Hi Robbie, I agree with Ed that you probably should not leave out your free > reflections in real-space under normal circumstances. >
Phoebe is right: you should not use free-r reflections in calculation of map that you are going to use for real-space refinement. Otherwise you will be biasing Rfree: the strength of the effect depends on how much model you will be real-space refining. I can clearly demonstrate it with a simple cctbx based script that I can post later of anyone interested. Ed's point about zeros is a good one, but here we are talking about specific set of non-zero reflections (free reflections) that we do not want to "see" any model, any refinement. If by "under normal circumstances" you mean real-space refinement of only a tiny fraction of the model (say a residue or a few residues) followed by reciprocal space refinement then this may not visibly impact the Rfree; however, still, technically this will make free-r reflections "see" your model and some refinement, which isn't cool I think. All the best, Pavel
