[phenixbb] Weighting in phenix.real_space_refine
Oliver Clarke
olibclarke at gmail.com
Tue Sep 13 08:12:14 PDT 2016
Hi Pavel,
So how do I interpret the weights in the output? For example, with a structure I am refining at the moment, I have the following:
"Weight determination summary:
number of chunks: 40
random chunks:
chunk 33 optimal weight: 0.9990
chunk 30 optimal weight: 10.0000
chunk 16 optimal weight: 9.9990
chunk 10 optimal weight: 9.9990
chunk 20 optimal weight: 9.9990
chunk 16 optimal weight: 9.9990
chunk 31 optimal weight: 0.0040
chunk 12 optimal weight: 5.9990
chunk 19 optimal weight: 10.0000
chunk 23 optimal weight: 0.8980
overall best weight: 9.4279”
Is low tight and high loose, as for phenix.refine? And are there any prospects for the future of varying weights across the structure? Often in EM we will have large regions at good resolution, say <4Å, and other regions which while well defined are at lower resolution, say 6Å - applying the same weights to both regions doesn’t seem ideal.
Would your suggested strategy at the moment be to split the structure domain-by-domain, refine domains separately and then recombine?
Cheers,
Oli
(Also, there seems to be a very minor bug in the output model stats - “Dist moved from start” changes, but “Dist moved from previous” is always 0.000.
Model statistics:
Map CC (whole unit cell): 0.662
Map CC (around atoms): 0.773
rmsd (bonds): 0.01
rmsd (angles): 1.04
Dist. moved from start: 0.060
Dist. moved from previous: 0.000
All-atom clashscore 4.47
Ramachandran plot:
outliers: 0.27 %
allowed: 12.24 %
favored: 87.49 %
Rotamer outliers: 0.54 %
C-beta deviations: 4)
> On Sep 13, 2016, at 11:01 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
>
> Hi Oliver,
>
>> So just to be sure - the average weight obtained with the randomly selected fragments is used for the entire model?
>
> correct.
>
> Pavel
>
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