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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 on I's and Rfree on F's, Rmerge of 5% should contribute 2.5% to Rfree; and furthermore errors add vectorially so it would be more like ,025/sqrt(2). I guess I have to take all those other errors that have to do with the inability of a simple atomic model to account for the diffraction of a crystal, lump them together and assume they have nothing to do with NCS and are not affected by the simple modification under consideration. I am thinking about the CHANGE in Fo-Fc at two sym-related reflections when the refinement program moves a single atom from position 1 to position 2. If we do not apply NCS, this is the only atom that will move, and for Fc we can definitely say there is no reason to expect the two Fc's to move in the same direction, therefore there is no coupling in the case we do not apply NCS. If we apply strict NCS then granted the sym related Fc's are equal before and after the change, so they move in the same direction. As I said, the argument is weaker now. If there are systematic errors contributing to the gap between Rfree and 0.5*Rmerge/sqrt(2), and if these systematic errors follow the NCS, then initial Fo-Fc is likely to be of the same sign at the related reflections and larger than the change in Fc, so Fo-Fc would go in the same direction. But to justify this you would have to explin why the systematic errors follow ncs. Crystal morphology related to ncs resulting in similar absorption errors? But how large are absorbtion errors, and is there any reason for morphology to follow NCS? After reading Dean Madden's latest- We might need some assumption here that we are reasonably close to the refined structure. If we start with random atoms then shoving the atoms around in a way that fits the density better might be seen as "improving the structure" from the point of modeling the density, but not from the point of approximating the real structure. But in this case the change in sign of Fc is completely decoupled between sym-related reflections, and if you enforce symmetry you will be enforcing the wrong symmetry and worsening both the structure and the fit to the density. I think Gerard Kleywegt has an example of enforcing NCS on a an erroneous structure, and it was not very effective at reducing Rfree? And in that case the structure may have had some resemblence to the density at low resolution,the NCS may have been somewhat correct. I guess there are two questions depending whether you are at the beginning at the beginning of a refinement and may have a completely wrong structure, or whether refinement isnearly complete and you want to know whether the further improvement you get on applg NCS is real. Jon Wright wrote: > Dear Ed, > > I don't see how you "decouple" symmetry mates in the case of a wrong > space group. Symmetry mates should agree with each other typically > within "R_sym" or "R_merge" percent, eg; about 2-5% . Observed and > calculated reflections agree within "R_Factor" of each other, so about > 20-30%. The experimental errors are pretty much negligible and > overfitting is not a question about error bars; it is about how hard to > push a round peg into a square hole? > > Cheers, > > Jon > > 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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