[phenixbb] WAS: changing TLS groups mid refinement

Ed Pozharski epozh001 at umaryland.edu
Mon May 17 14:29:53 PDT 2010

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.


"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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