I haven't tried it out, but it looks like all you have to do is apply a transformation to your model before you apply the set of rotations. You could create a set of matrices to do it all in one step, but that's more trouble than it's worth. Something like this should work: Jonathan ############################################### from chimera import openModels from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices icomats = icosahedral_symmetry_matrices(orientation = '222r') centerRot = (161.,161.,161.) tMat = ((1.0,0.0,0.0,-centerRot[0]), (0.0,1.0,0.0,-centerRot[1]), (0.0,0.0,1.0,-centerRot[2])) for rmat in icomats: m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model m.openState.xform = chimera_xform(tMat) # set translation to for center of rotation offset m.openState.xform = chimera_xform(rmat) # set rotation ############################################### On Mon, Jun 2, 2008 at 1:00 PM, <chimera-users-request@cgl.ucsf.edu> wrote:

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Message: 1 Date: Mon, 2 Jun 2008 12:18:25 -0400 From: Giovanni Cardone <cardoneg@mail.nih.gov> Subject: [Chimera-users] How to define a center of rotation when applying a symmetry To: chimera-users@cgl.ucsf.edu Message-ID: <919BC0E8-98BD-4F1A-97DD-13F048B71C13@mail.nih.gov> Content-Type: text/plain; charset="us-ascii"

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