Hmm. Shouldn't work that way. ROTATE BEST initializes with a "restore
orientation" (or, at least it effectively does that, because it multiplies
in the inverse of the current rotation quaternion).
What was the exact sequence of commands you used there? As far as I know,
the only way it can give a different rotation is
a) if you change the set of selected atoms, or
b) if you change the atom positions themselves.
I could be wrong, but the algorithm must give the same quaternion result
every time if it is using the same positions. Don't think I had a fixed bug
regarding that, but in any case, use
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.20.zip for testing,
please.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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