[phenixbb] Turn off side chain optimizations in phenix real space refine?
pafonine at lbl.gov
Fri Jun 11 10:15:07 PDT 2021
ok, great! Please send me an example once you have one and I will
You can disable it.. The option is local_grid_search. If you use GUI
just uncheck that box. Or remove "*" in front of it if you use parameter
file. Or don't include it into "run=..." if you use command line.
Note that will also disable using rotamer restraints which may result in
elevated counts of rotamer outliers.
On 6/11/21 05:13, Oliver Clarke wrote:
> Hi Pavel,
> I will definitely send an example the next time I come across one.
> There is no way to turn this off then? In most cases it is very
> helpful, but towards the end of the model building process I don't
> necessarily want phenix to alter rotamers that I have manually
> inspected. Yes, I am using dev-4158, the latest nightly available as
> far as I can see.
>> On Jun 11, 2021, at 2:24 AM, Pavel Afonine <pafonine at lbl.gov
>> <mailto:pafonine at lbl.gov>> wrote:
>> 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
>>> + 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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