> > Just to be sure, the issue is what to do with data that is in *pdb* > > columns 79-80. > > The issue is how to handle formal charges. > > In the case of .pdb files the charge data is stored in columns 79 & > 80. > > As to charges, I suppose 'charge' could be considered to be 'formal > > charge' > > That is what I thought it was.
Why do you think so? The PDB guide (quoted in my previous post) says 'charge', not formal charge. And the examples in the PDB guide are certainly consistant with ionic charge. Of course there may be more description somewhere else in the PDB specs, but I'd like to see it. > > but also not unreasonable to consider 'ionic charge' or the > > closely related 'oxidation number' or 'oxidation state'. The PDB > example> seems likely to be closer to the latter than the former. > > I have no idea what the difference is between these terms. For the moment, Miguel, I'm not going to ask you to learn the difference [smile]. --Phil ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
