Thanks, Nico, for releasing Jmol 12.2.9 and 12.3.9. Here are the details.
Also in this message is a bit about what is new in 12.3.10 in relation to
animations and IRC calculations. More to come on that, I think.
12.3.9/12.3.9 bug fixes
# bug fix: set isKiosk should:
# (a) not be reversible
# (b) not allow file saves other than logging
# (c) not allow prompt dialogs
# (d) not allow console or popup menu or ScriptEditor
# bug fix: background colors saved to state can be off very slightly
# bug fix: draw PLANE with three vertices problems after save -- four-atom
planes, not three
# bug fix: x = file("?") fails on Cancel
# bug fix: delay not allowed within try{...}
12.3.9 new features:
FRAME DELAY x.y
-- adds an additional delay (in seconds) in animation to a given frame
-- applies to all currently in-frame models (with FRAME RANGE, for
example)
12.3.10_dev (http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip)
new feature:
compare {...atomsFrom...} {...atomsTo...} FRAMES
This command option allows easy translation/rotation alignment of frames in
an IRC (intrinsic reaction coordinate) animation. The result can be
startling. See, for example, the difference between
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm?load%20data/cyclohexane_movie.xyz;animation%20mode%20palindrome;animation%20on
and
http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm?cd%20data%3Bscript%20cyclflip2.spt
Notice the completely different way that appears. And yet it is exactly the
same computational result.
It is the first-listed atom set that will be moved. The FRAMES option
automatically adds ROTATE TRANSLATE 0 and overrides any of those options
already given. You can add the SUBSET and/or ATOMS options to specify
exactly which atoms to use in the alignment calculation.
Very common would be to load a multi-model file and get all the frames
aligned with the first:
compare {*} {1.1} FRAMES
That's what I did with cyclohexane_movie.xyz to make that second example,
above.
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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