From chemistry-request@ccl.net Mon Jan 17 09:39:13 2005 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0HEdCsh015117 for ; Mon, 17 Jan 2005 09:39:13 -0500 Received: from oemcomputer (PPP13.fukuoka-ip.dti.ne.jp [211.132.92.13]) by smtp4.dti.ne.jp (3.10s) with SMTP id j0HEdAsV012900 for ; Mon, 17 Jan 2005 23:39:10 +0900 (JST) Message-ID: <001a01c4fca1$d2930080$0d5c84d3@oemcomputer> From: "Telkuni Tsuru" To: Subject: DBs for RNA Date: Mon, 17 Jan 2005 23:35:41 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, CCLers. I'm looking for DBs and web-sites which describe the relationship between RNA sequence and structure(including calculated structure). Although I know "Nucleic Acid Database" http://ndbserver.rutgers.edu/ , the site's sequence number is few to me. I can't find suitable data from "PDB" http://www.rcsb.org/pdb/ . And I don't know calculated structure DBs. If you know such DBs and sites, please let me know. When I receive replies, I will summarize them. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni$at$venus.dti.ne.jp From vdava@davapc1.bioch.dundee.ac.uk Mon Jan 17 15:29:34 2005 From: Daan van Aalten To: chemistry-request..at..server.ccl.net, jlabanow..at..nd.edu Subject: PRODRG available for download / release of PRODRG2.5 server (fwd) Message-ID: MIME-Version: 1.0 Dear all The PRODRG2 program, which generates coordinates and topologies from scratch (output formats: various PDB files with/without hydrogens and CNS, REFMAC, SHELX, WHAT IF, O, MDL Molfile, Mol2, Gromacs, Autodock (and others) topologies) is now available as a binary executable for free for academic users. Please download and use PRODRG locally if you want to, for instance, convert large libraries of small molecules - this will relieve some of the strain on the server, which is still there for anyone to use and always runs the most up-to-date/bug-fixed version. In addition, a new version, PRODRG2.5, is available for testing on the server (and will also soon be available for downloading). There are several improvements, the most significant improvement is compatibility with the Gromos96 force field. PRODRG2.5 is very much a beta version and we would welcome your feedback to help us improve it. The server/download page is at http://davapc1.bioch.dundee.ac.uk/prodrg Happy PRODRG-ing and best wishes for 2005! Alex Schuettelkopf & Daan van Aalten ############################################################################## Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979 Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764 School of Life Sciences E-mail: see WWW page Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk From chemistry-request@ccl.net Mon Jan 17 17:46:24 2005 Received: from web51304.mail.yahoo.com (web51304.mail.yahoo.com [206.190.38.170]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0HMkNxf011428 for ; Mon, 17 Jan 2005 17:46:23 -0500 Received: (qmail 17169 invoked by uid 60001); 17 Jan 2005 22:46:22 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=D7f1e2zCwbmJPeKuDXhWK+h09NUuH+WA9eRID99aulLbytUcYgpPwg12gM1GvB5+b7pCilwhJHVmIdkQjatHNx9s2u2vKXbhNt/m5a5hl8lv3/8Q0FEA9F9oJ6xyuBxRbyKrM+ijVOQtvpW9RWY1mzF7j6+AfWI5ah8zZVFuaaI= ; Message-ID: <20050117224622.17167.qmail{at}web51304.mail.yahoo.com> Received: from [24.152.168.117] by web51304.mail.yahoo.com via HTTP; Mon, 17 Jan 2005 14:46:22 PST Date: Mon, 17 Jan 2005 14:46:22 -0800 (PST) From: Sengen Sun Subject: CCL:orbitals and reality To: chemistry{at}ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I have been asked to make a summary on this year discussion on this subject. I received responces from 10 this year. 3 of them are neutral, 5 agree, and 2 disagree. I am specially interested in the disagreements and therefore post them here. I would think the first one might be meaningful. And we will have to see. I would be much happier if Mikael P Johansson and any one else could also critisize my earlier postings on the List as well :-). Here are two examples: http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+07+28+001; http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+06+02+016; The second disagreement is not specific enough. But I will address it later after Mikael P Johansson's next message or posting. Cheers! Sengen --- Mikael P Johansson wrote: > Well, if it helps, I disagree with you :-) I will > write up a "pro-orbital" > mail for CCL as soon as my work load permits. > > Happy New Year, > Mikael J. > http://www.helsinki.fi/~mpjohans/ > --- @yahoo.com> wrote: > Hello Dr. Sun, > > It's interesting to see your posts about that paper. > > > Since I am very busy I have not read the details of > the paper. However it > looks like what they did in the paper is very > important and meaningful. > > I think they derived some information about the > orbital from experiments > and data analysis, similar to the X-ray data > analysis in some sense. Also > they mentioned that the phase component of the wave > function is arbitary. > Very likely they derived the real part or the > imaginative part, or at > least some of either. So it's still very meaningful > > __________________________________ Do you Yahoo!? Yahoo! Mail - 250MB free storage. Do more. Manage less. http://info.mail.yahoo.com/mail_250