[Chimera-users] How to define a center of rotation when applying a symmetry

[Giovanni Cardone]

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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