Hi Chris, what would concern me is that one glucose have atoms with different occupancies or all of them. That is chemically unlikely. You should define sensible constraint groups, I think.
Cheers Christian
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.Best,ChrisOn Fri, Feb 5, 2016 at 6:38 PM, Pavel Afonine <pafonine@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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