<div dir="auto">Dear Tim and others,<div dir="auto"><br></div><div dir="auto">Thanks for your valuable insights. </div><div dir="auto"><br></div><div dir="auto">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?</div><div dir="auto"><br></div><div dir="auto">If I treat them separately I still have a multiplicity of 6 and completion of more than 95%. </div><div dir="auto"><br></div><div dir="auto">Thanks again.</div><div dir="auto"><br></div><div dir="auto"><br><br><div class="gmail_quote" dir="auto"><div dir="ltr" class="gmail_attr">On Thu, Jan 13, 2022, 00:24 Tim Gruene <<a href="mailto:tim.gruene@univie.ac.at" rel="noreferrer noreferrer" target="_blank">tim.gruene@univie.ac.at</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Pavel, hi Viney,<br>
<br>
you should NOT go back to data processing. Data processing should<br>
result in unmerged data, including I+ and I-. The refinement program<br>
(possibly under guidance of the user) should decide whether and how<br>
data should be merged for refinement purposes. This decision should<br>
also be reflected during data deposition when counting reflections,<br>
however, it is best practice to deposit unmerged data. Whether or not<br>
the PDB support deposition of unmerged data may be a different question.<br>
<br>
Cheers,<br>
Tim<br>
<br>
On Wed, 12 Jan 2022 09:19:35 -0800 Pavel Afonine <<a href="mailto:pafonine@lbl.gov" rel="noreferrer noreferrer noreferrer" target="_blank">pafonine@lbl.gov</a>> wrote:<br>
<br>
> Hi Viney,<br>
> <br>
> if your data are anomalous then you expect to have Fobs+, Fobs- and <br>
> singletons. If your data are not anomalous, you should not have +/- <br>
> mates in your data set. So then the real question is: since you do<br>
> not expect any anomalous signal and thus assume your data set isn't <br>
> anomalous (as you said), then how come you ended up with a data set<br>
> that contains Fobs+, Fobs- and singletons? Perhaps you should go back<br>
> to data processing step and make sure you don't get anomalous data<br>
> set in the first place.<br>
> <br>
> Now as to counting... Fobs+ and Fobs- are the two entries in the<br>
> array of float values, so they are counted as two, not one (in<br>
> Phenix).<br>
> <br>
> Pavel<br>
> <br>
> On 1/12/22 04:41, Viney Singh wrote:<br>
> > Dear all,<br>
> ><br>
> > First of all sorry for the novice question.<br>
> ><br>
> > I _processed_ one of my datasets using xds. Since I was not<br>
> > expecting an anomalous signal, I kept Friedel's Law = True.<br>
> > The number of unique reflections I got: *17,000*<br>
> > I used xds_ASCII.HKL after correct.LP and converted it to mtz using <br>
> > Phenix with 10% reflections for Rfree calculations.<br>
> ><br>
> > Now, when I am trying to_refine _the structure in Phenix, the <br>
> > structure is being refined against *32,300* reflections with *3230* <br>
> > reflections for Rfree calculation. Looks like refinement is<br>
> > treating Friedel's pair as two different reflections.<br>
> ><br>
> > When I am trying to upload PDB on rcsb, on the refinement tab, the <br>
> > number of reflections used for refinement and Rfree calculations<br>
> > are shown as 32,300 and 3220 respectively, while in the validation<br>
> > report, no. of reflections used for Rfree calculation are shown as<br>
> > *1700*.<br>
> ><br>
> > I would really appreciate if someone can guide me to resolve this <br>
> > discrepancy.<br>
> ><br>
> > Thanks in advance.<br>
> ><br>
> > Viney<br>
> ><br>
> > _______________________________________________<br>
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<br>
<br>
<br>
-- <br>
--<br>
Tim Gruene<br>
Head of the Centre for X-ray Structure Analysis<br>
Faculty of Chemistry<br>
University of Vienna<br>
<br>
Phone: +43-1-4277-70202<br>
<br>
GPG Key ID = A46BEE1A<br>
</blockquote></div></div></div>