From mckelvey@Kodak.COM Fri Feb 18 10:25:18 1994 Received: from Kodak.COM for mckelvey@Kodak.COM by www.ccl.net (8.6.4/930601.1506) id KAA26509; Fri, 18 Feb 1994 10:04:03 -0500 From: Received: from NTPROF.DECnet MAIL11D_V3 by Kodak.COM (5.61+/2.1-Eastman Kodak) id AA16489; Fri, 18 Feb 94 10:04:56 -0500 Date: Fri, 18 Feb 94 10:04:51 -0500 Reply-To: mckelvey@Kodak.COM Message-Id: <9402181504.AA16489@Kodak.COM> To: osc@Kodak.COM Subject: PSEUDOPOTENTIALS FOR THE BORON-IODINE SUBBLOCK NETTERS: RECENTLY SOMEONE INQUIRED CONCERNING HALOGENS, BASIS SETS AND PSEUDOPOTENTIALS. A SUGGESTION: Mol Physics V80 p1431-1441 (1993). Here the authors provide potentials and optimised bases for the 4x5 boron-iodine subblock.. For the chalcogens and halogens there are also optimised diffuse functions for anionic occasions. The valence orbitals are over 4 primitives, so contract as you see fit. John McKelvey Eastman Kodak From pmr1716@ggr.co.uk Fri Feb 18 10:52:11 1994 Received: from gate.ggr.co.uk for pmr1716@ggr.co.uk by www.ccl.net (8.6.4/930601.1506) id JAA26377; Fri, 18 Feb 1994 09:38:05 -0500 Received: from mailhub.ggr.co.uk by gate.ggr.co.uk; Fri, 18 Feb 1994 14:36:22 GMT Received: from ukwbf07 by mailhub.ggr.co.uk; Fri, 18 Feb 1994 14:33:49 GMT Received: from localhost by ukwbf07 (8.6.4/imd160294) id OAA04653; Fri, 18 Feb 1994 14:45:25 GMT Date: Fri, 18 Feb 1994 14:45:23 +0000 (GMT) From: Murray-Rust Dr P Subject: Substructure search software To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'd be grateful for any information about publicly available routines for substructure searching. Ideally the software should be modular rather than part of a larger program. It's for an academic collaborator who doesn't have access to this newsgroup. TIA Peter ------------------------------------------------------------------------------ Peter Murray-Rust | "Nothing exists except atoms and empty pmr1716@ggr.co.uk | space; all else is opinion" (Democritos). Protein Structure Group, Glaxo Group Research, Greenford, MIDDX, UB6 0HE, UK ------------------------------------------------------------------------------ From szilagyi@miat0.vein.hu Fri Feb 18 11:25:18 1994 Received: from sztaki.hu for szilagyi@miat0.vein.hu by www.ccl.net (8.6.4/930601.1506) id KAA27058; Fri, 18 Feb 1994 10:53:51 -0500 From: Received: by sztaki.hu with SMTP (5.67a8/SZTAKI-3.13) id kn27843; Fri, 18 Feb 1994 16:49:07 +0100 Received: by miat0.vein.hu with SMTP (5.61++/Vein-1.0) id AA08574; Fri, 18 Feb 94 16:52:30 +0100 Message-Id: <9402181552.AA08574@miat0.vein.hu> To: chemistry@ccl.net Cc: dmschn@bb1t.monsanto.com, szilagyi@miat0.vein.hu Subject: Re: CCL:MM2/3 <-> Sybyl MOL/MOL2 file conversion free!!! In-Reply-To: Your message of "Thu, 17 Feb 94 22:14:06 EST." <199402180314.WAA19061@hawkeye.ccl.net> Date: Fri, 18 Feb 94 16:52:30 +0100 X-Mts: smtp X-Charset: US X-Char-Esc: 0 select chemistry limit 200kb size 60kb cd software/mmconv get mmconv.tar.Z (you need UNIX and uudecode) get mmconv.tar.Z | untar.z (if you want each file separately) quit From chp1aa@surrey.ac.uk Fri Feb 18 11:42:28 1994 Received: from sun2.nsfnet-relay.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id KAA27068; Fri, 18 Feb 1994 10:54:37 -0500 Via: uk.ac.surrey; Fri, 18 Feb 1994 15:13:38 +0000 Via: central.surrey.ac.uk; Fri, 18 Feb 94 15:13:33 GMT Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA06276; Fri, 18 Feb 1994 15:13:31 GMT From: Mr Andrew D Allen Message-Id: <9402181513.AA06276@central.surrey.ac.uk> Subject: CCL: Homology searching on sequence data To: chemistry@ccl.net Date: Fri, 18 Feb 94 15:13:31 GMT Mailer: Elm [revision: 70.85] A colleague of mine has a protein sequence, but no x-ray structure, and wants to do sequence homology studies, to compare this sequence with other protein sequences. Does anyone have any ideas, code, or algorithms and programs to do this kind of study. I will summerise for the net... Andy. ################################################################################ Structural and Computation Chemistry Group, chp1aa@uk.ac.surrey - JANET. Department of Chemistry, phone +44(483)-300800-2632. University of Surrey, fax +44(483)-300803. Guildford, Surrey, GU2 5XH, UK. fpt 131.227.110.2 ################################################################################ From raman@bioc01.uthscsa.edu Fri Feb 18 14:01:30 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id