Dear Pavel, OK, will send you files. Normally we use older phenix version, so some parameters for this run with the latest version may be off. But would be still nice to be able to understand the meaning of all parameters. Best Leonid On 22.01.21 18:30, Pavel Afonine wrote:
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
-- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: [email protected]