Always Modelling Anomalous Signal

From: Jacob Keller
Date: 10 January 2012 20:00

Dear Crystallographers,

it seems to me that on a certain level we are always throwing away
(sort of) about half of our data when we merge Bijvoet pairs--why
shouldn't we keep them separate, since we know that they should be a
little bit different, especially in light of the higher multiplicities
which are more common now? Shouldn't modelling them give better
R-values, and wouldn't it just be more true? I guess a sort of proof
for this is that sulfurs are almost always detectable on anomalous
difference maps, implying that we are actually measuring those
differences accurately enough to see them (I don't think these things
can arise from model bias, as anomalous differences are not modeled.)
At least maybe at the final steps of refinement...?

JPK

--
*******************************************
Jacob Pearson Keller

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From: Felix Frolow


Who "We" ?
As a matter of protocol, for the last 25 years I keep anomalous signal
in my data for refinement, does not  matter what ignorant annotators say.
I do it for several reasons, one of them is matter of principle.
The problem is sometimes to deposit the data, which were used for the refinement.
Developers refuse to add the redundant information into the deposition file, annotators refuse to
accept the data file without averaged value for F or I, directors keep silent.
Be strong Jacob...

Dr Felix Frolow
Professor of Structural Biology and Biotechnology

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From: Ian Tickle


Jacob,

Actually the R factors including the Bijvoet pairs would be higher,
because the uncertainties in F(+) and F(-) are higher than that of
F(mean) by a factor of about sqrt(2).  R factors will always be higher
for unmerged data because averaging always reduces the uncertainty.
This means that we are in effect 'cheating' by throwing away the
relatively imprecise anomalous differences and getting falsely lower R
factors as a result!  But as you imply the model would improve if we
included the anomalous data in the refinement (assuming of course that
it is meaningful data).  This just demonstrates that low R factors do
not necessarily equate to a better model - especially if you
deliberately throw away the less precise data!  The model would
improve (marginally) because the anomalous differences would obviously
provide additional information about the anomalous scatterers and
therefore increase their precision, but wouldn't affect the precision
of the lighter atoms.  But is imprecision in the parameters of the
heavy (or heavier) atoms usually an issue? - since these have bigger
real scattering factors they will be more precisely determined than
the lighter atoms anyway.  So I don't think you would gain very much,
except maybe more truthful R factors!

Cheers

-- Ian

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From: Ethan Merritt

This has been an option in refmac refinement for some while now.
If you are using the GUI, select the option for "using SAD data directly"
rather than the default option "using no prior phase information".
Of course you must also make sure that appropriate scattering
factors are picked up by the program.

In my limited experience this has not led to improved refinement if
the anomalous differences are due only to sulfur, but has on occasion
led to noticeable improvement for true SeMet/SAD data.

       Ethan

--
Ethan A Merritt