[phenixbb] Global metrics for Ramachandran quality beyond %outliers?

Phoebe A. Rice price at uchicago.edu
Thu Feb 5 21:25:06 PST 2015

The Sosnick group (down the hall from me) has done a nice job evaluating the backbone as a whole - try the evaluation server here:


Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

773 834 1723; PRice at uchicago.edu<mailto:PRice at uchicago.edu>

From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Shane Caldwell [shane.caldwell17 at gmail.com]
Sent: Thursday, February 05, 2015 12:46 PM
To: Andreas Förster; phenixbb at phenix-online.org
Subject: [phenixbb] Global metrics for Ramachandran quality beyond %outliers?

I'm making a new thread because it's off the topic, but I have a question in response to this point<http://phenix-online.org/pipermail/phenixbb/2015-February/021691.html>:

> [Doggy structure improved, as shown by how] The Ramachandran plot tightened

This is interesting to me - other than eyeballing the plot, are there any quantitative metrics of Ramachandran distribution quality? At low-res or when refining a bunch of structures side-by-side it could be an additional indicator of quality of the model, without requiring having to inspect the plot. Of course manual inspection is always important in the end, but in early stages a global measure of spread could help guide refinement.

I've seen %outliers used for this purpose, but that ignores that while a residue can be "allowed" it can still be far from a statistically likely conformation. From what I've seen, some users only consult Ramachandran to tweak residues until they pop into the "allowed" regions and stop there, which isn't the same as globally improving the geometry.

Interested to hear thoughts (or it it's already in use, pointing me in the right direction!),

Shane Caldwell
McGill University

On Thu, Feb 5, 2015 at 5:06 AM, Andreas Förster <docandreas at gmail.com<mailto:docandreas at gmail.com>> wrote:
Dear Almudena,

I promise not to make a habit of advertising other programs on the Phenix mailing list, but just once I would like to encourage you (and the community) to try all the tools at your disposal.

Different refinement programs have different strength and weaknesses. Secondary-structure restraints in Phenix are great for low-resolution data, but so is jelly-body refinement in Refmac.  A dodgy 3.2 Å structure I'm currently working on was improved dramatically by Buster-TNT.  The Ramachandran plot tightened, and R free plunged by four percentage points.


On 05/02/2015 10:44, Almudena Ponce Salvatierra wrote:
Dear all,

I am refining my structure (data at 3 A), with a model that is complete.
However the Rs values are: R work= 0.25 and Rfree= 0.32. I have read
"Improved target weight optimization in phenix.refine" (In the
computational crystallographic newsletter 2011) and what I understand is
that just by marking the boxes "improve xray/stereochemistry weight" and
"improve xray/adp weight" it should work... giving me the best possible

I'm refining individual coordinates, occupancies, b-factors (isotropic
for all atoms), TLS, and using secondary structure restraints, automatic
ligand linking and experimental phases restraints. Also, I chose this
strategy because I have finished building the structure and according to
some of the suggestions in "towards automated crystallographic structure
refinement with phenix.refine".

I am actually quite confused and don't know what to think... is it a
matter of the weights? is it only that this is as good as it gets?

Any suggestions and comments are welcome.

Thanks a lot in advance,


Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen

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