[phenixbb] Trouble with occupancy refinement

Chris Fage cdfage at gmail.com
Fri Feb 5 10:09:17 PST 2016

Hi Pavel,

The B-factors of these atoms are quite high (most are 100+), so maybe the
occupancy is compensating as you said. After refinement, the maps don't
look much different. Perhaps it's not worth bothering with occupancy
refinement, then?

I think you got my question. I was asking if it is unusual that only 5/93
occupancies were refined to values other than 0 or 1.


On Fri, Feb 5, 2016 at 6:38 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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..
> Pavel
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