[phenixbb] why are my B factors being "refined"

Scott Classen sclassen at lbl.gov
Mon Apr 4 12:35:47 PDT 2011

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?


Scott Classen, Ph.D.
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Berkeley, CA 94720
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O) 510.495.2697
Beamline) 510.495.2134

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