[phenixbb] Weighting in phenix.real_space_refine

Pavel Afonine pafonine at lbl.gov
Tue Sep 13 07:54:25 PDT 2016

Hi Oliver,

unlike reciprocal space refinement where optimization of the weight 
requires systematically trying full refinement (which is very slow 
unless you use many cpus), in real space this can be done very quickly 
and the speed does not depend on model or map size.
The weight calculation procedure implemented in phenix.real_space_refine 
includes splitting the model into ten randomly picked continues 
ten-residue long segments, and finding the best weight for each segment. 
The best weight is considered to be the one that results in a model 
possessing pre-defined bond and angle rms deviations and that has best 
model-to-map fit among all trial weights. The obtained array of weights 
is filtered for outliers and the average weight is calculated and used 
as the best weight.

Parameters defining bond/angle rmsds as targets for weight optimization:

     target_bonds_rmsd = 0.01
     target_angles_rmsd = 1.0


On 9/12/16 14:14, Oliver Clarke wrote:
> Hi all,
> How does phenix.real_space_refine deal with restraint weighting? 
> Looking at the output of the program, I get the impression that it 
> splits the model up into  different chunks, and alters weights locally 
> based on some model/map correlation metric - is this the case (and are 
> there more specific details available), or how does it work otherwise?
> Cheers,
> Oliver.

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