Per the message below, it looks like Geoff Hutchison of the OpenBabel team as put a lot of thought into the color scheme that they define.
To me, his selection criteria are right on target.
As you know, we have already adopted OpenBabel's table of covalent and vdw radii. I believe that Jmol should seriously consider adopting the OpenBabel color scheme as the default. If there are colors that need to be changed, then we should coordinate those changes with the OpenBabel team.
I would support any synchronization between CDK/Jmol and OpenBabel parameterization. The OB mailing list is currently discussing atomtyping and the possibilities of altering parameters through commandline or other options and it would seem useful to have set(s) of parameters which can be used by either community. This greatly helps in comparing results of calculations and visualizations done in each.
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069
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