[phenixbb] Unexpected Occupancy refiniement for ligands...
yuri.pompeu at ufl.edu
Sat Aug 13 11:18:36 PDT 2011
Dear Ed and Pavel,
Some background, 1.5A, 0.14/0.16, P 63 2 2.
1- I figured out the occupancy problems. I had to define the ligands as
group occupancy rather than individual atoms...(duh!!...)
It looks better now.
2- Is there any case/resolution when one should try anisotropic
refinement for a ligand? I would think if its covalently attached
3- About the waters occupancies/B-factors I definetely see some density
peaks that correspond to waters (good distance and angles for H-bond
interactions with protein backbone on the surface)
Obviously they are weaker than peaks for waters that are ordered near
the active site. I modelled those in and I got some negative peaks in
the mFo-DFc map after isoptropic B refinement. That is what led me
to think I should try occupancy refinement.
4-Still on the same topic B-factors, I am also encountering the same
problem with surface side chains especially (D, E, Q). I am confident
they should be where they are. backbone density looks great.
But no matter where I put their side chains, I get negative peaks in
the diff. map. Their B-factors usually refine to ~55 vs ~25 for ordered
On Sat, 13 Aug 2011 12:45:32 -0400, Edward A. Berry wrote:
> Yuri wrote:
>> HETATM 6875 HC22 MLA L 3 33.760 -29.776 6.943 1.00 30.56
>> C H
>> Each atom is getting an individual occupancy assigned, which
>> is impossible :)
>> Any light?
>> Could it be my selection syntax?
> Could be- What was your selection syntax?
> For waters its probably not a good idea to refine occupancy - let the
> B factor
> take care of it unless you have really high resolution.
> For larger ligands I think it makes sense to refine occupancy (for
> whole ligand as a single occupancy group) and individual isotropic
> The ADP's can only spread the electrons around, cannot correct if
> the integrated electron density for the ligand is less than expected.
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