> 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. RasMol also supports this. It is not PDB standard. The openbabel guys & I talked about this several years ago ... but I don't recall their stance. Miguel ------------------------------------------------------- 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
