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Hi Arjen,<br>
<br>
thanks for pointing this out! I will have a look!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/13/16 08:06, arjen jakobi wrote:<br>
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cite="mid:CACTB1uMW3fW+5zL=Bb0bXzTfXR4aB4zhXAbq2Yz7qyNx_jy7qA@mail.gmail.com"
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<div>Hi Oliver, <br>
<br>
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).<br>
<br>
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Best,<br>
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Arjen<br>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On 13 September 2016 at 16:57, Oliver
Clarke <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:olibclarke@gmail.com" target="_blank">olibclarke@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks
Pavel!<br>
<br>
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?<br>
<br>
Cheers,<br>
Oli<br>
<div class="HOEnZb">
<div class="h5">> On Sep 13, 2016, at 10:54 AM, Pavel
Afonine <<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>>
wrote:<br>
><br>
> Hi Oliver,<br>
><br>
> 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.<br>
> 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.<br>
><br>
> Parameters defining bond/angle rmsds as targets for
weight optimization:<br>
><br>
>� � target_bonds_rmsd = 0.01<br>
>� � target_angles_rmsd = 1.0<br>
><br>
> Pavel<br>
><br>
> On 9/12/16 14:14, Oliver Clarke wrote:<br>
>> Hi all,<br>
>><br>
>> 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?<br>
>><br>
>> Cheers,<br>
>> Oliver.<br>
><br>
<br>
<br>
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