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Seeing as it is an important residue...
here's a suggestion that can work...
If q(A) is the occupancy of conformation A, and q(B) is the occupancy of
conformation B,
perform independent refinements with q(A) = 0 through 100 with steps of 5%,
with q(B) = 1 - q(A). Look at every result with corresponding Fo-Fc maps
displayed. Find Q1 = maximum q(A) such that you see positive Fo-Fc density
associated with conformation A. Find Q2 = minimum q(A) such that you see
negative Fo-Fc density associated with conformation A. (you should
similarly look at density associated with conformation B). Your occupancy
of (A) is the average of Q1 and Q2.
Note, however, that if your water molecules coincide with density of either
conformation then your problem is more complicated.
A problem with your in principle method is that it may be a bad assumption
that the atomic B-factors are the same in each conformation.
Anthony
At 11:25 AM 6/09/2005, OnLineHelpForm wrote:
I'd apreciate advice on following issue:
I've nearly finished refinement using Refmac of a structure with data to
1.7A in which a few side chains have 2 conformations. Normally I'd set the
occupancies at 0.5 and be done with it. In this case one of the ACs is in
the 'active site' and involves a glutamate side chain plus two water
molecules. Its clear that one conformer is preferred, as judged by fo-fc
maps refined at equal occupacies. Since thi is an important partt of the
structure I'd like to be as accurate as reasonable. My question is how to
proceed from here. Both conformers make H bonds with either ligand or
protein and so probably have similar b values... In principle I could fix
B and refine at occupancy steps of say 0.1 and look for fo-fc maps with
best residuals around this residue. Is there a better way? It would be
nice to refine occupancy automatically in refmac.
Thanks in advance,
Mark Mayer, [EMAIL PROTECTED]
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Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-3907 Fax. 61-2-9351-4726
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