[phenixbb] occupancy refinement
pafonine at lbl.gov
Wed Jan 28 07:16:41 PST 2009
> To this end, I set the occupancy of these atoms to 0.99 in Coot so that
> they would be picked up by occupancy refinement in phenix.refine (using
> version 1.4-3). Phenix however just put the value back to one. It
> looks like the occupancy refinement in phenix is meant for alternative
> conformations where the sum of the occupancies of the different
> conformations is 1.
No, phenix.refine can do individual, group, group constrained occupancy
If it put the value back to 1, then this means that this is what it
wants to refine to.
By the way, setting it to .99 is one way of prompting phenix.refine to
refine it. The other way is just give it a selection of atoms for which
you want to refine occupancies, for example:
phenix.refine model.pdb data.mtz refine.occupancies.individual="chain X
and resseq 123 and name OXT"
Since occupancies and B-factors are correlated, you can try to re-set
b-factors to some average value, and try again. Also, you may try
different staring value, say 0.5, and not .99.
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