> 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. Jmol also has support for partial charges, but .pdb files do not support that. > 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. > As I look at the 'Atom Block' of the *mol* file type, I see that field > 'ccc' is designated as 'charge', for which values are '0 = uncharged or > value other than > these, 1 = +3, 2 = +2, 3 = +1, 4 = doublet radical, 5 = -1, 6 = -2, 7 = > -3' , For .mol files, jmol converts these .mol file 'charge codes' to the associated formal charge value. > and Notes adds: '[Generic] Wider range of values in M CHG and M > RAD lines below. Retained for compatibility with older Ctabs, M CHG and > M RAD lines take precedence. Jmol does not support these extended fields for .mol files. > FWIW, in the *CIF* core dictionary, '_atom_type_oxidation_number' is > defined as: > 'Formal oxidation state of this atom type in the structure.' and 'The > permitted range is -8 -> 8 ' Currently the Jmol code ensures that values fall in the range [-4, +7]. This was based upon my misunderstanding of the ionic charge table data. Perhaps this range check should be expanded. > There is also '_chemical_conn_atom_charge', defined as 'The net integer > charge assigned to this atom. This is the formal charge assignment > normally found in chemical diagrams.', for which 'examples: 1, for an > ammonium nitrogen; -1, for a chloride ion' and 'The permitted range is > -6 -> 6' I am getting lost Q: What should the range of acceptable formal charge values be? Q: What should be done when charge values are given in the data files that do not have corresponding entries in the ionic charge tables? Miguel ------------------------------------------------------- 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_idv37&alloc_id865&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
