Your rot2 matrix is a left-handed axis system, not a right-handed one. That
matrix has a determinant of -1, not 1.
Jmol is considering your left-handed matrix
[-0.430167 -0.38484102 0.816611]
[0.693676 -0.719811 0.0261867]
[-0.57772803 -0.57772905 -0.57659] ]
and the proper rotation
[0.92022824 0.35561728 0.16345158]
[0.24758267 -0.8523756 0.46060687]
[0.3031219 -0.38339567 -0.8724247] ]
to be identical rotations.
On Mon, Mar 19, 2012 at 6:02 AM, Nikolay Bogdanov
<nikol.bogda...@gmail.com>wrote:
> Hi,
>
> I try to find out how to apply a rotation matrix to the model with jmol. I
> have a matrix to be applied to coordinates this way:
> matrix [[a1,b1,c1],[a2,b2,c2],[a3,b3,c3]]
> xnew=a1*x+b1*y+c1*z, ynew=a2*x+b2*y+c2*z etc
>
> It looks like I need just to do $ rotate selected @matrix. But it works
> for one matrix and doesn't with another (I've checked with manually
> multiplied
> coordinates). Then I decided to check how does jmol rotate coordinates
> with matrix and found that in one case transformation equal to matrix, and
> in
> other not. The same, as for my models.
>
> Is it a bug, or a feature, and how can I get rotation for the second
> matrix?
>
>
> $ show transform
> transform:
> [
> [1.0 0.0 0.0]
> [0.0 1.0 0.0]
> [0.0 0.0 1.0] ]
> $ show rot
> rot = [
> [0.0444209 -0.23927301 0.969936]
> [0.0448276 -0.969439 -0.24120401]
> [0.998007 0.0541943 -0.0323373] ]
> $ rotate @rot
> $ show transform
> transform:
> [
> [0.044420823 -0.23927324 0.9699356]
> [0.044827897 -0.9694386 -0.24120365]
> [0.99800664 0.05419464 -0.032337148] ]
>
> ... rotate back
>
> $ show transform
> transform:
> [
> [1.0 0.0 0.0]
> [0.0 1.0 0.0]
> [0.0 0.0 1.0] ]
> $ show rot2
> rot2 = [
> [-0.430167 -0.38484102 0.816611]
> [0.693676 -0.719811 0.0261867]
> [-0.57772803 -0.57772905 -0.57659] ]
> $ rotate @rot2
> $ show transform
> transform:
> [
> [0.9202282 0.35561728 0.16345158]
> [0.2475827 -0.85237557 0.46060684]
> [0.3031219 -0.3833956 -0.8724247] ]
>
> Thanks, Nick
>
>
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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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