[phenixbb] completeness in table1

Nathaniel Echols nechols at lbl.gov
Mon Jun 24 15:45:05 PDT 2013

On Mon, Jun 24, 2013 at 12:10 PM, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Mon, Jun 24, 2013 at 11:25 AM, Alexander Batyuk <batyuk at bioc.uzh.ch> wrote:
>> What could be the reason for discrepancy in completeness reported in XSCALE.LP (94.5% - 100.0%) vs from Table1: 89.57% (37.49%)?
> I don't know the explanation offhand, but I would check whether XSCALE
> is reporting the completeness relative to *merged* Friedel pairs.  If
> you have anomalous data, Phenix will always report the completeness
> with F+ and F- counted separately.

A correction: this statement is true for most CCTBX-based programs,
but I had actually implemented Table 1 (and the standalone merging
statistics program) so it always merges Friedel mates when calculating
these statistics, since that seems to be more in line with standard
practice (?).

Regardless, the explanation in this case is that the completeness is
calculated from the data you use in refinement, not the original
intensities.  And French-Wilson treatment throws out an unusually
large number of reflections - both Jeff's implementation in Phenix,
and ctruncate in CCP4 - almost all in the highest-resolution shell.  I
think we probably need to add a loud warning if a) our French-Wilson
routine discards more than X% of intensities, and b) if the
completeness calculated from unmerged intensities significantly
deviates from the completeness of the amplitudes in Table 1.


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