On Thu, Oct 18, 2012 at 8:45 AM, Katherine Sippel
<katherine.sippel(a)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...
-Nat
