>> Phil wrote: >> >> > ... I honestly can't see that there is a need to force a >> > special radius for that N...neither for calculating bonds nor for >> > spacefill display...since the formal charge doesn't enter into those >> > matters at all. >> >> I'm getting more confused. >> >> The formal charge *does* enter into the bonding radius. > > Not to the best of my understanding, and I'll dare to argue with the > code-meister. > > As I know it, as currently implemented in Jmol, the charge listed in pdb > column 79-80 is taken as ionic charge, or oxidation state, of that atom, > then compared against a table of ionic radii.
Basically correct ... with the exception that I would use the phrase 'formal charge' where you are using 'ionic' ... perhaps that is erroneous. > If a match in charge is > found, then that ionic radius is used in the bonding-by-proximity > calculations and spacefill ionic display. Correct > (And we learned over the past > year, that bonding-by-proximity calculations with Fe3+, Al3+, Si4+, > etc., fail b/c the radius of the neutral atom is _way_ too different > than the ionic radii and therefore way too big and therefore creates > 2x-4x extraneous bonds, and impossible bonds at that.) Agreed > To make it clear, from the chemistry side, the table of radii has > *nothing* to do with formal charge and everything to do with ionic > charge. Then apparently I have a fundamental flaw in my model ... and in the Jmol implementation. I thought that ionic == formal charge and the implementation reflects that. > Sometimes the ionic charge and the formal charge (btw, usually > zero on most atoms, but most common non-zero values I would guess to be > +1 and -1) may be identical values on a particular atom, but most often > not. As I stated before, the PDB Guide's example of the charge field > certainly leads one to believe that the ionic charge, or oxidation > state, was the intent of the format, hence MG2+ and FE3+ in the example. OK. I previously said that the PDB file contained a 'formal charge' because it was pretty clear that it was not a partial charge and I thought that there was only one other thing ... a partial charge. > Getting back to the start point on this issue, the original petition was > simply that charges that don't have a match in the ionic radius table > don't get overwritten with zero. Yes, I can do that. > And that should be fairly simply > accomodated without upsetting the cart on all the good things that can > be done with the ionic charge in cols 79-80. Correct. I can keep the charge value, allow its use for display purposes, use the bonding radius for the uncharged atom, and not look into it any deeper. That will solve the short-term issue. That does leave open the longer-term issue of my fundamental confusion between ionic charge and formal charge. > More questions? How about a phone call? Can't do it today ... perhaps next week. 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
