On Wed, Nov 3, 2010 at 6:46 AM, Dr. Christoph Gille <
christoph.gi...@charite.de> wrote:
> Hi Bob,
> thanks so much,
>
> viewer.scriptWait( ... ) would work in principle but there is a
> performance bug in jmol:
> The of scriptWait leads to a repaint of the JPanel.
>
Ah, yes, that's correct. If you had to do lots of these, that would slow you
down.
>
> But the bit-set method that you proposed works nicely for me.
>
> And this also gives me the right idea of how to perform the
> 3D-transformation:
> The BitSet tells me the atoms and then I can apply the transformation to
> each atom.
>
> Unless there is already a ready-to-use script command.
> What about "rotate"? Would this be applicable?
> It can rotate around axes but does it also take a matrix + translation
> vektor?
>
> yes, it does. You can pass a 3x3 matrix, an axis-angle, a 4x4 matrix, a 3x3
with a translation vector, etc. to the ROTATE command.
But understand that the standard ROTATE command just changes the view (of
all models, not just one). Jmol doesn't preserve a different viewpoint for
different models. If you need to move just one model relative to another,
use
ROTATE SELECTED option. These commands are pretty well documented. See
http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#rotate
> For this purpuse I will not use the built in superpositon beccause STRAP
> already has four different superposition methods
> and the state of the JMol-view should always be synchronized with what is
> in STRAP.
>
>
Jmol should do a very nice job of that.
> But perhaps, the 3d-superposition algorithm implemented in JMol could be
> used as a 5th option in STRAP?
> Is it a method of its own or is it one of the many superposition algorithms
> around?
> How does it compare e.g. to CE/CL?
>
>
It is strictly a 1:1 atom-for-atom mapping superposition. It's not a full
structure alignment algorithm. It uses Horn's closed-form quaternion
solution to pairwise superposition. I have some examples of the COMPARE
command at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=110
Bob
> Regards
>
> Christoph
>
>
>
>
>
>
>
>
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--
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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