>> 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?
Because within my (naive) binary-world-view there are only two types of charges ... formal and partial ... :-) Here is the model that is in my head and that is implemented in Jmol: - Formal charges are integer values in the range [-4, +7] ... (perhaps to be expanded a wee bit) - Partial charges are floats in the range [-1.0, +1.0] - ionic == formal I have no idea how closely this correlates with more realistic models of reality. :-) > 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. Well, they cannot be partial charges because there is no space for them. > Of course there may be more description somewhere > else in the PDB specs, but I'd like to see it. I doubt it. I would look and see how they convert these charges into mmCIF files. The mmCIF spec is a little more formal. That will tell you how the people at the PDB interpret this field. >> 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]. Thank you for your leniency :-) 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
