Robert Hanson said: > feature request. OK, done :-) It is #2962639 on http://sourceforge.net/tracker/?group_id=23629&atid=379136 ++++++++++++++++++++++++++++ Jmol has internal criteria based on atomic radii for auto-connecting atoms ("bonds"). bondTolerance and minBondDistance allow some modification, and distance ranges can also be specified. But it would be good to be able to specify a fractional range eg 0.8 to 1.2 of the sum of the pairs of atomic or ionic radii, perhaps connect 0.8 1.2 ionic (~cations) (~anions); connect 0.8 1.2 atomic (~cations) (~anions); where "ionic" means use ionic radii, and "atomic" use atomic radii. The use of ionic radii is essential for most inorganic structures. ++++++++++++++++++++++++++++
> On Wed, Mar 3, 2010 at 5:29 AM, Alan Hewat <[email protected]> wrote: > >> 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 >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > ______________________________________________ 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
