[phenixbb] real space rotamer restrains

Pavel Afonine pafonine at lbl.gov
Fri Jan 22 09:30:18 PST 2021


Hi Leonid,

with the latest version everything should just work at least the same as 
before and at most much better compared to the previous version. If this 
is not what you observe -- something must have gone wrong. Please send 
me input files (model before and after refinement, map and map 
resolution) and I will investigate as soon as I get files.

Pavel

On 1/22/21 08:58, Leonid Sazanov wrote:
> Hi,
>
> Is there somewhere a description of all the new parameters in 
> phenix.real_space_refine rotamer restrains?
>
> I mean
>
> rotamers {
>     fit = all *outliers_or_poormap outliers_and_poormap outliers poormap
>     restraints {
>       enabled = True
>       sigma = Auto
>       target = max_distant min_distant exact_match fix_outliers
>     }
>     tuneup = outliers outliers_and_poormap
>   }
>
>
> What is poormap?
>
> What is the range of Sigma?
>
> What are those types of target?
>
>
> With the latest nightly build, with default parameters starting model 
> with 1% of rotamer outliers ends up with 10% (not using local_search, 
> as it was done before).
>
> To minimise number of outliers, which parameters can be changed?
>
> Lower Sigma? Switch on tuneup?
>
>
> Thanks for any info!
>
> Leonid
>
>



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