With version 0.98 release, you can get this matrix as a standard 4x4
homogenous transformation matrix:
load targ.pdb
load prot.pdb
align prot, targ
print cmd.get_object_matrix("prot")
The matrix is returned as a tuple of 16 floats, where R is the rotation and
T the translation as follows:
(
R, R, R, T,
R, R, R, T,
R, R, R, T,
0, 0, 0, 1,
)
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
> Kristina Rogale Plazonic
> Sent: Wednesday, May 18, 2005 1:51 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] transformation matrix for align?
>
>
> Hi all!
>
> I'm new to pymol and I love it!
>
> I'm wondering if there is a way to obtain the affine
> transformation used to superimpose two structures with the
> align command? I'm a biopython user and I'd need this matrix
> for further processing...
>
> Thank you very much!
> Kristina
>
>
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