[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 

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.


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