numbers. Two such groups are Th and C3. Since Nov '92 a fix provided by Michel Dupuis has corrected the problem, and now calculations done in these groups are correct. Anyone interested in obtaining the fix should contact me at mike@si.fi.ameslab.gov. Mike Schmidt From h.rzepa@ic.ac.uk Wed Oct 20 15:09:29 1993 Message-Id: <9310201511.AA10529@cscmgb.cc.ic.ac.uk> Date: Wed, 20 Oct 1993 15:09:29 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Accurate masses to mol formula Does anyone know of a semi-intelligent program to do this? We have a quick and easy one written for PC, but it constantly offers "unreasonable" formulae, ie with 17 oxygen atoms, or 19 sulfurs etc etc in addition to the correct ones. It also does not handle metals and other elements more commonly found. (I dont want the other way around, from formula to acc mass, for which there are plenty of programs!). Many thanks. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.4, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From h.rzepa@ic.ac.uk Wed Oct 20 15:12:11 1993 Message-Id: <9310201513.AA10631@cscmgb.cc.ic.ac.uk> Date: Wed, 20 Oct 1993 15:12:11 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: IVS 3.2 (Videoconferencing) Is anyone using IVS with graphics card and camera for videoconferencing? We have a set up, and would love to try abroad. This thing peaks at about 200 kbits/sec, so it should be used with care. I have no idea if IVS is compatible with other such programs, but it certainly works across platforms (we have tried SGI to Sun etc). Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.4, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From CLETNER@DESIRE.WRIGHT.EDU Wed Oct 20 06:43:43 1993 Date: Wed, 20 Oct 1993 11:43:43 -0500 (EST) From: CLETNER@DESIRE.WRIGHT.EDU Subject: M/M of Protein To: chemistry@ccl.net Message-Id: <01H4C1EIAHMQ002WL6@DESIRE.WRIGHT.EDU> Hello all, I'm doing some molecular mechanics of small proteins, <100 A.A.. It isn't clear to me at what point I should concider the minumum reach a reasonable min. for the starting structure. Is it good enough to use .5 kcal/mol as the cutoff point or does that value need to be lower/higher? Also, what critera are important in deciding at what level to set this value? Thanks Charles Letner Department of Biochem. and Mol. Bio. Wright State University Dayton, OH 45435 e-mail: cletner@desire.wright.edu From krystek@alcor.bms.com Sun Oct 20 07:59:15 1993 Date: 20 Oct 1993 11:59:15 -0400 From: krystek@alcor.bms.com (Stanley Krystek) Subject: GRASP To: chemistry@ccl.net Message-Id: <9310201559.AA22791@alcor> GRASP is available from Anthony Nicholls at Columbia at E-mail nicholls@cuhhca.hhmi.columbia.edu. There is a small charge for the program but i can say it is well worth it. Anthony also responds to E-mail questions wich is a help in getting started. stan Stanley R. Krystek, Jr., Ph.D. Bristol-Myers Squibb Pharmaceutical Research Institute Department of Macromolecular Modeling P.O. Box 4000, Room H.3812, Princeton, N.J. 08543-4000 (609) 252-4100 FAX: (609) 252-6030 INTERNET: krystek@bms.com From youkha@iris75.biosym.com Wed Oct 20 03:19:19 1993 Date: Wed, 20 Oct 93 10:19:19 -0700 From: youkha@biosym.com (Philippe Youkharibache) Message-Id: <9310201719.AA29506@iris75.biosym.com> To: chemistry@ccl.net, Bernhard Anton Pabsch Subject: Re: GRASP >From: Bernhard Anton Pabsch >Dear netters, > >in the last two days on the LATSIS Symposium in Zurich on Horizons in >Structural Biology I learnd about the program GRASP from W Hendrickson. >Is that program publicly available by ftp? The program GRASP was written by Anthony Nicholls at Columbia. Although he is in the same department of Wayne Hendrickson, Wayne is just a user of GRASP. Anthony has set up an anonymous ftp account with 20 or so grasp pictures, with notes illustrating what the program can do, as well as an demo version. Its at cumbnd.bioc.columbia.edu (128.59.96.103). Anthony Nicholls can be reached at nicholls@cuhhca.hhmi.columbia.edu ************************************************************************** Dr. Philippe Youkharibache e-mail: youkha@biosym.com Biosym Technologies Inc. 9685 Scranton Road tel: (619) 546 5562 San Diego, CA 92121 fax: (619) 458 0136 ************************************************************************** From cramer@maroon.tc.umn.edu Wed Oct 20 07:41:40 1993 Message-Id: <0012cc57855023133@maroon.tc.umn.edu> From: Christopher J Cramer Subject: A priori prediction of 13C NMR Spectra To: chemistry@ccl.net Date: Wed, 20 Oct 93 12:41:40 CDT For a colleague -- Is anyone aware of a good (and cheap would be nice) program to predict 13C NMR spectra based on structure alone (no quantum chemistry here). My colleague has in mind something like the method described in Bremser et al.'s book "Chemical Shift Ranges in 13C Spectroscopy" which assigns chemical shift based on environment, connectivity, etc., but is quite complicated to plow through by hand. I will be happy to summarize responses for the net. Please don't tell me about IGLO approches, etc. While they interest me, they are not what the customer is looking for. CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 cramer@maroon.tc.umn.edu From cramer@maroon.tc.umn.edu Wed Oct 20 08:10:15 1993 Message-Id: <0012cc57f07001893@maroon.tc.umn.edu> From: Christopher J Cramer Subject: American Chemical Society gopher (fwd) To: chemistry@ccl.net Date: Wed, 20 Oct 93 13:10:15 CDT This is an outstanding idea whose time is long overdue. Perhaps this will