> On 10/11/11 12:58, Ethan Merritt wrote:
> > On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
> >> In the limit yes. however limit is when we do not have solution, i.e. when model errors are very large. In the limit map coefficients will be 0 even for 2mFo-DFc maps. In refinement we have some model. At the moment we have choice between 0 and DFc. 0 is not the best estimate as Ed rightly points out. We replace (I am sorry for self promotion, nevertheless: Murshudov et al, 1997) "absent" reflection with DFc, but it introduces bias. Bias becomes stronger as the number of "absent" reflections become larger. We need better way of estimating "unobserved" reflections. In statistics there are few appraoches. None of them is full proof, all of them are computationally expensive. One of the techniques is called multiple imputation.
> >
> > I don't quite follow how one would generate multiple imputations in this case.
> >
> > Would this be equivalent to generating a map from (Nobs - N) refls, then
> > filling in F_estimate for those N refls by back-transforming the map?
> > Sort of like phase extension, except generating new Fs rather than new phases?
> >
> > Ethan
Dale Tronrud wrote>
>
> Unless you do some density modification you'll just get back zeros for
> the reflections you didn't enter.
Sure. And different DM procedures would give you different imputations,
or at least that was my vague idea.
Garib N Murshudov wrote>
> Best way would be to generate from probability distributions derived after refinement, but it has a problem that you need to integrate over all errors. Another, simpler way would be generate using Wilson distribution multiple times and do refinement multiple times and average results. I have not done any tests but on paper it looks like a sensible procedure.
OK. That makes sense.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
|