NAA29361; Fri, 18 Feb 1994 13:38:02 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 18 Feb 1994 12:38:52 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA04299; Fri, 18 Feb 94 12:38:26 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9402181838.AA04299@bioc01.uthscsa.edu> Subject: Re: CCL:SESAM or SYBASE To: nittoli@pokey.chem.sunysb.edu (Thomas Nittoli) Date: Fri, 18 Feb 1994 12:38:24 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9402171921.AA05201@pokey.chem.sunysb.edu> from "Thomas Nittoli" at Feb 17, 94 07:21:45 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1907 Tom: > This message is about finding a program called SESAM or SYBASE > that I have come across in Proteins:Structure, Function, and > Genetics 11:59-76 (1991) by Huysmans, Richelle, and Wodak. Regarding the distribution of the protein structure database SESAM, you should contact Shoshana Wodak at the following address: shosh@ucmbcx1.ulb.ac.be This is very similar to the product IDITIS distributed by Oxford Molecular, but, when I spoke to Soshana last, there was no GUI implemented. Things could be different now. Here is the catch: SESAM is implemented under the commercial program RDBM, SYBASE. In order to run SESAM, you must have a license for this RDBM. A run-time version of this RDBM costs $5000. If you have this then SESAM is basically free. Alternatively. SESAM has also been implemented under ORACLE. Hope this helps. Cheers -raman P.S. I heard that a free RD oriented protein structure databse will soon be available from the UK. I will let you know if I hear more about this. In addition you might want to check out WHAT IF by Gerrit Vriend which implements a similar database and only bears a nominal cost for academia. -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From raman@bioc01.uthscsa.edu Fri Feb 18 15:01:28 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id OAA00324; Fri, 18 Feb 1994 14:11:24 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 18 Feb 1994 13:12:13 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA04363; Fri, 18 Feb 94 13:11:46 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9402181911.AA04363@bioc01.uthscsa.edu> Subject: Re: CCL:Homology searching on sequence data To: chp1aa@surrey.ac.uk (Mr Andrew D Allen) Date: Fri, 18 Feb 1994 13:11:45 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <9402181513.AA06276@central.surrey.ac.uk> from "Mr Andrew D Allen" at Feb 18, 94 03:13:31 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1646 Andy: > A colleague of mine has a protein sequence, but no x-ray structure, and wants > to do sequence homology studies, to compare this sequence with other protein > sequences. > Does anyone have any ideas, code, or algorithms and programs to do this kind > of study. There are many ways you could achieve this: 1. BLAST server 2. FASTA protocol 3. Server in Heidelberg You can obtain information on 1 & 2 by setting your gopher client to any of the biology gophers (e.g. fly.bio.indiana.edu). I like 3, since it not only provides the homology, but also the secondary structure prediction. This server is maintained by Chris Sander's group at EMBL, Heidelberg. To get instructions on using the server do the following: send email to the following address with no subject field: predictprotein@embl-heidelberg.de just include the word "help" in the body of the message. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From rks2@crux2.cit.cornell.edu Fri Feb 18 17:01:30 1994 Received: from crux2.cit.cornell.edu for rks2@crux2.cit.cornell.edu by www.ccl.net (8.6.4/930601.1506) id QAA01544; Fri, 18 Feb 1994 16:02:57 -0500 Received: by crux2.cit.cornell.edu (5.65/2.0) id AA27130; Fri, 18 Feb 1994 16:02:07 -0500 Date: Fri, 18 Feb 1994 16:02:06 -0500 (EST) From: "Rebecca K. Schmidt" Subject: Visualizing molecules on Indy To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, We are considering buying a Silicon Graphics Indy to run QUANTA and visualize proteins from molecular dynamics simulations. Apparently the Indy does not have a Z-buffer in the hardware. Therefore rotating larger proteins would be unsatisfactory since the depth-cueing must be done with software and is much slower. I would appreciate hearing about peoples' experience with the Indy in this regard and whether this limitation prevents it from being a useful graphics workstation for our needs. Thank you, Rebecca Schmidt