marginally slow down the proliferation of journal pages . . . > Date: Tue, 19 Oct 1993 17:53:13 -0500 (EST) > From: "Gary Wiggins, Indiana U. Chem. Lib., 812-855-9452" > > Subject: American Chemical Society gopher > Sender: CHEMICAL INFORMATION SOURCES DISCUSSION LIST > To: Multiple recipients of list CHMINF-L > Reply-to: CHEMICAL INFORMATION SOURCES DISCUSSION LIST > Message-id: <01H4B0J05NTEB7BQ9F@vx.cis.umn.edu> > X-Envelope-to: j-kemp@VM1.SPCS.UMN.EDU > Content-transfer-encoding: 7BIT > X-To: chminf-l@iubvm.ucs.indiana.edu > > There is now an American Chemical Society Gopher located at: > acsinfo.acs.org (port 70). > It contains supplementary material pages from the Journal of the > American Chemical Society from the beginning of 1993. Also: > > Copyright transfer form > Instructions for authors of the 24 peer-reviewed ACS journals. > --Gary Wiggins, Indiana University Chemistry Library > I have accessed this gopher, which currently only has volume 115 of JACS. The promise is that all Supplementary Material will be both ASCII and TIFF format (and that it will expand to other journals?). I can't seem to get my Word 5.0 to accomplish the TIFF conversion, but the README file on the gopher lists a number of pieces of software to do this, two of them available via anonymous FTP. This will really improve access to Suppl. Matl., and hopefully encourage its greater use for details which are critical to reproducibility, but of less than stellar interest otherwise. -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 cramer@maroon.tc.umn.edu From ross@cgl.ucsf.EDU Wed Oct 20 10:57:04 1993 Date: Wed, 20 Oct 93 17:57:04 -0700 Message-Id: <9310210057.AA19302@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: another free mol viz pkg I just spotted this on bionet.biology.computational. I haven't tried it. Bill Ross From: rasmol@dcs.ed.ac.uk (RasMol Molecular Graphics) Subject: RasMol 2.2 Molecular Graphics Package Available Keywords: RasMol, RasWin, molecular graphics Date: 14 Oct 93 16:55:43 GMT RasMol 2.2 Molecular Graphics Visualisation tool. Roger Sayle Biocomputing Research Unit University of Edinburgh October 1993 This posting is to announce the public release of RasMol 2.2 molecular graphics visualisation program. This package has been developed in the BRU over the last few years, and the latest version has a significant number of improvements over RasMol 2.1. These enhancements include protein ribbon diagrams, secondary structure assignment (based on Kabsch and Sander's DSSP algorithm), better amino acid classification, DNA hydrogen bonding, DNA backbone representations, stick representations of hydrogen bonds and disulphide bridges (either between backbone or sidechains), the ability to write out selected atoms to a PDB file, support for Alchemy format files, colouring of hbonds by their type, compressed PostScript output, extended atom expression syntax, increased scroll bar functionality, and many more additions (and bug fixes) too numerous to mention. For a complete list of modifications (and acknowledgements), refer to the distribution ChangeLog. RasMol is an X Window System tool intended for the visualisation of proteins and nucleic acids. It reads Brookhaven Protein Databank (PDB) files and interactively renders them in a variety of formats on either an 8bit or 24/32bit colour display. The complete source code and user documentation for both the UNIX/X11 version and the IBM PC/MS Windows 3.1 version may be obtained by anonymous ftp from ftp.dcs.ed.ac.uk [129.215.160.5] in the directory /pub/rasmol. The UNIX/X11 source code is contained in the file RasMol2.tar.Z and the MS Windows source code and executable in the file raswin.zip. Both of these files include a slightly dated version of the PostScript user reference manual. The program is intended for teaching and generating publication quality images. The program has both a menu system and a full featured command line interface. Different parts and representations of the molecule may be coloured or displayed in a number of formats independently. Currently supported formats include wireframe, ball and stick, backbone, space filling spheres and protein ribbon models. The space filling spheres may even be shadowed. The molecule may be manipulated using scroll bars, the interactive command line or from a dials box if attached. The resulting image may be saved at any point in PostScript, GIF, PPM, Sun rasterfile or Microsoft BMP formats. For more details see the RasMol user reference. It was claimed at a recent conference to be the fastest available uniprocessor program for drawing shadowed spacefilled molecules. On a SparcStation it can shadow a 10,000 atom protein in less than 10 seconds. The current version of the program has been tested on sun3, sun4, sun386i, hp9000, sequent, DEC alpha, IBM RS/6000 and SGI, DEC and E&S mips based machines compiled under both gcc and the native compiler. The version for Microsoft Windows requires version 7 of the Microsoft Optimizing C Compiler and the Microsoft Software Development Kit (SDK). The source code is public domain and freely distributable provided that the original author is suitably acknowledged. Any comments, suggestions or questions about the package may be directed to "rasmol@dcs.ed.ac.uk". Roger Sayle JANET: ros@uk.ac.ed.dcs Department of Computer Science UUCP: ..!mcsun!uknet!dcs!ros University of Edinburgh ARPA: ros%dcs.ed.ac.uk@nsfnet-relay.ac.uk Edinburgh EH9 3JZ, UK. Tel: (+44) 031 650 5163 (direct line) ---