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

Oliver Clarke olibclarke at gmail.com
Fri Jun 11 05:13:32 PDT 2021

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> 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
>> fit = all *outliers_or_poormap outliers_and_poormap outliers poormap Fit side-chains regimes
>> tuneup = outliers outliers_and_poormap Switch remaining (after map fit) outliers to the nearest rotamer
>> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210611/a9ff7d96/attachment.htm>

More information about the phenixbb mailing list