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