Or just boycott the journal...??
On 10/06/2021 14:02, Tim Gruene wrote:
Hi Graeme,
could you explain why Rmeas does not serve the same purpose as Rmerge?
I guess Manfred (and others) have no objection to reporting Rmeas just
instead of Rmerge.
@ Christy: If one of my manuscript were rejected solely because Rmerge
was not mentioned, I would make a phone call to the boss if the editor.
Afterall, Rmerge can be recovered from the unmerged data, which ideally
you did deposit at the PDB.
Best,
Tim
On Thu, 10 Jun 2021 12:42:10 +0000 "Winter, Graeme (DLSLtd,RAL,LSCI)"
<graeme.win...@diamond.ac.uk> wrote:
Once again I find myself jumping to the defence of this rather poor
statistic!
Yes, Rmerge is a very poor estimator of "data quality" and has many
well published flaws related to multiplicity, but the low resolution
Rmerge, if combined with a multiplicity > (say) 5, is a good
indicator of whether the data set is "good" or there is something odd
going on.
For example, if you claim a 1.6A structure with an inner shell Rmerge
of 0.11, 5-fold multiplicity and an overall I/sig(I) of 68 I would
"smell a rat"
To me it does have a value, as an unbiased estimator of your true
unmerged I/sigma as it does not depend on any manipulation you have
done to your sigmas. It is not a good estimator of where the
resolution should be cut or any other decisions.
The above situation could be an indicator that there was radiation
damage, for example
There are better ways of measuring damage - Rd, Rcp, ... but these
are not commonplace graphs as I understand it. This little number in
the middle of the table does give you that hint.
So while I would say rejecting a paper because it was not included
was very heavy handed, I would not like to see it erased from all
papers either.
All the best Graeme
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Manfred S. Weiss <manfred.we...@helmholtz-berlin.de> Sent: 10 June
2021 13:30 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Should Rmerge be reported?
Dear Cristy,
this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.
It has been shown many times that Rmerge is flawed
at various levels.
The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.
I would love to see it disappear.
All the best
Manfred
Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.
I have a question regarding Rmerge. In recent years, we have
published our crystallographic structures in highly respected
journals using CC1/2, I/sigma(I), completeness and multiplicity as
quality parameters for our diffraction data.
Recently this year, We submitted a paper using the same strategy, but
one of the reviewers asked us to provide the Rmerge, arguing that
providing this data was compulsory and it was important to estimate
radiation damage.
We replied to the editor arguing that Rmerge should not be used as a
quality parameter, as suggested by more recent literature, such as
the article published by Karplus and Diederichs
(10.1016/j.sbi.2015.07.003). We also argued that there are modern and
efficient methods to estimate radiation damage (
doi.org/10.1107/S1600576718005241<http://doi.org/10.1107/S1600576718005241>;
doi.org/10.1107/S0907444909040177<http://doi.org/10.1107/S0907444909040177>).
It is my opinion that an experienced crystallographer can even
monitor radiation damage over the course of data processing.
And our paper was rejected !!!!!!!!!!!!!!!! due to the fact I did not
provide Rmerge which I certainly could have done If I found necessary.
Journals like Nature ((https://www.nature.com › documents ›
nr-tables-xray<https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiigtb19uHwAhWS3YUKHSB1AdkQFjABegQIAxAD&url=https%3A%2F%2Fwww.nature.com%2Fdocuments%2Fnr-tables-xray.doc&usg=AOvVaw1RbfYvNeiEM07FBEOohMig>)
and even IUCr Journals
(https://journals.iucr.org/f/services/structuralcommunications/)
still list Rmerge as a data to be reported. I always took this as a
suggestion since there are people still using Rmerge for data cutoff,
but I never took this as if Rmerge was a compulsory data to be
reported.
I would like to hear the opinion of this community. Should we
compulsorily report Rmerge? If so, Why?
Cheers,
Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo
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--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
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Germany
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