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:

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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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

On Tue, Jul 23, 2013 at 8:35 AM, Felix Frolow wrote:

Were Ramachandran restraints in PHENIX reside now in the recent GUI's ? Once there were immediately visible as well as rotamer restraints.

Yes, I took them off the main interface because we (Jeff and I) found that a) people were using them far too aggressively in circumstances where they really shouldn't, and b) they tended to screw up local structure and almost always result in chemically insensible Ramachandran plots. I really don't think there's any excuse to use except in absolute desperation, and I actually think it would be better to deposit a structure with 1% outliers than to use the restraints. Usually if the overall weight on the geometry restraints is sufficiently high, the Ramachandran statistics will naturally get better. You can still find the parameter either by clicking the "Model interpretation" button, or by using the parameter search (in the Settings menu). But I would exhaust every other possible option before resorting to this. We never had rotamer restraints (although I guess the new RSR method uses them internally), just the fix_rotamers option, but that is now merged with the RSR code.

According to your mail from yesterday I wonder how can I treat Ramachandran outliers in very large molecules (close to 9000 residues).

Turn on weight optimization - this will almost always reduce both the number of Ramachandran outliers and the clashscore. The alternative is to set wxc_scale much lower, but I've always found that manual adjustment of the weights ends up taking far more manual effort and just about the same amount of time as the automatic optimization. -Nat