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:
http://www.phenix-online.org/documentation/refinement.htm#anch20

Pavel.

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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