Hailiang, r-free reflections should not participate in refinement, regardless whether it is real or reciprocal space one, done with machine driven minimizers or your hands moving atoms in Coot. Period. The issue of correcting the map appearance for missing data (resolution or completeness) is relevant but different. Removing the data is noticeable, but most of the time putting aside test set is not critical for map appearance (given that reflections are selected randomly and do not exceed a reasonable fraction of available data); and when it is critical, the cross validation should be done differently anyway.
So the answer to your question is: every time you compute a map not just to enjoy its appearance but to use it to improve your model, do not include test flagged reflections into it. Pavel. On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang <zhan...@umbc.edu> wrote: > Hi, > > I have a preliminary question. I understand Rfree reflection sets are > never used during automatic refinement, but, when generating the real > space density maps, do we have to exclude Rfree columns? Any references > will also be greatly appreciated! > > Best Regards, Hailiang >
