This problem pertains to autobonding and the 'covalent radius' of the noble gases.
-- Jmol must perform 'autobonding' when no bond connectivity data is present in the file ... .xyz for example. The algorithm that is currently used is derived from open babel. distance <= covalentRadius(atom1) + covalentRadius(atom2) + 0.45 // bond tolerance AND distance >= 0.4 // minimum bonding distance I know that open babel makes other checks to determine whether or not a bond is appropriate. But Jmol does not currently do any other checks ... if two atoms are close enough (but not too close) then they will bond. The table of covalent radii is taken directly from open babel. I observe that the noble gases all have non-zero bonding radii. This means that Jmol will bond these things together if they are close enough. That seems like a problem to me. Q: Why are there non-zero values for the covalent radii of the noble gases in openbabel? Q: Is there any reason why we should not set them to zero in Jmol? I am reluctant to set them to zero in Jmol unless that is also done in open babel. But, I am also somewhat reluctant to add more complexity to the bonding algorithms in Jmol. Its job is rendering, not calculating. Thoughts/suggestions? Miguel ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
