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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
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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,
multiplicity = 1.0?
On 14 Aug 2013, at 15:59, Yafang Chen yafangche...@gmail.com 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
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
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
Oxford OX1 3QU England - UK
Tel. 0044 1865 275339
From:
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
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
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
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
On Wed, Aug 14, 2013 at 10:31 PM, Edward A. Berry ber...@upstate.eduwrote:
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
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