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Re: [ccp4bb] B-factor & Space gr questions! |
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CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 05 June 2007Subject: Re: B-factor & Space gr questions! From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU Date: 2007-06-05 molecule has moved between the high-resolution and low-resolution datasets ? I would have thought that there was an effective information transfer between R-work and R-free once the rigid body movements became too large, which might provide one with an over-optimistic idea of what the R-free would be with the high-resolution model with the low-resolution data. Phil Princeton NJ Edward A Berry wrote: > Even if the free-R set is not preserved for the new crystal, > R and R-free tend to diverge rapidly once any kind of > fitting with a low data/param is performed, so I think > the new structure must not have been refined much beyond > rigid body (and over-all B which is included in any kind > of refinement). And that choice may be well justified. > Ed > > cdekker wrote: >> Hi, >> >> Your reply to the ccp4bb has confused me a bit. I am currently >> refining a low res structure and realise that I don't know what to >> expect for final R and Rfree - it is definitely not what most people >> would publish. So the absolute values of R and Rfree are not telling >> me much, the only gauge I have is that as long as both R and Rfree are >> decreasing I am improving the model (and yes, at the moment that is >> only rigid body refinement). >> In your email reply you suggest that even though a refinement to >> convergence that will lead to an increased Rfree (and lower R? - a >> classic case of overfitting!) would be a better model than the >> rigid-body-refined only model. This is what confuses me. >> I can see your reasoning that starting with an atomic model to solve >> low-res data can lead to this behaviour, but then should the solution >> not be a modification of the starting model (maybe high B-factors?) to >> compensate for the difference in resolution of model and data? >> >> Carien >> >> On 4 Jun 2007, at 19:38, Edward A Berry wrote: >> >>> Ibrahim M. Moustafa wrote: >>>> The last question: In the same paper, for the complex structure R >>>> and Rfree are equal (30%) is that an indication for improper >>>> refinement in these published structure? I'd love to hear your >>>> comments on that too. >>> Several times I solved low resolution structures using high resolution >>> models, and noticed that R-free increased during atomic positional >>> refinement. This could be expected from the assertion that after >>> refinement to convergence, the final values should not depend on >>> the starting point: If I had started with a crude model and refined >>> against low resolution data, Rfree would not have gone as low as the >>> high-resolution model, so if I start with the high resolution model >>> and refine, Rfree should worsen to the same value as the structure >>> converges to the same point. >>> >>> Thinking about the main purpose of the Rfree statistic, in a very >>> real way this tells me that the model was better before this step >>> of refinement, and it would be better to omit the minimization step. >>> Perhaps this is what the authors did. >>> >>> On the other hand it does not seem quite right submit a model that >>> has simply been rigid-body-refined against the data- I would prefer to >>> refine to convergence and submit the best model that can be supported >>> by the data alone, rather than a better model which is really the model >>> from a better dataset repositioned in the new crystal. >>> >>> Ed CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 05 June 2007 |
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