[phenixbb] special position

Karolina Michalska dziuba at amu.edu.pl
Mon Jul 9 16:01:18 PDT 2012

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.


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