From chemistry-request -8 at 8- server.ccl.net Thu Nov 29 17:19:46 2001 Received: from mail.axelero.hu ([195.228.240.83]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fATMJjN22548 for ; Thu, 29 Nov 2001 17:19:45 -0500 Received: (qmail 13663 invoked from network); 29 Nov 2001 22:18:46 +0100 Received: from adsl95.225.axelero.hu (HELO chemaxon.com) (195.228.225.95) by mail.axelero.hu with SMTP; 29 Nov 2001 22:18:46 +0100 Message-ID: <3C06A5C2.5060209 -A_T- chemaxon.com> Date: Thu, 29 Nov 2001 22:16:50 +0100 From: Ferenc Csizmadia Organization: ChemAxon User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us, hu MIME-Version: 1.0 To: maria.brandl # - at - # pharma.novartis.com, chemistry # - at - # ccl.net Subject: Re: CCL:mol-3D-2D References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Maria, >Does anybody know/currently write/ >need a tool that converts mol-files with 3D - coordinates >into mol-files with 2D - coordinates and correct stereo- >chemisty, up/down bonds etc.. and the same atom numbering >as the original file. > A tool that could reassign original atom numbering >of the 3D-file a correct 2D-file with changed order of atoms >would do as well. > There is a command-line tool that can do that in the Marvin Beans package of ChemAxon. The tool is called MolConverter. It interconverts various file formats (Molfile, SDF, SMILES, ....) and also creates image files. I guess you need Molfile to Molfile or SDfile to SDfile conversion. (The same atom numbering is applied in the generated 2D-file as in the original 3D file) If you would like to try MolConverter, select "Marvin" at http://www.chemaxon.com/products.html and then choose "Download". On the download page select "Downloads for web and software developers. (Applets and JavaBeans) ". (I guess, you are not a software developer, but usually developers are interested in Marvin Beans) Since Molconverter is in Java, you need to install a Java Runtime Environment before running it. The page explains how to register before downloading and how to get Java. When you are done, select the marvinbeans-.....zip link. Unzip the file, go to the marvinbeans directory (in a Command Prompt or a Unix shell window) and run bin_MSWIN\molconvert mol -2:O1 filename (in Windows) bin/molconvert mol -2:O1 filename (in Unix) (if you need a format other than Molfile, then replace "mol" with the abbreviation of another format) A user guide for Molconverter is available at http://www.chemaxon.com/marvin/doc/molconvert.html. Another product called JChem (it is for chemical database handing) also includes the MolConverter. But probably you are better off with Marvin Beans, since it is smaller. Please let me me know if you need help. Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988