I think the correlation between occupancy and B-factor depends
also on the size of the ligand (relative to resolution).
Bob Stroud, I think, has estimated occupancy by comparing
the integrated electron density of the ligand with that of
a well-defined, isolated water (assumed to be at unit occuancy?).
In principle the integrated electron density is not affected
by applying a B-factor, it is just spread out over a wider
area. In the case of a single atom at 3 A resolution, it
is spread out under the neighboring atoms and effectively
lost, so it is hard to distinguish high B-factor from low
occupancy.
In a large ligand most of the atoms are inside the ligand,
so their spread-out density remains inside the ligand
and gets counted in the integrated density. In that case
high B-factor has a very different effect than low occupancy,
as only the latter reduces the total electron density of
the ligand.
During a previous reincarnation of this thread I did the
simple test of refining occupancy and B-factor for a
stretch of the protein (holding the rest of the protein
at unit occupancy) in CNS 1.1, and I felt the results
were quite satisfactory (don't have the specifics now).
Ed
Anastassis Perrakis wrote:
>> I have already changed occupancies as Eleanor mentioned, and got
>> approximate values. But my hope is to try to get much precise ones if
>> possible.
>>
> I never expected to preach the 'Kleywegt Gospel' in the ccp4bb,
> but in this case what you need is more accurate answers, not more
> precise ones
> (or better both, but precision alone can be a problem, and you can
> easily get
> 'precise' but inaccurate data easily by making the wrong assumptions
> in your experiment)
>
> http://en.wikipedia.org/wiki/Accuracy
>
>> I have heard from my colleague SHELX can refine occupancies, and
>> got its license. I'll next try SHELX.
>
> I think that phenix.refine can also do occupancies ?
> The problem is not if the program can do it, but if at your specific case
> you have enough information to do that in a meaningful way.
>
> For a soaking experiment and 1.5 A data, I would say that Eleanor's
> suggestion
> of tuning Occ based on B, is as close as you would get, accurate enough
> given the data,
> although not necessarily too precise.
>
> Tassos
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