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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008Subject: Re: an over refined structure From: Dean Madden drm0001 {- at -} DARTMOUTH {- dot -} EDU Date: 2008-02-07 This is an intriguing argument, but I know (having caught such a case as a reviewer) that even in cases of low NCS symmetry, Rfree can be significantly biased. I think the reason is that the discrepancy between pairs of NCS-related reflections (i.e. Fo-Fo') is generally significantly smaller than Fo-Fc . (In general, Rsym (on F) is lower than Rfree.) Thus, moving Fc closer to Fo will also move its NCS partner Fc' closer to Fo' *on average*, if they are coupled. Dean Edward Berry wrote: > Actually the bottom lines below were my argument in the case > that you DO apply strict NCS (although the argument runs into > some questionable points if you follow it out). > > In the case that you DO NOT apply NCS, there is a second > decoupling mechanism: > Not only the error in Fo may be opposite for the two reflections, > but also the change in Fc upon applying a non-symmetrical > modification to the structure is likely to be opposite. So there > is no way of predicting whether Fo-Fc will move in the same > direction for the two reflections. I completely agree with Dirk > (although I am willing to listen to anyone explain why I am wrong). > > Ed > > > Edward Berry wrote: >> Dean Madden wrote: >>> Hi Dirk, >>> >>> I disagree with your final sentence. Even if you don't apply NCS >>> restraints/constraints during refinement, there is a serious risk of >>> NCS "contaminating" your Rfree. Consider the limiting case in which >>> the "NCS" is produced simply by working in an artificially low >>> symmetry space-group (e.g. P1, when the true symmetry is P2): in this >>> case, putting one symmetry mate in the Rfree set, and one in the >>> Rwork set will guarantee that Rfree tracks Rwork. >> >> I don't think this is right- remember Rfree is not just based on Fc >> but Fo-Fc. Working in your lower symmetry space group you will have >> separate values for the Fo at the two "ncs-related" reflections. >> Each observation will have its own random error, and like as not >> the error will be in the opposite direction for the two reflections. >> >> Hence a structural modification that improves Fo-Fc at one reflection >> is equally likely to improve or worsen the fit at the related reflection. >> The only way they are coupled is through the basic tenet of R-free: >> If it makes the structure better, it is likely to improve the fit >> at all reflections. >> >> For sure R-free will go down when you apply NCS- but this is because >> you drastically improve your data/parameters ratio. >> >> Best, >> Ed > -- Dean R. Madden, Ph.D. Department of Biochemistry Dartmouth Medical School 7200 Vail Building Hanover, NH 03755-3844 USA tel: +1 (603) 650-1164 fax: +1 (603) 650-1128 e-mail: dean.madden@dartmouth.edu CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008 |
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