The intensity of the reflection (hkl) being zero is a piece of
information, provided there are other reflections in that resolution
shell that are not zero (above sigma). If all of the reflections in the
resolution shell are essentially zero (<< sigma), then the
resolution cut-off is too optimistic.
There are two somewhat separate questions here: (1) what data to
use in refinement and (2) how to define a "nominal resolution"
How do you see those questions being separate? Let say you collected
data to resolution A (edge or corner of detector), then refined to
resolution B. You probably looked at the data and considered that the
data beyond B are either compromised by experimental setup or just
absent. Why would anyone consider calling the resolution of the refined
model or resolution of the presented structure other than B? One may
state in the main body of the paper that the crystal actually
diffracted to much higher resolution A but for such and such reasons we
were able to use the data only till resolution B.
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
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