Jmol users,
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.17.zip
adds the feature of calculating the smallest box that can contain a
selected set of atoms. It is only an approximation, using 1495
pre-calculated quaternion-based orientations, but I think it is pretty
good. On my machine, 3cc2, with 99,000 atoms, takes about 5 seconds.
Selecting just the 6,641 alpha carbons and phosphorus atoms takes about a
second.
I plan to release 13.3.4 and 13.2.4 early next week. This new feature is
only in 13.3.4.
new feature: rotate BEST
-- rotates the model to a position such that dx > dy > dz
-- calculation is based on selected atoms only, (so, for example,
for large proteins one might first select *.CA).
-- uses 1495 pre-calculated quaternion-based alternatives
new feature: rotate SELECTED BEST
-- rotates the selected atoms, changing their actual coordinates
new feature: show ROTATION BEST
-- operates on currently selected atoms
-- reports "{quaternion}"
new feature: quaternion("best")
-- delivers actual quaternion
new feature: show ROTATION VOLUME
-- calculates approximate best box
-- reports "<volume> {dx dy dz}"
-- where <volume> is the volume,
-- and {dx dy dz} are the dimensions, where dx > dy > dz
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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