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
