[phenixbb] occupancy refinement

[Pavel Afonine]

Hi Nicole,

> 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 
refinement.
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.

Pavel.