[phenixbb] Real space refinement
Pavel Afonine
pafonine at lbl.gov
Mon Feb 17 20:56:33 PST 2014
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
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