[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 


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