From owner-comp-bio@hgmp.mrc.ac.uk Sun Dec 24 18:33:30 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CEB0A17A79; Sun, 24 Dec 2000 18:33:29 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 7839817A60; Sun, 24 Dec 2000 18:33:28 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id CA4C017A43; Sat, 23 Dec 2000 21:57:37 +0000 (GMT) Received: from briar.org (backdraft.briar.org [192.207.123.123]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D317D41626 for ; Sat, 23 Dec 2000 21:57:28 +0000 (GMT) Received: (from smap@localhost) by briar.org (8.9.1b+Sun/8.6.12) id QAA08873 for ; Sat, 23 Dec 2000 16:57:27 -0500 (EST) X-Authentication-Warning: backdraft.briar.org: smap set sender to using -f Received: from mail.fu-berlin.de(160.45.11.165) by backdraft via smap (V2.1) id xma008869; Sat, 23 Dec 00 16:57:03 -0500 Received: by mail.fu-berlin.de (Smail3.2.0.98) from Curry.ZEDAT.FU-Berlin.DE (160.45.10.36) with esmtp id ; Sat, 23 Dec 2000 22:57:00 +0100 (MET) Received: by Curry.ZEDAT.FU-Berlin.DE (Smail3.2.0.98) from news.fu-berlin.de with bsmtp id ; Sat, 23 Dec 2000 22:57:00 +0100 (MET) To: bionet-biology-computational@moderators.isc.org From: Kristian Rother Newsgroups: bionet.biology.computational Subject: Re: cDNA-PDB mapping Message-ID: <3A451F5B.17C70BEB@chemie.fu-berlin.de> References: Reply-To: krother@chemie.fu-berlin.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: fu-berlin.de 977608619 6229937 62.180.167.138 (16 [61713]) X-Mailer: Mozilla 4.7 [de]C-CCK-MCD QXW0322g (Win98; I) X-Accept-Language: de,en Date: Sun, 24 Dec 2000 18:33:28 +0000 (GMT) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk Dear Iddo, > I am well > aware of ISSD, but it seems to be rather small. And it does not seem to be up to date, either. Recently, I had the same problem. After two weeks, I abandoned the experiment for this problem was growing too large to fit into a two-month practical course. I think someone might have to write something new that finds the best matches between Swiss-Prot and Pdb. That would really improve a lot of studies. > Or, if someone has written any code which does that, and is willing to > share, that will be great too. I have written some classes that read and write PDB data in Java and Python. The code cares for the atomic coordinates most. Actually, organism and molecule information is still ignored. You can find the latest version of both on: http://userpage.chemie.fu-berlin.de/~krother/bioinf/protein.html or http://www.mandalay.de.vu (main page) (Unfortunately, its all in German, Sorry) Let me know if You want to something with the code, I might give some additional advice. Kristian .