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Re: [ccp4bb] how to improve Rfree? |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: how to improve Rfree? From: Bart Hazes Bart {- dot -} Hazes {- at -} UALBERTA {- dot -} CA Date: 2009-10-19 The RFREE SHELL command in sftools is another way to select thin shells. However, for the purist there is no clean way of getting rid of correlations between the Rwork and Rfree sets that I know of. To do it properly, the thickness of the thin shell should be larger than the radius where the G-function has strong features. In practice that makes the shells so thick that you can have only a few which likely causes artifacts. Even then, the reflections at the edge of the shells are still contaminated so you'd have to exclude the ones near the edge from both the Rwork and Rfree sets. I'm pretty sure that there has been a publication long ago on thick shells (It may have been Ian, Phil or some other CCP4BB regular). An improvement would be to go from shells to donuts, basically the intersection of the spherical shell and a plane through the origin perpendicular to the NCS rotational symmetry axis. One step further is Fred's suggestion to use the explicit NCS relationships to select groups of NCS-contaminated reflections, but only works if the NCS symmetry forms a closed group. One step further again would be to use an explicit low resolution G-function model to find the strongest NCS correlations and only group those together. Enough fodder for purists to fight over but when sftools users ask me, my general response includes the fact that the higher your NCS the greater the NCS-contamination problem, but also the smaller the model bias/overfitting problem, assuming NCS restraints are used appropriately in refinement. As a reviewer I would have a problem with authors patting their backs for a small Rwork-Rfree difference without noting the impact of NCS. But if they report a low Rwork-Rfree difference and comment on the fact that the difference is likely underestimated due to NCS effects I have no problems, with or without thin shells, as long as I feel the refinement protocol and final model are acceptable for the biological interpretations that they make. Bart Vellieux Frederic wrote: > Hi Ian (& ccp4bb'ers), > > NCS ties reflections in reciprocal space by the interference > G-function effect. Nothing more. So you get an R-free value that is > lower than if you don't have NCS. One should be aware of that, and > referees should be aware of that. > > I currently have a structure that has 12-fold NCS in the asymmetric > unit. The free R-factor is lower than the R-factor. I expect that > future referees will not view that kindly. > > A number of people have suggested to use different approaches to get > rid of this reciprocal space binding effect. One of these people (Bart > Hazes I think, correct me if I'm wrong) suggests to take reflections > for the R-free as thin shells in reciprocal space. The thin shell is > omitted completely from the target for refinement (I suppose omitting > a shell of data completely will also have deleterious effects on the > refinement, I don't know by how much). Problem is, none of the data > processing programs or suites of programs has implemented this as far > as I know. A better approach would be to use the NCS operator (the > transpose and the inverse of the rotation matrices in fact, including > the identity matrix for all cases including the cases where the only > NCS is 1-fold NCS, i.e. the presence of solvent in the asymmetric unit > or unit cell) to select the subset of reflections that are going to be > omitted from the refinement target: take one reflection, select all > equivalents that are bound to it by the interference effect, and > repeat the process until you have reached the required number of > reflections to be omitted. But this requires serious programming... > And someone willing to modify all data processing suites to include > this approach. But that would satisfy referees because it is the only > approach that is valid. > > Fred. > > Ian Tickle wrote: >> The problem is that real life is never simple! - >> and NCS really messes things up! >> >> Cheers >> >> -- Ian >> -- ============================================================================ Bart Hazes (Associate 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 ============================================================================ CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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