Well, that's an idea, anyway. How common do you think it is to have the
actual matrix and not other information?
On Wed, Mar 21, 2012 at 6:30 AM, Nikolay Bogdanov
<nikol.bogda...@gmail.com>wrote:
> Thanks! Thus I do a proper rotation (which is my matrix multiplied by (-1)
> ) and then INVERTSELECTED, and that gives me what I want.
>
> Shouldn't this be a default action for the left-handed matrix rotation?
> Because now Jmol does something strange when one tries to apply a
> rotation/reflection matrix as rotation. It just rotate with some other
> matrix and does not say anything. In principle it could imply mistakes, if
> someone will just trust Jmol and do not check is the matrix right- or
> left-handed...
>
> Nick
>
> On 03/19/12 20:48, Robert Hanson wrote:
> > 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 <mailto: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>
> > <mailto: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 <tel: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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--
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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