I tried to test sth related to the TransformationSymmetry on rigid
bodies and I fail to get it work properly in the below simple example.
In the example I create four copies of a chain, create four-fold
symmetry constraints and try to generate the updated configuration using
model.update(). In the resulting model.rmf, three chain copies are fine
and follow the symmetry but one copy of the chains is weirdly rotated.
Your script looks OK to me. I would need to see your input PDB to say
for sure, but TransformationSymmetry on a rigid body sets the reference
frame of the body, i.e. the coordinate system used for all particles in
that body, not the global coordinates of the member particles. I expect
if you examine the rigid bodies' reference frames, you'll see they're
related by the transformation correctly. The initial reference frame of
a rigid body is (usually) the principal axes of the members, not the
origin of the global coordinate system, so my guess is that these don't
all line up in your case.