Hi Scott, yes, I just reproduced it using a fake one-atom model and generated Fobs... The output B-factors are different because of anisotropic scaling: the trace of overall scale matrix is subtracted from it and is added to Bsol and all atomic B-factors. This is described in details in: http://www.phenix-online.org/newsletter/ see "On atomic displacement..." article. I agree, strictly speaking you are right: you did not ask phenix.refine to do anything with atomic B-factors, so they must be the same in input and output files. I guess I make this sure in most of other case, but I most likely overlooked rigid-body refinement case (it has its own bulk-solvent correction and scaling step). I just made this change, so B-factors will stay the same in your case. It will be available in a next build (in a day or two). Pavel.
Hello Phenix community,
I'm currently using nightly build 718, but this behavior is exhibited since sometime in the 1.6.xx releases too.
I've turned off ADP refinement (only doing rigid_body refinement) and set the b_iso specifically as such:
modify_start_model { selection = None adp { atom_selection = None randomize = None set_b_iso = 55 convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None }
Yet the output PDB file has all b-factors in the 100s.
Whazzup with that?
Thanks, Scott