Re: [Jmol-users] fun with COMPARE

[Paul P. <pau...@ac...>]

Congratulations Bob, this is really awesome !
I was wondering if it would be possible to make such a structural alignment between two different applets  included in the same webpage ?
Once both molecules are aligned, the applets could be synchronized thus allowing a comparison between both structures.
Thanks,
Paul
Le 28 mars 2010 à 04:46, Robert Hanson a écrit :

> 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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