From chemistry-request@ccl.net Tue Apr 20 15:21:16 2004 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3KKLFuR005029 for ; Tue, 20 Apr 2004 15:21:15 -0500 Received: (from igorf@localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id i3KKEF615794890; Tue, 20 Apr 2004 16:14:15 -0400 (EDT) Date: Tue, 20 Apr 2004 16:14:15 -0400 From: "Igor Filippov [Contr]" To: Richard Wood cc: "chemistry..at..ccl.net" Subject: Re: CCL:converting an sdf database into a chemfinder database In-Reply-To: <40851F13.7010108..at..cornell.edu> Message-ID: References: <4316.129.123.250.158.1082407282.squirrel..at..webmail.cornell.edu> <40851F13.7010108..at..cornell.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.3 required=7.5 tests=FCS_URI_NODOTS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Richard, Is it possible that you're talking about NCI database processed by our group (CADD @ LMC @ NCI-Frederick) ? The website is http://cactus.nci.nih.gov where you can download public portion of NCI database (processed). As the whole processing was done in CACTVS it is hard to imagine that one is not able to read/write the structures anymore. If you downloaded NCI database somewhere else then it is, of course, impossible to tell what did you get and what the problem with it might be. Regards, Igor Filippov Contractor - SAIC-Frederick Computer Aided Drug Design group Laboratory of Medicinal Chemistry National Cancer Institute On Tue, 20 Apr 2004, Richard Wood wrote: > Hi all > > I should note that the file that I am trying to open and convert, > CANS03.sdf, is a file that I obtained from the NCI database (I don't > have the url with me, it's at work), and it originally couldn't be > opened with CACTVS, until someone at the NCI "fixed" it. CACTVS now > reads it, but won't write it out, at least not the whole file. The part > that CACTVS does write out, can be read by Chemfinder, however. CACTVS > will currently write out the first 37 structures I believe and then not > write anymore, but only if I write the first 15 and then append the next > 15 and so on. SO it writes two sets of 15 structures and then 7 of the > next 15 and then stops. I'm doing this using the CACTVS browser, btw. > > I hope this helps all of those that responded with questions/suggestions. > > TIA, > Richard > > Richard L. Wood wrote: > > >Hi all > > > >I'm wondering if there is anyway to convert an sdf database into something > >that Chemfinder can read easily. > > > >Chemfinder is supposed to be able to import sdf databases, but the file I > >have must not be formatted correctly, because chemfinder can't read it. > > > >Thanks in advance, > >Richard > > > > > > > > > > > > > > > > -- > Richard L. Wood, Ph. D. > Computational Chemist > SynVax, Inc. > N. Logan, UT 84341 > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY..at..ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > >