[phenixbb] special position

Pavel Afonine pafonine at lbl.gov
Mon Jul 9 15:04:51 PDT 2012

Hi Karolina,

both ways you described should work.. Could you send me the inputs 
(off-list) so I have a closer look?


On 7/9/12 4:01 PM, Karolina Michalska wrote:
> Hi all,
> I'm refining a structure with a phosphate ion on a 3-fold axis. I set
> occupancy manually to 0.33 and after refinement the ion has huge
> B-factor (close to 100) and there is a lot of positive electron density.
> I found somewhere that phenix recognizes special positions and there is
> not need to adjust occupancy manually. so I set it to 1 again and
> re-refined. This time my phosphate sits in a mixture of negative and
> positive density with B factor around 90 (for comparison Refmac refines
> it to ~20). Now I'm confused which procedure to follow.
> Karolina
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