[phenixbb] Weighting in phenix.real_space_refine
Pavel Afonine
pafonine at lbl.gov
Tue Sep 13 08:30:30 PDT 2016
Hi Arjen,
thanks for pointing this out! I will have a look!
Pavel
On 9/13/16 08:06, arjen jakobi wrote:
> 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
> <mailto: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
> <mailto: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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