Carlos,
> Is it possible to output to the console the superposition matrix after pair
> fitting?
# yes, for example:
load $TUT/1hpv.pdb
extract chA, chain A
extract chB, chain B
align chA, chB
print cmd.get_object_matrix("chA")
# which dumps the 4x4 homogenous transformation matrix
> 2- Is it possible to apply these transformation matrices to mesh objects
> (from electron density maps)?
load chA_map, chA_map
matrix_copy chA, chA_map
isomesh chA_mesh, chA_map, 1.0, chA
# etc.
Cheers,
Warren
________________________________________
From: Carlos Martinez Fleites [mailto:marti...@ysbl.york.ac.uk]
Sent: Tuesday, March 24, 2009 11:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] mesh and pair fitting questions
Hi,
I would like to do the following task:
I have three complexes of three different ligands with the same enzyme and I
would like to rotate/translate the electron density maps of two of these
complexes in order to superpose them onto the first complex. I need to do the
superposition based on the coordinates of the ligands and not on the common
enzyme residues since there are conformational changes that differ in the three
complexes. I can nicely superpose the ligands using Pymol "Pair fitting" wizard
but then my questions are:
1-Is it possible to output to the console the superposition matrix after pair
fitting ?
2- Is it possible to apply these transformation matrices to mesh objects (from
electron density maps)?
Thanks,
Carlos
-----------------------------------------
Carlos Martinez Fleites
Structural Biology Laboratory
Department of Chemistry
The University of York
Heslington
York YO10 5YW
United Kingdom
Tel: +44 1904 328278
Fax: +44 1904 328266
E-mail: marti...@ysbl.york.ac.uk
