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

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 <[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