r!
>
>> -Original Message-
>> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
> On
>> Behalf Of George M. Sheldrick
>> Sent: 31 May 2009 17:20
>> To: Patrick Loll
>> Cc: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] cou
t; Sent: 31 May 2009 17:20
> To: Patrick Loll
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] coupling between occupancy and b-values in
> refinement
>
> Dear Pat,
>
> You don't say how large your ligand is, but if the occupancy is
> refined as a single
Dear Patrick
Long ago we (Cheetham et a (1992) J Molec Biol 224:613-628) did some
refinements on hen lysozyme + substrate complexes at 1.75A and 2A
resolution and showed that B and occupancy are negatively correlated,
especially at 2.0A. In simplistic terms this is because at medium
reso
Simple test is to vary the occupancy (say increments of 0.1) and check for
residual densities following quickie refinements on each. Then at least you
know if you can make a conclusion or not.
I suppose you could also try refining coupled occupancies on ligand-sized
chunks of the protein to g
The other approach is to choose a reasonable B-factor from the atoms and
ligands in the vicinity, fix the B's, and then refine the occupancy.
It is true that the occupancy and B-factor of an atom are highly
correlated with full-matrix least-squares refinement. The only
discrimination comes from hi
Dear Pat,
You don't say how large your ligand is, but if the occupancy is
refined as a single parameter so that all the atoms in the ligand
are constrained to have the same occupancy, it should be rather
well-defined and not highly correlated with the B-values. By
the way, I was not your referee!
If there is serious doubt of a full occupancy of the ligand and it is
of importance for the interpreation it can in fact be handled and even
at lower resolution (we have done it 2.8 Å resolution for PDB 2C8K for
example) - I'm not the referee but maybe he/she is right ;-)
You need not refine
Hi all,
I'm looking for a reference to bolster my response to a referee, in
which I defend my decision not to refine the occupancy of a ligand in
structure refined at around 2 A resolution (note the ligand binding
slte lies on a two-fold crystallographic axis, so the maximum
occupancy is
