[phenixbb] Occupancy refinement of anomalous scatters

Chen Zhao c.zhao at yale.edu
Tue Sep 2 11:50:33 PDT 2014

Hi all,

I have a question about the occupancy refinement of the anomalous scatters.
This is because when I went through all the HA sites, I found that some of
them has too high B factor and too high occ. I manually adjusted the occ
and fed the model into refinement, but the B factor and occ came back to
around their original level again. It seems that those have a stronger peak
in the anomalous difference Fourier map has a higher occupancy after
refinement, but this does not necessarily equals to a strong density peak
in 2Fo-Fc map (some of them even disappear after refinement), and this
might be related to their high B factor. Am I doing something wrong in the
refinement? I am basically using phenix.refine default setting, but with
TLS+isotropic B factor refinement and occupancy refinement of a small
region (5-8 residues). The resolution is 3 A, and the refinement is already
at the final stage. I am still at the learning stage and your input will be
greatly appreciated.

Thank you!

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