> >> > 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)
Step up to the backboard, Miguel. Formal charges are those values that fall out of an electron dot diagram...they are 'formally' right, but that is a guarded term. I can see why a computer scientist might prefer something that is formally right over all others, but that is only one type of charge in chemistry. > - Partial charges are floats in the range [-1.0, +1.0] > > - ionic == formal No, but both ionic and formal are integers. Are you sure you want to continue? Someone else want to take over?? > 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. That is an interesting approach. Like learning Greek by studying the loan words in Latin. > Thank you for your leniency :-) Actually, I'm ducking this a bit b/c I've never taught introductory chemistry and there are many nuances, as well as history, to all this. --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
