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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: Edward Berry eaberry {- at -} LBL {- dot -} GOV Date: 2008-02-07 > Hi Ed, > > 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. OK, I see that now, the systematic errors must be related to "NCS" in this case because we know if we reduced the data in the higher space group, our Rsyms would be OK. I stand educated. But it is difficult to go from there to real ncs where the large unaccounted errors may not be related to ncs. Furthermore if you don't enforce NCS the structural changes are asymmetric and there is no reason to believe Fc will move in the same direction, even in this artificial case. So Dirk's assertion still stands, I believe. > > 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 >> > CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008 |
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