There are two opposing views on this.
First: Rmerge doesn't matter. Don't even look into that column in
scalepack output, you will be upset over nothing. If you collect twice
as much data (360 sweep instead of 180) from the same crystal, your
Rmerge will go up due to higher redundancy, but the dataset will
actually get better because you measuring every reflection twice more
and your I/sigma will increase by ~40%.
Second: Rmerge is very important, because if it is, say, 100% (oh,
those zeros in the scalepack output) it means that symmetry-related
reflections vary by about 100%, so your data is a pile of garbage (at
least in that resolution shell). Cut your data at the resolution where
Rmerge is 30% and you will be rewarded by really low Rfactors for your
final model. Plus, if you keep all the data to where I/sigma~1, your
Rmerge is guaranteed to be 0.00 in the output, and what are you going to
tell reviewers of your paper?
Of course, truth is somewhere in the middle. If I collect on two
crystals of the same type (assuming everything else is the same, such as
redundancy), and one has much higher Rmerge, then I should probably
choose the other one. If you cut resolution at I/sigma~1, and your
overall Rmerge is about 10%, I think it's normal. But if it's 30%, you
may have some unusually high level of noise in your data (satellite
crystal? twinning? evil xray fairy messing with you?). So Rmerge does
tell you something, but only in context with all the other information.
After all, the only thing that matters is if your electron density map
is interpretable. I dare to say that the quality of the map you get
does correlate with Rmerge, but would I discard a dataset just because
Rmerge is high without trying to solve the structure and take a look at
the density? Never.
Cheers,
Ed.
Mischa Machius wrote:
OK, that brings us back to a more substantial question: is any of
these R values actually suitable to judge the quality of a given
dataset? Instead of introducing novel R factors, one could also simply
ignore them altogether, make sure that the error models have been
properly chosen and look at I/sigma(I) as the main criterion. [QUOTE
]If anyone then still wants to present low R factors, one can always
divide by 2, if necessary. [/QUOTE]
Best - MM
On Jan 18, 2008, at 1:02 PM, Salameh, Mohd A., Ph.D. wrote:
Thank you all, it was very, very helpful discussion. However, I
collected crystal data and the Rmerge overall was very high around 0.17
at 2.6A resolution and I'm wondering what is the acceptable value
(range) of R-merge that worth the time to continue processing! Very
anxious to hear your thoughts. Thanks, M
****************************************************
Mohammed A. Salameh, Ph.D.
Mayo Clinic Cancer Center
Griffin Cancer Research Building
4500 San Pablo Road
Jacksonville, FL 32224
Tel:(904) 953-0046
Fax:(904) 953-0277
[EMAIL PROTECTED]
****************************************************
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Chris Putnam
Sent: Friday, January 18, 2008 1:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] differences between Rsym and Rmerge
On Friday 18 January 2008 09:30:06 am Ethan A Merritt wrote:
Rmerge is an average over replicate measurements of the intensity for
identical [hkl]. Rsym is an average over the measurements for all
symmetry
equivalent reflections.
In the presence of anomalous scattering, Rsym will be higher than
Rmerge
because the Bijvoet pairs, although symmetry related, do not have
identical
intensities.
One might logically report two values for Rsym, one which averages
over the Bijvoet-paired reflections and one which does not.
This has been an eye-opening discussion for me. I've been really
surprised
that there's been such a diversity of opinion about what these common
terms ought to refer to, and the fact that my understanding was wrong.
I always thought that Rsym was an average over all symmetry equivalent
reflections from the same crystal (including Bijvoet pairs) and Rmerge
was
properly restricted to cases of multi-crystal averaging. (My versions
of
Table 1's from single crystals have used "Rsym" rather than "Rmerge".)
I wonder if the problem here is that the terms have become overloaded
(and
hence non-specific). In that sense "Rmerge" is a particularly
unfortunate
name as every R that we're discussing is a really a merge of some sort
or
another. (In the most naive sense, "Rmerge" might be thought to be the
R
for whatever variation of reflection merging the experimenter chooses to
do.)
One possible solution would be to push the community towards a new set
of
terms with clearly defined meanings (and whose names would be used
explicitly by new releases of MOSFLM, HKL2000, etc. and changes for
new entries in the PDB).
If new terms were to be adopted, they ought to specifically distinguish
between single crystal and multi-crystal merging. I see three such
R values that might be useful (I've arbitrarily chosen names to
distinguish
them from each other and the older terms):
Rhkl - R of identical hkl's
Rrot - R of symmetry-related hkls, but not Bijvoet pairs
("rot" coming from the concept that all symmetry-related
reflections can be found via rotations in reciprocal space and
the fact that "sym" has already been used)
RBijvoet - R of symmetry-related and Bijvoet-related hkls
(including reflections related by both rotations and an inversion
center in reciprocal space)
Rhkl,multi - multi-crystal version of Rhkl
Rrot,multi - muti-crystal version of Rrot
RBijvoet,multi - multi-crystal version of RBijvoet
The downside of adopting new names is that it makes the previous
literature
obsolete, but I wonder if the older terms were ambiguous enough that
that's
not such a problem.
--Christopher Putnam, Ph.D.
Assistant Investigator
Ludwig Institute For Cancer Research
--------------------------------------------------------------------------------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
