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Dale Tronrud wrote: > Bart Hazes wrote: > >> Dale Tronrud wrote: >> >>> [log in to unmask] 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 >> > Dear Bart, > > I agree that the way one uses the test set depends critically on the > question you are asking. In my letter I was focusing on that aspect > of the pseudo centered crystal problem where the strong/weak divide can > be used to particular advantage. > > I have not thought as much about the matter of using the test set > to estimate the level of uncertainty in the parameters of a given model. > My gut response is that the strong/weak distinction is still significant. > Since the weak reflections contain information about the differences > between the two, ncs related, copies I suspect that a great many systematic > "errors" are subtracted out. > > For example, if your model contains isotropic B's when, of course, > the atoms move anisotropically, your maps will contain difference features > due to these unmodeled motions. Since the anisotropic motions are > probably common to the two molecules, these features will be present in > the average structure described by the strong reflections but will be > subtracted out in the "difference" structure described by the weak > reflections. This argument implies to me that the strong reflections > need to be judged by the Sigma A derived from the strong test set and > the weak reflections judged by the weak test set. > > Dale Tronrud Hi Dale, I agree with the above but think there is yet another way to think about this which may also suggest a more general solution. In a case of pseudo-translational NCS you can separate three effects. 1) An overal modulation of reflection intensity that depends just on the pseudo translation vector (x,y,z) and the reflection indices (h,k,l). 2) Deviations from pure translation due to the NCS axis not being perfectly parallel to the crystallographic axis. 3) Deviations from pure translation due to local structural deviations between NCS-related molecules. The problems I was referring to are due to the first effect, which messes up the expected structure factor intensity distribution. Your comments relate to the second and especially third effects where the weak reflections inform about actual differences between the NCS-related molecules. Sigmaa calculations already correct for expected intensity effects due to crystallographic symmetry but not for pseudo-translation effects. Given the translation component of the pseudotranslational symmetry it is possible to estimate the expected intensity for a reflection and I would think that could be used as a correction factor just like we do with normal crystallographic symmetry. This correction would basically transform the bimodal intensity distribution due to strong and weak subsets of reflections back to a normal unimodal distribution which, in an ideal world, only differs from normal data in the fact that the weak subset will have a poor F/SigF ratio compared to the strong subset. As long as the standard deviation is accounted for this could allow us to consider all data on equal footing. 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 =============================================================================