Hi, I used the --gen3D option, so something like
babel -isdf chemdraw.sdf -osdf chemdraw3d.sdf --gen3D babel -isdf chemdraw3D.sdf -osdf chemdraw.sdf --gen2D cheers, Doug Quoting cadeddu <cade...@unistra.fr> on Tue, 06 Mar 2012 13:39:28 +0100: > can you specify which 3D format? I've tested this series > > babel -h -i cdxml benzeneACS.cdxml -o c3d1 benzeneACSvi.c3d > babel -h -i c3d1 benzeneACSvi.c3d -o pdb benzeneACSviac3d.pdb > > and I still have 14.9 angstrom for a benzene double bond. > > Did someone has already produced a stylefile (.chm?), and want to share > it? that will be of tremendous help, and eventually be a fast patch > > > On 6/3/12 12:52 PM, Douglas Houston wrote: >> Yes, this is a serious problem in Chemdraw. I found that using >> OpenBabel to convert to 3D then back to 2D adjusted the bonds to the >> correct dimensions. >> >> >> Quoting cadeddu<cade...@unistra.fr> on Tue, 6 Mar 2012 03:06:02 >> -0800 (PST): >> >>> seems that files converted from the cdx or cdxml have wrong bond >>> lenght (I've >>> the feeling that is related to the document properties in chemoffice); >>> benzene bond lenght --> 70Angstrom >>> anyone has already find a solution? I'm thinking to something like a >>> "feed2babel" style, or something similar. >>> thanks anyone >>> >>> >>> >>> -- >>> View this message in context: >>> http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html >>> Sent from the General discussion mailing list archive at Nabble.com. >>> >>> ------------------------------------------------------------------------------ >>> Keep Your Developer Skills Current with LearnDevNow! >>> The most comprehensive online learning library for Microsoft developers >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >>> Metro Style Apps, more. Free future releases when you subscribe now! >>> http://p.sf.net/sfu/learndevnow-d2d >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >> >> >> >> >> _____________________________________________________ >> Dr. Douglas R. Houston >> Lecturer >> Room 3.23 >> Institute of Structural and Molecular Biology >> Michael Swann Building >> King's Buildings >> University of Edinburgh >> Edinburgh, EH9 3JR, UK >> Tel. 0131 650 7358 >> > > > -- > Andrea Cadeddu > > -- > Nanochemistry Laboratory > Institut de Science et d'Ingénierie Supramoléculaires (I.S.I.S.) > Université de Strasbourg > 8, allée Gaspard Monge > F-67000 Strasbourg (France) > Tel: +33-(0)3-68855185 > Fax: +33-(0)3-68855161 > cade...@unistra.fr > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > _____________________________________________________ Dr. Douglas R. Houston Lecturer Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
