>>The algorithm is as follows: >> - if an atom has no charge, then the covalent radius is used >> (data values from OpenBabel) >> - if an atom has a charge, then it is looked up in the ionic table >> * if it is not found in the ionic table, then the >> covalent radius is returned > > I may have missed (or forgotten) some of this discussion.
Phillip and I probably exchanged a few emails without cc'ing everyone. Here is the issue ... What happens if I see an element/charge combination that is not in the table? For example, I open a file which has a carbon atom with a charge of +7. Based upon my brief discussion with Phillip, I decided that a 'covalentRadius' was most closely related to a charge of 0 ... therefore the default was to use the covalentRadius. > Are you talking about "used" for determining the presence of a > covalent bond, or "used" in the spacefill rendering? Certainly the former ... "used" as the radius for determining covalent/ionic bonds. And the latter too, but only for 'spacefill ionic', not for 'spacefill on'. > If the latter, do you really mean covalent radii? > As stated in > http://www.umass.edu/microbio/rasmol/rasbonds.htm > RasMol uses van der Waals radii or "united atom radii" by default for > spacefill. > I think Jmol should do the same for backward compatibility. Agreed. 'spacefill on' uses vdw radii (although the values I am currently using are taken from OpenBabel) 'spacefill ionic' will use ionic/covalent radii > I've never been clear about the rationale for using vdW radii in > spacefill rendering instead of covalent radii. Certainly *I* don't have any idea :-) If you think any of this is incorrect behavior, please speak up. Miguel ------------------------------------------------------- This SF.net email is sponsored by: Perforce Software. Perforce is the Fast Software Configuration Management System offering advanced branching capabilities and atomic changes on 50+ platforms. Free Eval! http://www.perforce.com/perforce/loadprog.html _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
