[phenixbb] Ramachandran and clashes

Pavel Afonine pafonine at lbl.gov
Tue Jul 23 08:25:59 PDT 2013

Hi Felix,

> Hi Pavel
> According to your mail from yesterday I wonder how can I treat 
> Ramachandran outliers in very large molecules (close to 9000 residues). 

- fix them manually first and then run refinement;
- if after refinement some of them come back as outliers then you 
consider them for including into Ramachandran restraints.

Ramachandran restraints are good at keeping correct conformation from 
becoming an outlier (due to poor density for instance), and NOT for 
fixing wrong one.

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