Some .pdb files have CONECT records. Jmol currently ignores them. I have read the PDB file format specification http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html and have looked at some .pdb files ... and I am a little confused about what I should do.
It looks like to me that the spec says that CONECT records are used for special cases. The implication is that CONECT records are not needed within standard residues. And in fact, many .pdb files have relatively few CONECT records ... so that seems consistent to me. That seems to imply that (in this case) Jmol should build its own bonds and add the CONECT bonds. But I have seen other .pdb files which *do* seem to have all the CONECT records there. And, in general, Jmol will not calculate bond connectivity information if this information is in the file. In this case, Jmol should *only* use the connectivity specified in the CONECT records. Q: How do I tell if the CONECT records are for 'all' the bonds or only for the 'nonstandard' bonds? Q: It seems I recall seeing something about a format 'extension' where a CONECT record could be specified more than once in order to define a double/triple bond. Is that true? Another factor ... the RasMol documentation for the 'connect' command says: The RasMol 'connect' command is used to force RasMol to (re)calculate the connectivity of the current molecule. If the original input file contained connectivity information, this is discarded. So, that doesn't seem right to me in the case where a file is following the PDB format specification and standard connectivity is not included in the CONECT records. Q: What should the connect command do? Miguel ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
