I was under the impression that the differences arise due to XDS uses SIGNAL/NOISE >= -3.0 as the cutoff, thus allowing some negative reflections, while phenix use a strict cutoff of 0? Note, that the completeness in the high res. shell is lower in phenix than XDS (90.6 vs 99.7), a behavior I have seem several times solving different structures. XDS will show high completeness at high res. and then in phenix.refine it always drops.

Am I wrong thinking this?

Thanks for any insights!
-Bjørn
--
Bjørn Panyella Pedersen
Macromolecular Structure Group
University of California, San Francisco


On Fri, Oct 19, 2012 at 8:15 AM, Nathaniel Echols <nechols@lbl.gov> wrote:
On Fri, Oct 19, 2012 at 8:07 AM, Kay Diederichs
<Kay.Diederichs@uni-konstanz.de> wrote:
> I just want to point out that one possible source of discrepancy between
> I/sigma reported by a data processing program, and I/sigma reported by a
> program that uses the relevant cctbx routine is the following: that cctbx
> routine calculates the variance of merged data as max("internal variance",
> "external variance") which is different from what the data processing
> programs do (they calculate the "internal variance" - I hope I didn't get it
> the wrong way round). SHELXC and SHELXL also calculate the variance of the
> merged data like the data processing programs do.

Good point.  However, this particular CCTBX routine is only used when
merging non-unique data, which would not be the typical input here (at
least in the official release).

> I dislike this "feature" of cctbx but I do not know if phenix.table_one
> actually uses this routine for this purpose.

It does.  But I may change this, if I can be certain it won't screw
things up for the small molecule folks.  I'm just not sure why it was
written that way in the first place...

-Nat
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