[phenixbb] Ramachandran and clashes

[Mark J van Raaij]

Hi Felix,
we recently refined a structure with about 4800 residues, and here the secondary structure restraints as implemented in Phenix helped a lot. Admittedly the resolution was a bit better, 3.0 A.
I also used NCS extensively to get all chains the same unless clear electron density was present to suggest otherwise - and yes, it was a lot of manual intervention.
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij





On 23 Jul 2013, at 16:51, Felix Frolow wrote:

> 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 : - \
> FF
> 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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