Jmol users,
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
OK, we are going to have fun with this! Jmol now has atom-pair comparisons
built into the scripting in the form of a COMPARE command and also a nifty
ROTATE option:
ROTATE COMPARE {atoms1} {atoms2} -nSeconds
does a smooth motion animation over nSeconds time moving atoms1 to the
absolute best fit at the positions of atoms2 in a straight line motion. It's
really a combination of a rotation and a translation -- which, by the way,
constitutes a helical or screw motion. (The negative sign is necessary
because for the rotate command, a positive number is degrees per second.) So
there is also a HELIX option that lets you visualize that screw motion. (I'm
betting Dean Johnston is getting ideas already....)
ROTATE HELIX COMPARE {atoms1} {atoms2} -nSeconds
Note that you need at least 3 atoms to do this. Otherwise the pathway is
undefined. Watch those crystallographic molecules zoom around their screw
axes:
ROTATE HELIX COMPARE {symop=1} {symop=4} -3
right? (no, we can't invert through a plane or center of inversion yet...)
Also, you can compare two sets, but then move another based on that
comparison:
ROTATE COMPARE {2.1 and *.CA} {1.1 and *.CA} {2.1} -3
This moves the whole model 2.1 based on a comparison of just the alpha
carbons -- what PyMol and other programs typically do, without the fun of
animation.
Also, in this release will be the organic chemist's stereochemical
inversion, which is technically a 180-degree rotation. A nice example of
that is up there as well as feature #110. It looks like this:
select {*}
invertSelected STEREO {atomno=12} {atomno=11 or atomno=13}
This will invert the groups around atomno=12 that are NOT atoms 11 or 13.
Hmm. Come to think of it, I should probably change that to the center and
the atoms you DO want inverted, right? OK.... This one's not quite ready, I
think.
Bob
--
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
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