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

Andreas Förster docandreas at gmail.com
Mon Feb 9 02:57:43 PST 2015

Since I started this, I should comment - though I don't have access to 
all the files at the moment.

With tightening of the Ramachandran plot, I meant that the number of 
residues in the allowed region decreased dramatically.  Favored went 
from 88% or so to 96%.  Visually, the plot changed from the million star 
motel to well defined areas of spots.

In Phenix, I used secondary-structure restraints on what were during the 
initial built mostly ideal helices, individual B values, NCS, TLS and 
weight optimization (no phi/psi angles restraints).

Buster-TNT with NCS and TLS restraints and pretty much all defaults 
tidied up the Ramachandran plot and improved R values by more than four 
percentage points.  I know that what matters is the electron density and 
the side chains I can place with confidence, in particular in the active 
side.  There, the situation is less clear, but I'm still working on this.



On 05/02/2015 7:56, Nathaniel Echols wrote:
> The %favored is also important - if you only have 1% outliers but 20%
> are "allowed", that's still not a very realistic structure.  On the
> other hand, it is entirely possible to generate a model that has 98%
> favored but an equally unrealistic distribution, if you try to make the
> plot too "tight" (i.e. forcing residues into particular sub-regions of
> favored).  But there isn't any metric for this that I'm aware of - it's
> very qualitative and based entirely on visual intuition.
> -Nat
> On Thu, Feb 5, 2015 at 10:46 AM, Shane Caldwell
> <shane.caldwell17 at gmail.com <mailto:shane.caldwell17 at gmail.com>> wrote:
>     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.
>         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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