> 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. If a match in charge is found, then that ionic radius is used in the bonding-by-proximity calculations and spacefill ionic display. (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.) 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. 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. 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. 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. More questions? How about a phone call? --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
