[phenixbb] Alternate occupancies

Pavel Afonine pafonine at lbl.gov
Thu Aug 4 13:33:28 PDT 2011

Hi Yuri,

> If tell phenix.refine to do occupancy refinement on resname HOH, will 
> it still perform the default refinement for residues with alternate 
> conformers?

Yes. It will add whatever selection you specified to the default 
selections. Note, that would apply to only existing waters with HOH 
resname. Occupancies of newly added waters (with ordered_solvent=true) 
will not be refined. To refine their occupancies as well you need to set 
True the corresponding parameter under ordered_solvent {...} scope of 


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