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Have a look at (for example) D. E. Tronrud Introduction to macromolecular refinement Acta Cryst. (2004). D60, 2156-2168 It gives a general overview on refinement and provides answers to your questions. R. Peter Adrian Meyer ([EMAIL PROTECTED]) wrote: > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi all, > > Anthony Duff wrote (regarding R-fac and R-free from mapfiles?) > > 2. CNS does a worse job of refining a structure in the late stages, > even > > accounting for differences in default restraint weights. (I don't know > why > > this would be so, with both using maximum likelihood... maybe the CNS > algorithms are inferior?) > > This reminded me of a question I've been wondering about for a bit: Does > maximum likelihood refer to a scoring function (generate gradients to > optimize while refining), or both a scoring function and refinement > menthod? As far as I understand, it's the first (based on what I've seen > of poking around in the internals of programs that do ML refinement vs > other types of refinement). But least-squares is a special case of > maximum likelihood, and least-squares (again as far as I know) is both a > scoring function and refinement method. > > Could somebody more knowledgable about maximum likelihood clear this up? > > Thanks, > > Pete > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > > > > > > > >
