[phenixbb] Refinement of occupancy 0 residues

Pavel Afonine PAfonine at lbl.gov
Mon Aug 3 06:48:31 PDT 2009

Hi Jose,

occupancies of any atoms that have 0 values are not normally refined in 
phenix.refine. I'm not sure why they get refined in your case. Could you 
please send me your PDB file before and after phenix.refine refinement 
run, and also the exact command you used?

Here are some details about occupancy refinement in phenix.refine:


On 8/3/09 4:41 AM, Jose M Casasnovas wrote:
> Dear phenix users.
> I have a question regarding use of phenix.refine.  We recently moved 
> from Refmac to Phenix and found out that residues with occupancy 0.00 
> were refined by phenix.refine, whereas those residues set to q=0 in 
> Coot were not refined in Refmac.  How can we avoid refinement of those 
> residue in phenix?  During the refinement is quite convinient to keep 
> residue with q=0, which can be included in the refinement upon map 
> improvement.
> Thanks so much.
> Jose M Casasnovas
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