Hi Leonid, with the latest version everything should just work at least the same as before and at most much better compared to the previous version. If this is not what you observe -- something must have gone wrong. Please send me input files (model before and after refinement, map and map resolution) and I will investigate as soon as I get files. Pavel On 1/22/21 08:58, Leonid Sazanov wrote:

Hi,

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     restraints {       enabled = True       sigma = Auto       target = max_distant min_distant exact_match fix_outliers     }     tuneup = outliers outliers_and_poormap   }

What is poormap?

What is the range of Sigma?

What are those types of target?

With the latest nightly build, with default parameters starting model with 1% of rotamer outliers ends up with 10% (not using local_search, as it was done before).

To minimise number of outliers, which parameters can be changed?

Lower Sigma? Switch on tuneup?

Thanks for any info!

Leonid

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