[phenixbb] Table 1 stastics

Nathaniel Echols nechols at lbl.gov
Thu Oct 18 12:07:49 PDT 2012

On Thu, Oct 18, 2012 at 8:45 AM, Katherine Sippel
<katherine.sippel at gmail.com> wrote:
> Part of the problem could lie in whether he input the original mtz as
> intensities or not. In older versions of phenix some intensities were
> dropped if they were below the cutoff and particularly for high res data the
> completeness would go down significantly. I know you have implemented the
> French and Wilson conversion in the newer versions but if he comes from a
> lab like my old one and is refining off of intensities that could be the
> culprit.

This is a good point, but it depends on the version of Phenix, the
type of input data, and how the data file was processed.  I checked my
code for Table 1 and if the input data are intensities, the negative
observations should *not* be discarded.  The same goes for
phenix.refine, among other programs.  However, if amplitudes were used
as input for Table 1, and had previously been filtered through a
program that does not perform the French & Wilson treatment, they may
be missing some data (most of which will probably be at high
resolution).  One caveat: the reflection file editor in Phenix has an
option to convert intensities to amplitudes, but this will not run
F&W, which is perhaps a bug...


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