[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.
Pavel
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