Thanks Garib, but my task was not real space refinement (just manual model building/adjustment). Following is my previous post. Thanks!
"""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?""" Hailiang > It should be remembered that refining in real space is equivalent to > refinement in the reciprocal space (through Parseval's theorem). If you > want to do consistent refinement then you need to use exactly same > reflections for free and working set. If you do not use the same set of > reflections for real and reciprocal space refinements then you may get > very interesting results. > > Garib > > > > > On 23 May 2011, at 21:17, Hailiang Zhang 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? >> >> Hailiang >> >> >>> On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang <zhan...@umbc.edu> >>> wrote: >>> >>>> 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! >>>> >>> >>> If you are going to run overall real-space refinement on the structure, >>> you >>> should absolutely exclude the test set reflections from the map. If >>> you >>> are >>> only going to run local refinement of small parts of the model in Coot >>> or >>> equivalent, it's debatable - in practice, I think most people/programs >>> leave >>> them in. >>> >>> -Nat >>> > > >
