Well, it's not a valid matrix for rotation. What you have right now in rot2
is an improper rotation -- a rotation/reflection. As interesting as that
might be, it's not a rotation, doesn't correspond to a quaternion (which is
what Jmol turns that matrix into), and therefore shouldn't be used with the
ROTATION command. If you want to invert the atom positions, use the
INVERTSELECTED command.
On Mon, Mar 19, 2012 at 10:18 AM, Nikolay Bogdanov <nikol.bogda...@gmail.com
> wrote:
> But they are not identical:
> Point (1.0, 1.0, 1.0) goes into (0.0016, 0.0000, -1.7320) with my
> left-handed matrix, and to (1.4393, -0.1442, -0.9527) with Jmol's rotation.
>
> If I multiply the rotation matrix with (-1) and thus make it right-handed.
> This is fine for me now, because I need only axes orientation, but not the
> direction.
>
> However, it could be something wrong with the switching to right-handed
> rotation algorithm.
>
> Thanks, Nick
>
> On 03/19/12 14:55, Robert Hanson wrote:
> > 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 <mailto: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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--
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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