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

11 Jun 2021

      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