[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.
Best.
Andreas
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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