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

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 mailto:[email protected]> 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