[phenixbb] real space rotamer restrains

Pavel Afonine pafonine at lbl.gov
Fri Jan 22 10:02:12 PST 2021

Hi Leonid,

> Is there somewhere a description of all the new parameters in 
> phenix.real_space_refine rotamer restrains?
> I mean
> rotamers {
>     fit = all *outliers_or_poormap outliers_and_poormap outliers poormap

means work on:
- all residues, or
- only on outliers or residues that fit map poorly, or
- only on outliers that do not fit map well, or
- outliers only, or
- residues that do not fit map well.

> restraints {
>       enabled = True

Enables rotamer restraints.

> sigma = Auto

Defines strength of these restraints. In a default run it is 
self-adjusting starting with 5 for the first macro-cycle and going down 
to 1 for the final macro-cycle. Using more or less macro-cycles changes 
the rate of change of sigma.

> target = max_distant min_distant exact_match fix_outliers

Choices for rotamar target for rotamer restraints. None selected means 
the choice made by the program based on specific situation.

>     }
>     tuneup = outliers outliers_and_poormap

Post-refinement adjustment of rotamers: work on outliers only or both 
outliers and poorly fitting residues.

All the default settings are consensus result of thousands of trial 
refinements and weeks of experimenting. This is why I find it very 
unlikely (but perhaps still possible, may be..) that someone ever needs 
to change these settings.


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