Hi George,
It doesn't matter that much which space one does the refinement in does it?
indeed, it does not matter if we are talking about real-space refinement as minimization of SUM(rho_obs-rho_calc)**2 instead of its reciprocal space equivalent SUM(Fobs-Fcalc)**2 . But I think it does matter a lot if we think of real-space refinement as an accumulation of various methods. In real-space you can afford doing things a) locally and b) if needed. Therefore you can use optimization tools that have way greater convergence radius. For example, instead of gradient-driven minimization you can use such tools as sampling in torsion angle space to fit rotamers or use morphing. You can identify regions that need refinement and refine only these regions. It could be good runtime saving if we are talking about a handful of residues out of whole ribosome. You can utilize various local repacking techniques. And so on, and so on... This is exactly what is being implemented in phenix.real_space_refine. Pavel