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Re: [ccp4bb] B-factor & Space gr questions! |
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CCP4bb navigationCCP4bb <-- 2007 <-- June 2007 <-- 04 June 2007Subject: Re: B-factor & Space gr questions! From: Edward A Berry eaberry {- at -} LBL {- dot -} GOV Date: 2007-06-04 > 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 <-- 04 June 2007 |
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