[phenixbb] Occupancy refinement of anomalous scatters

Pavel Afonine pafonine at lbl.gov
Mon Sep 8 23:59:11 PDT 2014

Hi Chen,

my apologies for the late reply, somehow I managed to overlook your 
email.. Ok, here it is (better late than never!):

> 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.

HA sites may be partially occupied. Try this for HA with high B: set 
occupancy of HA to some number less than 1 and reset B to mean B, then 
run phenix.refine (make sure occupancy refinement is enables, which is 
the default).
If this does not help then please send me files and I will have a closer 


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