[phenixbb] regarding number of unique reflections

[Viney Singh]

Dear Tim and others,

Thanks for your valuable insights.

Will it be okay if I treat Friedel's pair as separate reflections, even if
there is no anomalous signal for structure refinement. Can such reflections
(Friedel's pair) be considered unique reflections in that case?

If I treat them separately I still have a multiplicity of 6 and completion
of more than 95%.

Thanks again.



On Thu, Jan 13, 2022, 00:24 Tim Gruene <tim.gruene at univie.ac.at> wrote:

> Hi Pavel, hi Viney,
>
> you should NOT go back to data processing. Data processing should
> result in unmerged data, including I+ and I-. The refinement program
> (possibly under guidance of the user) should decide whether and how
> data should be merged for refinement purposes. This decision should
> also be reflected during data deposition when counting reflections,
> however, it is best practice to deposit unmerged data. Whether or not
> the PDB support deposition of unmerged data may be a different question.
>
> Cheers,
> Tim
>
> On Wed, 12 Jan 2022 09:19:35 -0800 Pavel Afonine <pafonine at lbl.gov> wrote:
>
> > Hi Viney,
> >
> > if your data are anomalous then you expect to have Fobs+, Fobs- and
> > singletons. If your data are not anomalous, you should not have +/-
> > mates in your data set. So then the real question is: since you do
> > not expect any anomalous signal and thus assume your data set isn't
> > anomalous (as you said), then how come you ended up with a data set
> > that contains Fobs+, Fobs- and singletons? Perhaps you should go back
> > to data processing step and make sure you don't get anomalous data
> > set in the first place.
> >
> > Now as to counting... Fobs+ and Fobs- are the two entries in the
> > array of float values, so they are counted as two, not one (in
> > Phenix).
> >
> > Pavel
> >
> > On 1/12/22 04:41, Viney Singh wrote:
> > > Dear all,
> > >
> > > First of all sorry for the novice question.
> > >
> > > I _processed_ one of my datasets using xds. Since I was not
> > > expecting an anomalous signal, I kept Friedel's Law = True.
> > > The number of unique reflections I got: *17,000*
> > > I used xds_ASCII.HKL after correct.LP and converted it to mtz using
> > > Phenix with 10% reflections for Rfree calculations.
> > >
> > > Now, when I am trying to_refine _the structure in Phenix, the
> > > structure is being refined against *32,300* reflections with *3230*
> > > reflections for Rfree calculation. Looks like refinement is
> > > treating Friedel's pair as two different reflections.
> > >
> > > When I am trying to upload PDB on rcsb, on the refinement tab, the
> > > number of reflections used for refinement and Rfree calculations
> > > are shown as 32,300 and 3220 respectively, while in the validation
> > > report, no. of reflections used for Rfree calculation are shown as
> > > *1700*.
> > >
> > > I would really appreciate if someone can guide me to resolve this
> > > discrepancy.
> > >
> > > Thanks in advance.
> > >
> > > Viney
> > >
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>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
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