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There are two somewhat separate questions here: (1) what data to use in
refinement and (2) how to define a "nominal resolution" that will give the
outside world a good idea of how far out the data extended, which needs
some vague sort of uniform standard. I'd suggest the answers are (1) any
datum you believe you really did measure should be thrown into the pot and
(2) the reported nominal resolution should be where I/sigI falls below 2,
perhaps with the output statistics from scalepack or whatever was used
included as supplementary material to show that the sigmas are not grossly
mis-estimated. Unfortunately this creates logistical problems with
deposting coordinates, etc. if you want to call the official "resolution"
something other than that of the farthest-out fly speck you refined against.
At 09:29 AM 4/28/2006, Bart Hazes wrote:
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This is an interesting conceptual question. A reflection with an intensity
of virually zero does not contribute to your electron density map, so can
it be data? If it is can I claim to have a 0.02 Angstrom structure
although all intensities beyond 2 Angstrom are virtually zero?
The answer to question 1 is YES it can be data
The answer to question 2 is NO KEEP DREAMING
A very weak reflection does not contribute to your map so leaving it out
doesn't hurt since missing a reflection is equivalent to assuming it is
zero, not a bad approximation. However, a lot of our maps are of the
2Fo-Fc and Fo-Fc types. Similarly refinement a depends on |Fobs-Fcalc|.
Thus, if Fcalc is big and you measured it as being near zero then the
discrepancy is large and the reflection has a large contribution to
refinement and these kinds of maps. Had you not measured the reflection
then its contribution would be ignored (equivalent to Fo-Fc being zero).
The difference at the high resolution limit is that Fcalc starts to
approach zero as well as Fobs. So now both Fobs and Fo-Fc are virtually
zero and small relative to the errors in Fo and Fc. So this time there
really is no information left to speak of.
Bart
[EMAIL PROTECTED] wrote:
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What is "observable data"? If I observe a reflection by passing it through
the Ewald sphere I can measure its intensity
Phil
Here's what Acta Cryst has to say about resolution-
From the "Notes for authors 2006" from Acta Cryst D:
http://journals.iucr.org/d/issues/2006/02/00/me0308/index.html
"11.1. Resolution
The effective resolution should be described clearly. Values of the
internal
agreement of the data, Rmerge, together with the multiplicity, the mean
value
of I/ and the percentage completeness of the data are required for the
overall
data set and the highest resolution shell together with the limits of that
shell in Å. For high-quality data obtained with synchrotron radiation,
values
of Rmerge < 20%, completeness > 93% and observable data > 70% should
be
achievable for the highest resolution shell. A complete table listing the
above
criteria as a function of resolution should also be submitted, but will
normally
be included in the supplementary material..."
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
