On 06/20/2013 01:07 PM, Douglas Theobald wrote:
> How can there be nothing "wrong" with something that is unphysical? Intensities cannot be negative.
I think you are confusing two things - the true intensities and observed
intensities.
True intensities represent the number of photons that diffract off a
crystal in a specific direction or, for QED-minded, relative
probabilities of a single photon being found in a particular area of the
detector when it's probability wave function finally collapses.
True intensities certainly cannot be negative and in crystallographic
method they never are. They are represented by the best theoretical
estimates possible, Icalc. These are always positive.
Observed intensities are the best estimates that we can come up with in
an experiment. These are determined by integrating pixels around the
spot where particular reflection is expected to hit the detector.
Unfortunately, science did not yet invent a method that would allow to
suspend a crystal in vacuum while also removing all of the outside
solvent. Neither we have included diffuse scatter in our theoretical
model. Because of that, full reflection intensity contains background
signal in addition to the Icalc. This background has to be subtracted
and what is perhaps the most useful form of observation is Ispot-Iback=Iobs.
These observed intensities can be negative because while their true
underlying value is positive, random errors may result in Iback>Ispot.
There is absolutely nothing unphysical here. Replacing Iobs with E(J) is
not only unnecessary, it's ill-advised as it will distort intensity
statistics. For example, let's say you have translational NCS aligned
with crystallographic axes, and hence some set of reflections is
systematically absent. If all is well, <Iobs>~0 for the subset while
<E(J)> is systematically positive. This obviously happens because the
standard Wilson prior is wrong for these reflections, but I digress, as
usual.
In summary, there is indeed nothing wrong, imho, with negative Iobs.
The fact that some of these may become negative is correctly accounted
for once sigI is factored into the ML target.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
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