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). Ralf