Thanks Angel. bondTolerance and minBondDistance look useful, but only to add a fixed distance for deciding to bond atoms, or to set a fixed minimum requirement for bonding. I would like to be able to say "bond if the atoms are within the sum of their radii plus/minus some fraction".
And of course for inorganic structures I would like to use ionic radii rather than atomic radii to decide whether to draw bonds or not. I guess "bond" is not really the correct term here; I prefer "connect". The "bonds" that we draw, especially for ionic materials, are only there to indicate which pairs of atoms are within the sum of their radii plus/minus some fraction. Alan. Angel Herráez said: > 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. ______________________________________________ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE <[email protected]> +33.476.98.41.68 http://www.NeutronOptics.com/hewat ______________________________________________ ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
