Ian and Herman,
does one want to convolute the electron density at all? I was under the
impression that current thinking favors convolution of the model
instead, i.e. placing both the helices in both orientations at partial
occupancy and letting the refinement program figure things out?
Andreas
[email protected] wrote:
Dear Ian and Margriet,
You are right, the correction needs to be done on F, not on |F|^2. If I recall
correctly (I did not do it myself), the assumption was that Fobs = 0.5*Fobs(A)
+ 0.5*Fobs(B), so Fcorrected(A) = 2*Fobs - Fcalc(B) where A and B are the two
orientations. Since one does not have an observed phase, one would have to take
calculated phases. I am unsure though, if that was done in practise and one did
not just subtract the absolute values. Since the inhibitor is usually only a
small part of the total scattering mass, the phases might not differ too much
and therefore the error would not be too big. In case of superposition of base
pairs, I guess that the differences in scattering between the different
base-pairs is not too much, so one might also be able to get away with not
using phases, but here you are the expert.
Using this method, one could much better interpret the convoluted electron
density, but one has to be very careful not introducing severe model bias. I
would look in the literature in detail, what people from the HIV protease field
had done to solve this problem.
Cheers,
Herman
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
