Hi Alan
Maybe you can use this:
http://www.stolaf.edu/academics/chemapps/jmol/docs/#setbondstyles
set bondTolerance (decimal)
When autobonding, the value of bondTolerance is added to the two bond radii
of atoms
being tested for a bond. A larger bondTolerance allows atoms that are further
apart than the
sum of their listed radii to still be bonded. This parameter should be adjusted
prior to file
loading for proper maintaining of the Jmol state.
set minBondDistance (decimal)
Sets the minimum bond distance for autobonding. Should be set prior to file
loading for
proper maintainence of the Jmol state.
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