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@nih.gov

=============================================