I've uploaded new files for 13.1.17_dev_2013.06.16:
http://chemapps.stolaf.edu/jmol/jsmol.zip
http://chemapps.stolaf.edu/jmol/Jmol-13.zip
Thanks to Nick Greeves for spotting that Jmol.getPropertyAsArray was not
returning auxiliaryInfo and that the vibration demo would not work because
of that.
See now
http://chemapps.stolaf.edu/jmol/jsmol/vibrate.htm
Also in this version is the new ANIMATION MORPH, which if you haven't seen,
allows you to load two models from one or two files as trajectories and
then do a standard linear morph between them:
load trajectory =1cdr
animation morph 10
animation on
produces a smooth transition between NMR models, with 10 "frames" per
model. Or, if you had two individual PDB files with a 1:1 mapping of
coordinates, you can now do this:
load trajectory state1.pdb state2.pdb
animation morph 30
animation on
Basically just a standard morph between two forms.
*Dihedral-driven morphs*
But, of course, linear morphing could produce some very strange results.
Art Cox and I wondered if an animated "flexible fit" would work. The new
feature allows you to do a bond mapping between two models and then do a
flexible fit -- rotating dihedral angles only -- to transform one model
into another or to take one model to the closest resemblance of another
simply by driving dihedral angles. Art and I have all sorts of ideas where
this might be useful; what do you think?
You can check it out here:
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
center column link "flexible fit," which runs the following script. Several
new ideas there:
load files "$tyrosine" "$lysergamide"
select 2.1; translateSelected {10 0 0}
frame *;zoomto 0 {*} 0
select {2.1}
wireframe only
display remove 1.1 and _H
delay 1
// use a SMARTS string to find the key atoms in both molecules
sm = "c1ccccc1CCN"
keyatoms = {*}.find(sm)
select keyatoms
selectionHalos on
// optional way to get dihedral lists based on SMARTS
//print {1.1}.find(sm, "BONDS")
// get an array of numbers indicating the dihedrals, their current values,
and their target values based on a SMARTS match.
x = compare({1.1},{2.1},sm,"BONDS")
// rotate using a new option to rotate a whole series of dihedrals
concurrently
rotate branch @x 1
// overlay one model on another with a fit based on the same SMARTS match
compare {1.1} {2.1} SMARTS @sm rotate translate
// fly in to the model
zoomto 1 {*} 0
// new distance option -- minimum distances to another atom set
{1.1}.property_d = {1.1}.distance.min({2.1})
select {1.1}
// new option -- color balls only, not bonds, like PyMOL color spheres
color balls property_d
// highlight the key atoms
select {1.1 and keyatoms}
set echo top
echo molecule 1 colored by distance |to molecule 2
Enjoy!
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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