Dear All,
In addition to Paul Adams point, I would note that people have sometimes
been confused by different definitions of completeness and resolution
when looking at Staraniso data, particularly if there is significant
anisotropy. It would be worth checking not only which shell but which
definition the 38% completeness figure refers to, and what the
anisotropic diffraction limits are.
Yours,
Rasmus Fogh
On 28/02/2024 17:58, Paul Adams wrote:
By setting wxc (weight of the X-ray term) to 0.1 there is good chance
that the refinement is dominated by the geometry term and the model
isn’t really seeing the effect of the X-ray data. I suspect this would
result in R-factors that are similar. Why they are so low is less clear,
but as others have pointed out 38% completeness is a problem. It would
be good to check if that is 38% overall, or just very incomplete in the
higher resolution shells. If it is complete at lower resolution you
might be able to do something with the dataset, but not using the
default parameterization in refinement programs - you’ll need to apply
constraints and additional restraints if you can, and look at the
weighting (by modifying wxc_scale, not wxc).
There is a Phenix mailing list you might want to use as well (I assume
you are using phenix.refine):
https://phenix-online.org/mailman/listinfo/phenixbb
<https://phenix-online.org/mailman/listinfo/phenixbb>
On Feb 28, 2024, at 8:21 AM, Justin Cruite
<[email protected]> wrote:
Thanks everyone,
I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å
dataset. The data was processed using autoProc and the staranisano mtz
was used for MR. The completeness is only 38%. It could be that the
Rfree and Rwork reflection sets are small because of this? What is the
best way to check the number of reflections used for Rwork and Rfree?
Is this dataset usable at all?
Thanks!
Justin
On Wed, Feb 28, 2024 at 10:21 AM nicfoos <[email protected]
<mailto:[email protected]>> wrote:
Hello Justin,
There is something weird in your results. You mention Rwork/Rfree of
0.1837.
This means a pretty good refinement and also is very unusual to be
obtain for a resolution of 3.37.
Additionally you should not have Rfree = Rwork.
I suspect something wrong with you Rfree reflections sets. What
size is
it ? Is your dataset complet ?
How did you cut the res. ?
I hope this may help you.
Nicolas
On 2024-02-28 16:10, Justin Cruite wrote:
> Hi everyone,
>
> What does it mean if your Rwork and Rfree are exactly the same?
>
> I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
> cycles of refinement with wxc = 0.1. Everything else at default. The
> Rwork and Rfree are both 0.1837. Is this bad?
>
> Thank you!
>
> Justin
>
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