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 > > > > > > ------------------------------------------------------------------------------ > > This SF email is sponsosred by: > > Try Windows Azure free for 90 days Click Here > > http://p.sf.net/sfu/sfd2d-msazure > > _______________________________________________ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > <mailto:Jmol-users@lists.sourceforge.net> > > <mailto:Jmol-users@lists.sourceforge.net > <mailto:Jmol-users@lists.sourceforge.net>> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > > > -- > > 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 > > > > > > > > > > ------------------------------------------------------------------------------ > > This SF email is sponsosred by: > > Try Windows Azure free for 90 days Click Here > > http://p.sf.net/sfu/sfd2d-msazure > > > > > > > > _______________________________________________ > > Jmol-users mailing list > > Jmol-users@lists.sourceforge.net > <mailto:Jmol-users@lists.sourceforge.net> > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > <mailto:Jmol-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > 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 > > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
