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What about being very pragmatic: the latest stage of data processing is
data conversion to a 'standard' data file format, done using XDSCONV.
The latest version has the following input lines:
!This omits reflections with I/sigma(I) below a specified cut-off
!NEGATIVE_INTENSITY_CUTOFF=0
So if you use this input line and cut below (say) I/s(I) < 0 then I
believe you should state the corresponding figures. If you cut below, say,
I/s(I) < 1 then you report the corresponding values and so forth.
How's that sound?
Fred.
On Thu, 28 Sep 2006, 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!
--
s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
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