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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008Subject: Re: an over refined structure From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2008-02-08 > price@UCHICAGO.EDU wrote: > > Rotational near-crystallographic ncs is easy to handle this way, but > > what about translational pseudo-symmetry (or should that be > > pseudo-translational symmetry)? In such cases one whole set of spots is > > systematically weaker than the other set. Then what is the > > "theoretically correct" way to calculate Rfree? Write one's own code to > > sort the spots into two piles? > > Phoebe > > > > Dear Phoebe, > > I've always been a fan of splitting the test set in these situations. > The weak set of reflections provide information about the differences > between the ncs mates (and the deviation of the ncs operator from a > true crystallography operator) while the strong reflections provide > information about the average of the ncs mates. If you mix the two > sets in your Rfree calculation the strong set will tend to dominate > and will obscure the consequences of allowing you ncs mates too much > freedom to differ. I haven't had to deal with this situation but my first impression is to use the strong reflections for Rfree. For the strong reflections, and any normal data, Rwork & Rfree are dominated by model errors and not measurement errors. For the weak reflections measurement errors become more significant if not dominant. In that case Rwork & Rfree will not be a sensitive measure to judge model improvement and refinement strategy. A second and possibly more important issue arises with determination of Sigmaa values for maximum likelihood refinement. Sigmaa values are related to the correlation between Fc and Fo amplitudes. When half of your observed data is systematically weakened then this correlation is going to be very high, even if the model is poor or completely wrong, as long as it obeys the same pseudo-translation. If you only use the strong reflections for Rfree I expect that should get around some of the issue. Of course it can be valuable to also monitor the weak reflections to optimize NCS restraints but probably not to drive maximum likelihood refinement or to make general refinement strategy choices. Bart ============================================================================== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================== CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008 |
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