Re: [ccp4bb]: Refinement of ligand occupancy

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Daniel Copeland wrote:
> 
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> I am a graduate student working on my first structure determination of a
> heme protein (HOPEFULLY) bound to a ligand.  The assumption is that the
> ligand will displace AN axially bound water molecule.  I have run into a
> problem with trying to refine the occupancy of the ligand.  I have already
> attempted to use CNS to refine the occupancy of the ligand.  I have used
> both the q-group and q-individual and harmonically restrained (with various
> intensities) all or part of the ligand.  I generated another Fo-Fc electron
> density map after the>refinement step and did not see any improvement.  I
> have a few questions and any opinions would be helpful.


  Here are some general comments - I am not an expert on CNS

1) the behavior will depend very much on the resolution of your data. at
3A it will be hard to judge - at 1.2A you can use the peak heights to
estimate the occupancy.
This will also affect the B factor/ occupancy correlation.

2) I presume the whole ligand is there in some of the unit cells, so it
will still need a full set of restraints.

  You ask about positive and negative peaks, but in what sort of map? 


 I would look very carefully at a 2mFoDFc map without the ligand
present. Leave out some side cchain  too in the vicinity to see the
relative heights of the 2 features.

But it is very difficult to refine occupancy without high resolution
data, as you are finding! 

Eleanor