[phenixbb] Ramachandran and clashes

Felix Frolow mbfrolow at post.tau.ac.il
Tue Jul 23 07:51:34 PDT 2013

Hi Pavel
According to your mail from yesterday I wonder how can I treat Ramachandran outliers in very large molecules (close to 9000 residues). Despite 
R=0.22 and Rfree=0.29 there is still a lot of changes to do. It was molecular replacement project with 28 subunits 14 and 14 and with about 50% identity and some small insertions deletions. map is 3.4 A and after permissive CC1/2 decision - about 3.05 .  A lot of clashes, a lot of Ramachandran
outliers ( about 6% after COOT Ramachandran improvement and about 9% after refinement.
What I need is not elimination of manual intervention, but minimisation of it : - \
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 22, 2013, at 20:21 , Pavel Afonine <PAfonine at lbl.gov> wrote:

> Hi Joel,
> from http://www.phenix-online.org/version_docs/dev-1439/CHANGES :
> - Local RSR: residue-by-residue, replaces old fix_rotamers option
>   - fits both main chain and sidechain
>   - only applies to residues with rotamer outlier, poor CC, or clashes
>   - new residue fit serves as torsion restrains for subsequent macro-cycle
>   - currently not performed when explicit hydrogens present
> To turn this off simply exclude real-space refinement from refinement strategy.
> Note, RSR above means Real-Space-Refinement, and not Reciprocal-Space-Refinement.
> Pavel
> On 7/22/13 9:33 AM, Joseph Noel wrote:
>> Dear Pavel,
>> To clarify, in the latest nightly build, 1435, do you have to click on real space refinement to carry out side chain rotamer fitting? If you just refine xyz I assume side chain rotamer fitting is not enabled, correct?
>> Joe Noel
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