[Chimera-users] How to define a center of rotation when applying a symmetry
Giovanni Cardone
cardoneg at mail.nih.gov
Mon Jun 2 09:18:25 PDT 2008
Hi,
I would like to apply a rotation to a pdb model, in order to place
copies of it in equivalent symmetry points (icosahedral symmetry).
I am not sure I understand all the different coordinate systems in
chimera, but digging into the program code, I was able to write the
following script.
I am not sure it is the best way to do it, and obviously at the
moment it does not work properly, because I am not specifying the
center of rotation.
With respect to the coordinates of the pdb model, I know the center
of symmetry, let's say (161,161,161), but I don't know how to impose it.
I tried to assign these coordinates to the parameter 'cofr', but the
result does not change.
Does anyone know how to apply, inside a script, a rotation matrix
around a given point?
Any other feedback on the correctness of the script is very welcome.
Thank you.
Giovanni
###############################################
from chimera import openModels, Point
from PDBmatrices import chimera_xform
from Icosahedron import icosahedral_symmetry_matrices
icomats = icosahedral_symmetry_matrices(orientation = '222r')
for rmat in icomats:
xf = chimera_xform(rmat)
m, = openModels.open('/dummy/dummy.pdb') # open a copy of the
model
m.openState.xform = xf # set rotation
###############################################
=============================================
Giovanni Cardone
Laboratory of Structural Biology Research
National Institutes of Health
50 South Drive (Building 50), Room 1511
Bethesda, MD 20892-8025 USA
Tel: (301) 451-8247
FAX: (301) 480-7629
Giovanni_Cardone at nih.gov
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