What I meant is that for small denominators (i.e. weak data, i.e. high
resolution), Rmerge is a quantity that does not have a statistically
meaningful average.
As James Holton pointed out before (can't find the original post, but
see links below):
Rmerge is (like?) a Cauchy distribution (check
Great! and (oops) now I realize what I meant to say was compare cc* with
cc-work and cc-free.
eab
Nat Echols wrote:
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry mailto:ber...@upstate.edu>> wrote:
If you refine once in phenix you can use phenix.cc_star to calculate cc*
and compare wit
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry wrote:
> If you refine once in phenix you can use phenix.cc_star to calculate cc*
> and compare with R and R-free; from the output mtz file and your unmerged
> .sca file.
>
FYI, this should also work with structures refined in Refmac, assuming it
But it is highly unlikely that sum(I) in the denominator is zero if I/sig(I) is 2 as reported (providing the sig(I) is
valid- what was chi^2 in the last shell and overall?).
I sort of disagree that R-merge values over 1.0 are meaningless, provided not too far over. Granted R-meas is more
meanin
This HKL2000 (scalepack) feature is actually extremely sensible: an
Rmerge that high is mathematically meaningless, it quite literally tells
you nothing at all about he signal in your data.
So I second James's advice: just put "n/a" in your table 1.
If the reviewer complains, point them to K
No matter what the value printed out for Rmerge in the outer shell is, I
recommend using "-" or "n/a" in your paper. This is because
sum(|I-I0|)/sum(I) actually is equal to "n/a" when sum(I) = 0.
-James Holton
MAD Scientist
On Wed, Aug 14, 2013 at 8:41 AM, Pietro Roversi <
pietro.rove...@bioch
The wwPDB partners are pleased to announce that new X-ray structure
validation reports are now being provided to depositors as part of the
structure annotation process. For the full announcement, see:
http://www.wwpdb.org/news/news_2013.html#02-August-2013
The reports can be used by depositors
Hello Yafang,
The answer lies in the fact that you used HKL2000. Scalepack has a long
standing "feature" where it reports Rmerge > 100% as zero. Quite why they do
that is a mystery, but your Rmerge in the outermost shell is NOT zero - the
Rmerge for the lower resolution shells will show up as
HKL2000 sets to 0 the Rmerge in any shell where it is higher than 100%
OUCH
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Dr. Pietro Roversi
Oxford University Biochemistry Department - Glycobiology Division
South Parks Road
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Tel. 0044 1865 275339
From:
Dear All,
Here are some more details about the question I asked earlier about "Rmerge
is 0 in the last shell". I processed the data using HKL2000. The space
group is I213. Redundancy is 10.2 (10.3). I/sigma is 34.8 (2.3). Rmerge is
6.5 (0.0). Since I/sigmaI is more than 2 in the last shell, I pref
multiplicity = 1.0?
On 14 Aug 2013, at 15:59, Yafang Chen wrote:
> Dear All,
>
> I recently processed a dataset, in which I/sigmaI of the last shell is 2.3,
> while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0?
> The completeness is 100 (100). Thank you so much for your
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Hash: SHA1
Dear Yafang,
a mathematically simple answer would be you collected no symmetry
equivalent reflections, although experimentally this is probably
difficult to achieve, unless your space group is P1. If you could tell
the name of the software you used, t
Dear All,
I recently processed a dataset, in which I/sigmaI of the last shell is 2.3,
while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0?
The completeness is 100 (100). Thank you so much for your help in advance!
Best,
Yafang
--
Yafang Chen
Graduate Research Assistant
Me
The project will involve structural, functional and mechanistic studies on
different heme proteins, including neutron crystallography and single
crystal resonance Raman spectroscopy. This work is a collaboration of
Peter Moody in the Department of Biochemistry and Emma Raven in the
Department of C
Hi everybody,
I would like to bring to your attention the following job offer:
==
The University of Konstanz with its “Institutional Strategy to promote
Top-Level Research” has been receiving continuous funding since 2007
within the framework of the Excellence Initiative by the
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