[phenixbb] Alternate occupancies

[Pavel Afonine]

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 
parameters.

Pavel.