On Tuesday, 21 February, 2017 16:53:06 Hunter Moseley wrote:
> Is there a straight-forward way to estimate the amount of missing electron
> density that a particular protein structure is missing based on the
> difference between Fo and Fc?
Short answer: no.
> It appears that the normalization of the Fc due to the employing of a
> maximum entropy method that keeps Fo and Fc comparable to the standard
> deviation of Fo would make this difficult.
Maximum entropy is not the issue. Your Fobs have no intrinsic scale.
They are not a count of photons-per-second or a fractional intensity of
the direct beam. In order to refine a model you must introduce an
ad hoc scale factor to make Fobs approximately equal to Fcalc on average.
"On average" is a somewhat sloppy description (that's where use of
maximum likelihood weighting may come in) but in the end we normally
calculate and display difference-density maps such that the mean
difference density is zero. You won't end up with a map that is
overall negative even if your model has spurious extra bits and you
won't end up with a map that is overall positive even if your model
is missing large chunks. The best you can hope for is that your
missing chunks will manifest in the map as connected blobs of positive
difference density balanced out by diffuse/disconnected regions of
negative difference density elsewhere.
Longer answer: still no.
The distribution of differences between Fobs and Fcalc can provide an
estimate of how good/bad wrong/right your current model is.
But that still doesn't tell you whether the current model is bad because
pieces are missing or bad because existing pieces are in the wrong place.
Ethan
> Or am I missing something?
>
> Cheers,
> Hunter
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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