[phenixbb] Positive density at metal ions

Pavel Afonine pafonine at lbl.gov
Thu Sep 3 09:20:41 PDT 2015

Hi Jan,

see pages 8-14 here:

If this does not help, please send files to me (off-list) and I will 


On 9/3/15 09:11, Jan van Agthoven wrote:
> Hi everyone,
> I work on a structure of about 3 A resolution. The structure is almost 
> done except for 3 metal ions which remain positive in the density. The 
> metal is clearly Mn (refinement works fine for an other very similar 
> structure) and has been set at full occupancy.
> I tried to reset the B factor at lower values, which solves the 
> problem for 2 metal ions but not the 3rd one. Is there anything else I 
> can do?
> Jan
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