From chemistry-request@ccl.net Fri Jul 2 02:24:48 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i627Ol8a001902 for ; Fri, 2 Jul 2004 02:24:47 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id i627U92a032868 for ; Fri, 2 Jul 2004 09:30:09 +0200 (CEST) X-Ids: 164 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i627U68E052048; Fri, 2 Jul 2004 09:30:06 +0200 (MEST) Date: Fri, 2 Jul 2004 09:30:06 +0200 (MEST) From: Michel Petitjean Message-Id: <200407020730.i627U68E052048|at|ds10.itodys.jussieu.fr> To: chemistry|at|ccl.net Subject: CCL: Re[2]: software to convert XYZ format to PDB ? X-Miltered: at shiva.jussieu.fr with ID 40E50F01.002 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: chemistry|at|ccl.net Subject: CCL:software to convert XYZ format to PDB ? Konrad Hinsen wrote: > On Jul 1, 2004, at 11:57, Michel Petitjean wrote: > > Imagine that you are the programmer: how could you know from > > the atomic symbols and the X,Y,Z coordinates what could be > > the residue ? The N,CA,C,O coordinates of all residues of > > all known proteins in the PDB offer quite similar 3D patterns. > > If I had to do this (fortunately I don't), I'd first identify the > peptide planes as patterns of pairwise distances (they are quite > rigid). I'd then identify the sidechains atom by atom starting from the > C-alphas, again by distance criteria. Not a trivial task, but not an > impossible one either. Sure... if you have the side chains ! (were not indicated in the example) It needs other assumptions: true residues, no HETATM, lexicographical ordering coherent with the PDB conventions... Michel Petitjean, Email: petitjean|at|itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean|at|ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From chemistry-request@ccl.net Fri Jul 2 04:20:11 2004 Received: from vscani-a.ucl.ac.uk (vscani-a.ucl.ac.uk [144.82.100.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i629KAFY011599 for ; Fri, 2 Jul 2004 04:20:10 -0500 Received: from socrates-a.ucl.ac.uk ([144.82.100.160]) by vscani-a.ucl.ac.uk with esmtp (Exim 4.24) id 1BgKIP-0003OQ-43; Fri, 02 Jul 2004 10:25:25 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.7p1+Sun/8.9.3) id i629PO424025; Fri, 2 Jul 2004 10:25:24 +0100 (BST) Message-Id: <200407020925.i629PO424025*at*socrates-a.ucl.ac.uk> Subject: Re: CCL:NMR for Nitrogen atom in Gaussian 03 To: sterzel*at*chemia.uj.edu.pl (Mariusz Sterzel) Date: Fri, 2 Jul 2004 10:25:24 +0100 (BST) Cc: chemistry*at*ccl.net In-Reply-To: from "Mariusz Sterzel" at Jul 01, 2004 08:21:24 PM From: Tanja van Mourik X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCL-MailScanner-Information: Please contact the UCL Helpdesk, helpdesk*at*ucl.ac.uk for more information X-UCL-MailScanner: Found to be clean X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Mariusz, > I have run NMR calculations and I don't know for which nitrogen isotope, > N^{14} or N^{15}, my calculations were performed. > Can someone help me with this? There is nothing written in a gaussian > log file. If you have not specified the isotope explicitly, then Gaussian calculated the NMR properties for N^{14}. In Gaussian 03, you can specify the N^{15} isotope in xyz coordinate input by N(Iso=15) x y z Hope this helps, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik*at*ucl.ac.uk London WC1H 0AJ, UK home: tanja*at*van-mourik.me.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html =================================================================