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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 13 February 2008Subject: Re: an over refined structure From: Edward Berry eaberry {- at -} LBL {- dot -} GOV Date: 2008-02-13 > ---- > In summary, this argument depends on two assertions that you can > argue with me about: > > 1) When a parameter is being used to fit the signal it was designed > for, the resulting model develops predictive power and can lower > both the working and free R. When a signal is perturbing the value > of a parameter for which is was not designed, it is unlikely to improve > its predictive power and the working R will tend to drop, but the free > R will not (and may rise). > > 2) If the unmodeled signal in the data set is a property in real > space and has the same symmetry as the molecule in the unit cell, > the inappropriate fitting of parameters will be systematic with > respect to that symmetry and the presence of a reflection in the > working set will tend to cause its symmetry mate in the test set > to be better predicted despite the fact that this predictive power > does not extend to reflections that are unrelated by symmetry. > This "bias" will occur for any kind of "error" as long as that > "error" obeys the symmetry of the unit cell in real space. > Dear Dale, Thanks for taking the time to think about my problem and for composing what is obviously a well-thought-out explanation. I am a little over my head here, but I think I see your point. Inappropriate fitting of this residual error has poor predictive power so does not reduce {Fc-Fo for general free reflections. However the error is symmetrical, so attempts to fit it will result in symmetrical changes which reduce Fo-Fc for those free reflections that are related to working reflections. I need to read the references that were mentioned in this discussion, and think about it a little more in order to resolve some remaining conflicts in my thinking. But I don't need to bother everyone else with my struggles, unless I come up with something useful. Thanks for the guidance! Ed CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 13 February 2008 |
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