[phenixbb] Turn off side chain optimizations in phenix real space refine?

Pavel Afonine pafonine at lbl.gov
Thu Jun 10 23:24:48 PDT 2021

Hi Oliver,

rotamer fitting is designed to do better or leave things alone 
untouched. If your experience is different, I'd appreciate seeing an 
example (so that I can make it better!).

Also, I assume you are using one of latest nightly builds..


On 6/10/21 12:41, Oliver Clarke wrote:
> From the phenix docs, I can see how to modify this behaviour, but not 
> how to switch it off without just switching to rigid body fitting:
>   * rotamers
>       o fit = all *outliers_or_poormap outliers_and_poormap outliers
>         poormap Fit side-chains regimes
>       o tuneup = outliers outliers_and_poormap Switch remaining (after
>         map fit) outliers to the nearest rotamer
>       o restraints
>           + enabled = True Use rotamer restraints
>           + sigma = Auto The smaller the value, the stronger the
>             restraints
>           + target = max_distant min_distant exact_match fix_outliers
>             Choice for the reference conformation to restrain to
>> On Jun 10, 2021, at 3:20 PM, Oliver Clarke <olibclarke at gmail.com 
>> <mailto:olibclarke at gmail.com>> wrote:
>> Hi,
>> Is there any way to turn off rotamer fitting/side chain optimization 
>> in phenix.real_space_refine? Sometimes it seems to do more harm than 
>> good, and repositions sidechains completely out of the density, but I 
>> couldn't find how to switch it off.
>> Cheers
>> Oli
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