[phenixbb] Weighting in phenix.real_space_refine

[arjen jakobi]

Hi Oliver,

indeed this can be beneficial. We have done this e.g. for a cryo-EM map of
Pol III where for the apo models we see substantial resolution variation
(doi:10.1038/nature16143; doi:10.1111/febs.13732).

Best,
Arjen


On 13 September 2016 at 16:57, Oliver Clarke <olibclarke at gmail.com> wrote:

> Thanks Pavel!
>
> So just to be sure - the average weight obtained with the randomly
> selected fragments is used for the entire model? Or different weights are
> used for different regions? I guess the latter would be in some ways
> preferable for large structures in cryoEM where there is a substantial
> variation in local resolution?
>
> Cheers,
> Oli
> > On Sep 13, 2016, at 10:54 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> >
> > 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
> >
> > Pavel
> >
> > 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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