[phenixbb] Ramachandran and clashes

Felix Frolow mbfrolow at post.tau.ac.il
Tue Jul 23 08:35:58 PDT 2013

Thank you for the fast reply.
Were Ramachandran restraints in PHENIX reside now in the recent GUI's ? Once there were immediately visible as well as rotamer restraints.
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfrolow at post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jul 23, 2013, at 18:25 , Pavel Afonine <PAfonine at lbl.gov> wrote:

> 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.
> Pavel
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