[phenixbb] weight optimization

Pavel Afonine PAfonine at lbl.gov
Sun Mar 29 16:57:03 PDT 2009

Hi Peter,

although occupancy refinement is listed among the strategies performed 
by default, in fact phenix.refine by default will only refine 
occupancies of atoms that are 1) not equal to 1.0 in your input PDB 
file, 2) having multiple conformations (alternative conformations).

If you don't have such atoms in your input PDB file, then no occupancy 
refinement will be performed. At 3.0A resolution, I wouldn't think you 
have any partially occupied sites (well, they may be present in the 
actual structure but you wouldn't see it at this rather low resolution), 
therefore you probably shouldn't worry about turning the occupancy 
refinement off.


On 3/29/09 12:40 PM, peter hudson wrote:
> Hello all
> I am very new to this field. I am refining a dataset of 3.0A 
> resolution. I want to perform the weight optimization. while weight 
> optimisation, occupancy refinemnet is default. I donot want torefine 
> the occupancy of any of the atoms from my model. How can i set to 
> occupancy_refinemnet=false. I will appreciate the suggestions.
> Thanks in advance
> Peter
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