[phenixbb] B factors of zero after refinement
Pavel Afonine
PAfonine at lbl.gov
Thu May 13 15:42:50 PDT 2010
Hi Kyle,
> I have been performing standard refinement of atomic coordinates and B
> factors (ADP) in phenix.refine using NCS and bulk solvent correction
> without anisotropic scaling. The program has been returning a handful
> of atoms with B factors of zero after refinement, and I'm not sure
> why. I tried using adp.set_b_iso to reset all B factors before
> refinement but some still come back down to zero. Has anyone else
> noticed something similar, or has a suggestion on what to do?
is it a water oxygens? Typically, if a water oxygen gets placed into a
heavier atom density (ion, metal) then its B-factor refines to much
smaller value, sometime close to zero. So I would investigate this
possibility.
If it's not the water, then I don't know what's happening. And to tell
more I would need to look at the data and model and probably run some
refinement myself.
Pavel.
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