[phenixbb] Table 1 stastics

Bjørn Pedersen bjopp at msg.ucsf.edu
Thu Oct 25 09:59:39 PDT 2012

I was under the impression that the differences arise due to XDS uses
>= -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 Panyella Pedersen
Macromolecular Structure Group
University of California, San Francisco

On Fri, Oct 19, 2012 at 8:15 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Fri, Oct 19, 2012 at 8:07 AM, Kay Diederichs
> <Kay.Diederichs at 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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