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Dear Florian,
since it's not good practice to apply a sigma-cutoff in refinement, I
take _all_ the data from XDS up to the maximum resolution (here I stick
to the rule that in the outer shell the completeness should be >= 50%
and >= 50% of the observed reflections should have an I/sigma(I) >= 2),
and therefore report the XSCALE statistics for all data with
signal/noise > -3.0.
Best regards,
Dirk.
Florian Schmitzberger wrote:
Dear All,
I would have a question about reporting diffraction data quality
indicators (for pdb-submission and publication) for data processed with
XDS/XSCALE. XSCALE(.LP) lists data quality indicators such as
completeness, mean <I>/sigma<I>, R-meas etc. for several signal/noise
cutoffs descending to negative values for the latter (up to -3.0).
I was wondering whether it makes more sense to report data quality for
data with a signal/noise > 0 (or indeed 1) rather than report the data
quality for (all) data with a signal/noise >-3.0.
Whereas I imagine for error estimates and standard deviation
calculations (in ML-based refinement) including the quality of the
negative intensity reflections (signal/noise >-3.0) is still meaningful
to know, these reflections probably did not contribute significantly to
the diffraction, calculation of the electron density, and the final model.
I am asking this since I observe the following difference (I suppose
because of the altered sd estimates) between the tables for the 0.0
(Rmeas=94% (flame on, I am aware) and I/sigmaI= 1.83) and -3.0 (and
Rmeas=106.4%, I/sigmaI= 1.51) signal/noise cutoff.
I am aware this question is of a rather cosmetic nature and the data
will of course be the same (but reporting may have slightly different
effects on referees, I could imagine).
Thank you very much in advance for any comments!
Regards,
Florian
--------------------------------------------
Florian Schmitzberger
Medical Biochemistry and Biophysics
Karolinska Institute
Scheeles vaeg 2
SE-171 77 Stockholm, Sweden
Tel: +46-8-524-86875
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Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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