Re: [phenixbb] Ramachandran and clashes

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: [email protected] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608

On Jul 22, 2013, at 20:21 , Pavel Afonine wrote:

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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:

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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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