[phenixbb] Unexpected Occupancy refiniement for ligands...

Yuri 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 
side chains.


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 
>> physically
>> 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 
> the
> whole ligand as a single occupancy group) and individual isotropic 
> ADP.
> The ADP's can only spread the electrons around, cannot correct if
> the integrated electron density for the ligand is less than expected.

Yuri Pompeu

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