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
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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