Hi Robbie, I agree that you bias R-free after the real-space refinement
well, ok, isn't it enough to realize that this is bad and should be avoided ? (I guess we all know we should never bias Rfree!) > My point was that we normally do not calculate R-free after real-space > refinement, It's not about whether you compute something or not. It's about whether you expose free-r reflections to refinement and to current model, given that they should never ever see any refinement or model or optimization under any circumstances. Otherwise they immediately become non-free. > but after reciprocal space refinement. Here the bias is removed again. Hm.. How you know this? I guess it requires a great deal of effort to prove this!. > In practical terms we have to choose the best option: > 1) Refine against maps with missing reflections and the possibility of > artefacts that lead to suboptimal results. This keeps R-free unbiased, even > directly after real-space refinement. > 2) Refine against maps with test reflections set to Fcalc. This biases > against the current model, but should have less artefacts. This too keeps > R-free unbiased directly after real-space refinement. > 3) Refine against maps with all reflections. This should give the best > fitting results, but does introduce bias to the test set. However, this bias These are all valid points. However they do not advocate for biasing Rfree. Yuo can always fill in missing reflections with something else (different from your genuine free-r set of reelections) and thus address two issues at once : eliminate missing terms and not use free-r reflections for this! Pavel
