From chemistry-request@server.ccl.net Mon Nov 18 03:30:01 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAI8U0u14710 for ; Mon, 18 Nov 2002 03:30:00 -0500 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id gAI8Sfcm001821; Mon, 18 Nov 2002 09:28:41 +0100 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id gAI8Se3T001818; Mon, 18 Nov 2002 09:28:40 +0100 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Mon, 18 Nov 2002 09:28:40 +0100 (CET) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: William Wei cc: CCLers Subject: Re: CCL:Homology modeling software? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id gAI8U1u14713 Hy, I think that one of the best homology modelling software (open source for accademics) is Modeller, downloadable at http://guitar.rockefeller.edu/modeller/modeller.html It's very powerfull and flexible Best reguards Alessandro Contini Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Fri, 15 Nov 2002, William Wei wrote: > Hi all, > > Does anyone know about more functional Homology modeling software than > Composer in sybyl package. What I want is I can interact more while I do the > modeling, for example, I want a "gap" some where, it is very difficult to do > that in Composer. Thank you for any information. > > Regards, > > William > > ------------------------- > William Wei > Faculty of Pharmacy > 19 Russell Street > Toronto, ON. M5S 2S2 > Tel: 1-416-946-8469 > Fax: 1-416-978-8511 > Email: william@phm.utoronto.ca > william.wei@utoronto.ca > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon Nov 18 03:38:00 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAI8bxu14835 for ; Mon, 18 Nov 2002 03:37:59 -0500 Received: from humagne.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.12.3/8.12.6) with ESMTP id gAI8bxVb005397 for ; Mon, 18 Nov 2002 09:37:59 +0100 (MET) Received: from humagne.ethz.ch (localhost [127.0.0.1]) by humagne.ethz.ch (8.12.3/8.12.3) with ESMTP id gAI8bwIP007963 for ; Mon, 18 Nov 2002 09:37:58 +0100 (MET) Received: (from portmann@localhost) by humagne.ethz.ch (8.12.3/8.12.3/Submit) id gAI8bwnX007962 for chemistry@ccl.net; Mon, 18 Nov 2002 09:37:58 +0100 (MET) Date: Mon, 18 Nov 2002 09:37:58 +0100 (MET) From: chem-support@cscs.ch Message-Id: <200211180837.gAI8bwnX007962@humagne.ethz.ch> X-Authentication-Warning: humagne.ethz.ch: portmann set sender to chem-support@cscs.ch using -r To: chemistry@ccl.net Subject: MOLEKEL: New Release Dear Computational Chemists CSCS (http://www.cscs.ch) is proud to announce the release of MOLEKEL version 4.3. There are only minor changes to version 4.2. * bugs fixed. * file parsers updated. * support for a new data format: list of points on a surface with an associated value (please check the manual). The release is mainly due to the fact that I will leave ETHZ/CSCS end of November 2002. As a consequence, I also have to leave MOLEKEL behind me. CSCS will further maintain the software. MOLEKEL is an interactive molecular graphics program to visualize molecular and electronic structure data from a number of electronic structure program outputs (Gaussian, Gamess, ADF...) as well as from XYZ and PDB files. MOLEKEL is able to render the molecular structure in different styles, display orbitals, electron densities, map and color code properties on any surface, display and animate vibrational normal modes, animate a sequence of coordinates and produces great graphics... Look and see! More information, a precompiled binary for SGI, SUN, LINUX systems and WINDOWS PC's and detailed documentation is available from http://www.cscs.ch/molekel/. Best regards Stefan Portmann From chemistry-request@server.ccl.net Mon Nov 18 06:08:53 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAIB8ru18318 for ; Mon, 18 Nov 2002 06:08:53 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18Djho-0005E6-00 for chemistry@ccl.net; Mon, 18 Nov 2002 11:04:40 +0000 Date: Mon, 18 Nov 2002 11:04:40 +0000 (GMT) From: Szilveszter Juhos To: Computational Chemistry List Subject: PDB H atom name convention Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, I could not find a definitive guide how the hydrogens in PDB files should be called. There is an advisory with some IUPAC->PDB hints at http://www.rcsb.org/pdb/lists/pdb-l/199907/msg00013.html , but I hope there is a concise on-line version somewhere since this list does not include nucleic acid residues I need. The article they are referring to J.L.Markley, et al., "Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids," Pure & Appl. Chem., 70 (1998): 117-142 is still a recommendation or an accepted standard? If you know an URL (or an article) that serves as the standard, please let me know. Thanks: Szilva