Hi Giovanni, To convert icosahedron rotation matrices that act about origin 0,0,0 to instead use a different center of rotation (cx,cy,cz) you would first shift by -cx,-cy,-cz then apply the rotation then shift by cx,cy,cz. I've attached an example script. Note that "a.premultiply(b)" means to multiply b to the left of "a" which means that b acts after a. Note that the Chimera Multiscale dialog (Tools / Higher-Order Structure / Multiscale) will apply icosahedral symmetry and load the coordinates (use select all, then style show wire). It doesn't allow you to change the icosahedron origin to something different from 0,0,0 but you could modify your PDB coordinates to make that the origin. Tom from chimera import openModels, Xform from PDBmatrices import chimera_xform from Icosahedron import icosahedral_symmetry_matrices pdb_path = '/dummy/dummy.pdb' cx = cy = cz = 161 # Center of icosahedron icomats = icosahedral_symmetry_matrices(orientation = '222r') for rmat in icomats: xf = Xform.translation(-cx, -cy, -cz) xf.premultiply(chimera_xform(rmat)) xf.premultiply(Xform.translation(cx, cy, cz)) for m in openModels.open(pdb_path): # open a copy of the model m.openState.xform = xf # set rotation