On Mon, May 23, 2011 at 1:17 PM, <zhan...@umbc.edu> wrote: > Thanks Nat! I am not doing real space refinement. Actually I am only using > the maps for manual model building/adjustments. In this case, if some > Rfree reflections have strong scattering intensities, removing them may > lead to featureless density maps. However, if we just leave them in, do > you think we may have the so-called model-bias issue?
I've always seen "model bias" used to describe phases, which don't really involve R-free. I suppose there is theoretically some slight risk of biasing your R-free value if the test set is not excluded from the maps during manual rebuilding, but it's minimal compared to what happens during refinement. The real danger is in global optimization algorithms (gradient minimization, and especially simulated annealing), which are so powerful that they can occasionally make a completely incorrect model - say, traced backwards - look reasonable (as judged by the R-factor and fit to density) after many rounds of refinement. It is very difficult to do this with modern refinement programs, regardless of what reflections are used in the maps. -Nat
