Re: [Jmol-users] extract rotation + translation performed by compare command

[Robert H. <ha...@st...>]

2011/8/3 Angel Herráez <ang...@ua...>

> I am using the "compare" command to align 2 conformations of the same
> protein. The effect
> is great, but I would like to isolate the translation + rotation that is
> being applied.
>
> 1. I load protein1.pdb (which I want to stay as it is oriented)
> 2. I load (append) protein2.pdb (which I want to align to the first)
> 3. frame all
> 4. compare {2.1} {1.1} SUBSET {protein} rotate translate //does a nice job,
> moving model2
> towards model 1
>
> I can save everything to a JMOL file and it works nicely, but the file is
> much larger than the
> sum of the 2 original files.


Right, because it contains all the new atom positions.


> Also, I am losing some control on things I was doing beforehand
> on the first model (I'd prefer not to have to recalculate or redo my
> scripts).
>

???


> To the point: what I would like is to have the rotation+translation that
>  has been applied to
> model 2 during the compare command
>

Yes. First save the coordinates in a variable:

oldCoord = {*}.xyz.all

Now you have a reference. Provided you are not moving PARTS of the model
(one chain, for example, relative to another), after any number of moves you
can determine the quaternion for the overall change in coordinates. That's
all you need to reproduce that particular rotation and translation, again
with the COMPARE command. This is illustrated at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=115

That the idea?

>
> Any way to extract that info?
>
> Thanks
>
>
>
>
>
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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