[phenixbb] Difference Map positive peaks in release dev-798

[Pavel Afonine]

Hi Yuri,

> 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 
> occupancy.
> 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?

Pavel.