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

Hi Oli, ok, great! Please send me an example once you have one and I will investigate. 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. Pavel 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 mailto:[email protected]> 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 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