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

Pavel Afonine pafonine at lbl.gov
Fri Jun 11 10:15:07 PDT 2021

Hi Oli,

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.
> Cheers
> Oli
>> 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..
>> Pavel
>> 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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