[phenixbb] Weighting in phenix.real_space_refine

[Pavel Afonine]

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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