[phenixbb] Difference Map positive peaks in release dev-798
pafonine at lbl.gov
Sat Jun 25 15:50:30 PDT 2011
> I was wondering if anything changed (weights or something) in the way
> the difference maps are calculated?
no, I did not change anything recently that would affect the mFo-DFc map.
> I just ran refinement on a 1.3 structure and a hexacoordinated Mg2+
> ion has significant positive density peak even at occupancy 1.0. I had
> not noticed that before.
When the change occurred (between which version numbers)? Does the peak
disappear if you do the same calculation using an older version?
> My ligand also does have positive peaks, but refine gives it a .91
> I wonder if I am missing some parameter cif file or some definition
> that would make the positive peaks decrease?
There is no general remedy - it's all case-dependent.
Does its B-factor differ significantly from surrounding atoms?
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