[phenixbb] Turn off side chain optimizations in phenix real space refine?
pafonine at lbl.gov
Thu Jun 10 23:24:48 PDT 2021
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
> + 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:
>> 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.
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