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

Shane Caldwell shane.caldwell17 at gmail.com
Thu Feb 5 10:46:27 PST 2015

I'm making a new thread because it's off the topic, but I have a question
in response to this point

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

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>

> 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.
> Andreas
> 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
>> Rfree.
>> 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,
>> Best,
>> Almudena
>> --
>> Almudena Ponce-Salvatierra
>> Macromolecular crystallography and Nucleic acid chemistry
>> Max Planck Institute for Biophysical Chemistry
>> Am Fassberg 11 37077 Göttingen
>> Germany
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