[phenixbb] Table 1 stastics

Nathaniel Echols nechols at lbl.gov
Thu Oct 25 10:57:51 PDT 2012

On Thu, Oct 25, 2012 at 9:59 AM, Bjørn Pedersen <bjopp at msg.ucsf.edu> wrote:
> 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.

Phenix used to have a strict cutoff, but it now runs French&Wilson
treatment by default, so negative intensities are allowed.  However:
Kay pointed out that in another piece of code, I am calculating
I/sigma starting from amplitudes, which are always positive.  For
Table 1, if you use intensities as input, this won't matter, but if
you use amplitudes and many of the original intensities were negative,
it may be overestimating I/sigma.  Fixing this now.

It still doesn't explain why the completeness would be so far off, however.


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