Dear Warren (and others who might be interested - Zac, Robert ?):
Thank you for the cmd.get_object_matrix(object-name), this is what we
were looking for. Or almost, here are a few comments :
1) We were also looking for an equivalent "cmd_set_object_matrix" or
something like that, but could not find it. Does it exist somewhere ?
2) "reset" and "undo" do not seem to reinitialize the matrix
3) moving the molecule with the commands rotate/translate instead of
with the rotF/movF from the mouse, the matrix does not get updated.
4) We get some numerical instabilities. For example, using the following
function a few times (on a pdb file "mono") gives values which are
greater than 1 for the cos/sin of the rotation matrix, and then quickly
diverge :
from Numeric import *
print cmd.get_object_matrix('mono')
cmd.transform_object('mono',[cos(1.57), 0, -sin(1.57), 0.0, 0, 1, 0,
0.0, sin(1.57), 0, cos(1.57), 0.0, 0, 0, 0, 0.0])
print cmd.get_object_matrix('mono')
cmd.transform_object('mono',cmd.get_object_matrix('mono'),0,0,'',0,1)
print cmd.get_object_matrix('mono')
Note that it diverges also but more slowly when replacing the second
transform line by :
cmd.transform_object('mono',[cos(1.57), 0, sin(1.57), 0.0, 0, 1, 0,
0.0, -sin(1.57), 0, cos(1.57), 0.0, 0, 0, 0, 0.0])
Can you help us with some of these issues ?
Thank you very much.
--Xavier (w/ Leandro and Stefano)
ps : thank you Zac & Robert for your help !
> Provided objects are moved in their entiretly, recent PyMOL betas may
> provide what you want via
>
> cmd.get_object_matrix(object-name)
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
>
>
> > -----Original Message-----
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > Xavier Siebert
> > Sent: Friday, September 16, 2005 10:01 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] rot+trsl matrices
> >
> > Hello,
> >
> > I would like to dock several molecules into a map and display
> > a score in real time (i.e., as the molecules are moved around
> > with the mouse).
> >
> > For that I have to retrieve the rotation+translation matrix
> > for each molecule while it is being moved around, to feed it
> > into a scoring algorithm.
> >
> > Do you know how to get these matrices ?
> > Thank you !
> > --X.
> >
> > -------------------------------------------------
> > Xavier Siebert, Ph.D.
> > Laboratoire de Virologie Mole(c)culaire & Structurale UMR 2472
> CNRS-GIF
> > 1 Av. de la Terrasse, Bat. 14 B
> > 91198 Gif-sur-Yvette, FRANCE
> >
> > tel : (++33)-1-69.82.38.56
> > fax : (++33)-1-69.82.43.08
> >
> >
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> >
>
