[phenixbb] Trouble with occupancy refinement

Pavel Afonine pafonine at lbl.gov
Fri Feb 5 09:38:07 PST 2016

Hi Chris,

> I've built several glucose molecules from my cryosolution into regions 
> of weaker electron density. Attempting to refine the occupancies of 
> the corresponding atoms, I set the value of each to 0.25 in the pdb 
> file. However, after running phenix.refine, most of the atoms still 
> have occupancies of 1.00:

perhaps they are fully occupied but highly mobile which explains weak 
density? Or B-factor refines to larger value so that occupancy tries to 
compensate? How maps look like after refinement?

> 14 atoms with occ = 0.00
> 5 atoms with 0.00 < occ < 1.00
> 74 atoms with occ = 1.00
> Is this unusual?

Do you mean is it unusual to have 5 atoms in your structure with 
occupancies between 0 and 1? Hm.. I don't know, may be not! I think I'm 
not understanding what's the real question here..


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