I will check it out.
On Tue, Dec 16, 2014 at 9:05 AM, <sschm...@tue.mpg.de> wrote:
>
> Hey,
>
> I would like to represent superpositions of an external tool in jsmol.
>
> The rotation/tranlation matrix (4x4 matrix) of the external tool looks
> like:
>
> m_ext=[
> [0.80521651, 0.204535829, -0.5565891350000001,
> 42.002786661]
> [-0.21990044800000003,-0.76870466, -0.6006138010000001,
> 47.417337482]
> [-0.550699704, 0.6060183490000001, -0.573996163,
> 27.924563443]
> [0, 0, 0, 1]
> ]
>
> However, the superposition fails - the translation seems to be wrong:
>
> model 1.1 - superposed chain A of the mobile structure,
> chain B the target structure
> model 2.1 - the original coordinates of the mobile structure
>
> select 2.1
> rotateSelected @m_ext
>
>
> So, I loaded the superposed structure and compared it to the original
> coordinates
>
> m = compare( {*A.CA:2.1}, {*A.CA:1.1})
>
> m=[
> [0.8034722620457098, 0.20782335713182248, -0.5578904698537244,
> 28.646307053941896]
> [-0.21910626765164903,-0.7680943038972581, -0.6016839567383779,
> 31.022614107883825]
> [-0.5535564719149386, 0.6056736683652718, -0.5716070677047655,
> -9.882908713692924]
> [0, 0, 0, 1]
> ]
>
> So, it looks like the rotation matrix (3x3 matrix) looks fine. Just the
> translation is wrong...
>
> Any idea what I missed?
>
> Best
> Steffen
>
> P.S. The example I used was the superposition of 1thf (target) with 1qo2A
> (mobile) using tmalign
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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