sorry, slipped a space into the middle of the file name.
On Sun, Jun 16, 2013 at 2:00 PM, Bays Philip <pb...@saintmarys.edu> wrote:
> Bob:
> I get an unrecognized file type in the ....vibrate.htm link
>
>
> On Jun 16, 2013, at 1:21 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> 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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>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
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>
--
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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