[phenixbb] WAS: changing TLS groups mid refinement

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon May 17 13:00:06 PDT 2010

> The person(s) in charge of cctbx can give more specific answer, but I
> suspect this is not the case.  While the main format is mtz (and thus
> NaN is used to specify missing reflections), it appears to me from a
> quick look at mmtbx module that internally missing reflections are
> exactly that - missing from corresponding python data structures.

That's true, but the whole story is slightly more complicated.
Reflections with Fobs=0 are ignored at the mtz reading stage if
Sigma=0 or Sigma=NaN.

> On Mon, 2010-05-17 at 12:49 -0400, Edward A. Berry wrote:
> > The problem seems to be that phenix is using Fobs=0 as a "missing
> > number flag" which
> > precludes its use as a valid measurement.

I think we could fairly easily change phenix.refine to use Fobs=0 if
Sigma > 0. I'll add that to the low-priority to-do list (since there's
the truncate workaround).


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