On Mon, 2010-05-17 at 13:00 -0700, Ralf W. Grosse-Kunstleve wrote:
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.
That's good since both 0 and NaN values for sigma are unreasonable.
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).
I guess truncate is not a workaround but rather something one must do. But this option may be useful when one inherits an incorrectly processed dataset. Few reflections will be of Iobs=0 in every dataset (just checked and got 8 reflections out of ~18000 with I=0.0 in scalepack output). Truncate, however, will push them into positive territory. Of course, if one got such a crazy dataset with a lot of zeros, a simple trick would be to increment every Fobs by a very small number. Would cheat the Fobs>0 check. Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs