[phenixbb] regarding number of unique reflections

[Gerard Bricogne]

Dear Tim,

     Your final question suggests that you might have missed the answer
contained in the following announcement

https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3

that clearly states that the deposition of unmerged data is now supported.
These extensions of the mmCIF dictionary included the tidying up of the
definitions related to the deposition of anomalous data.

     Your active participation in the on-going efforts to promote such 
depositions into the PDB would be of great benefit to the project. More
information available on request :-)) .


     With best wishes,

          Gerard.

--
On Wed, Jan 12, 2022 at 07:54:57PM +0100, Tim Gruene 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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