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.