On Tue, 2005-04-19 at 12:34 -0400, Miguel wrote: > > Hi, I have an SDF file that contains a C=O bond and it displays fine in > > Jmol. However when I use babel to convert it to a PDB file, the > > resultant PDB file does not show the C=O double bond. > > > > Does anybody have any idea why this would happen? > > The standard PDB format does not bond orders. > > > The coordinates in the > > PDB file are to 3 decimal places and in the SDF file to 4 decimal > > places, but I would'nt think that this would affect the bond type > > recognition. > > > > Is there a way to indicate bond type in the PDB format? I tried > > converting the ATOM records to HETATM records but that did'nt seem to > > work. > > You can use the CONECT record to explicitly bond two ATOM or HETATM records. > > You specify a source and one or more targets in a CONECT record. > > If you specify a target more than once then Jmol will recognize it as a > double/triple bond.
Aah, thanks for the pointer ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> <http://jijo.cjb.net> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Breadth-first search is the bulldozer of science. -- Randy Goebel ------------------------------------------------------- This SF.Net email is sponsored by: New Crystal Reports XI. Version 11 adds new functionality designed to reduce time involved in creating, integrating, and deploying reporting solutions. Free runtime info, new features, or free trial, at: http://www.businessobjects.com/devxi/728 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
