Woops! Sorry. I was thinking Rpim, which is always lower than Rmerge.
Rmeas is always higher, and more correctly estimates the
infinite-multiplicity Rmerge.
Sorry for the confusion, and thanks for the many reminders I just got
about the definition!
-James Holton
MAD Scientist
On 3/29/2013 10:28 AM, Tim Gruene wrote:
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Hi James,
you misquote me: I was saying that Rmeas should be replacing Rmerge,
and I guess everything you say holds for Rmeas, too, but still it is a
better statistical quantity than Rmerge. So please replace Rmerge with
Rmeas.
Best,
Tim
On 03/29/2013 06:08 PM, James Holton wrote:
I must disagree with Tim on the statement "Rmerge should not be
published anymore". That would be a shame. Perhaps even a crime.
When Uli Arndt introduced Rmerge he was in no way, shape or form
proposing that it be used for resolution cutoffs, or anything else
about the quality of the "structure". He was, however, trying to
define a good statistic to evaluate a diffractometer system, and
Rmerge is still VERY useful for that!
Any halfway decent modern detector/shutter/beam system should be
able to measure reasonably strong spots to within 5% of their
"true" intensity. Note that this is the _overall_ Rmerge value.
The Rmerge divided up in resolution bins is pretty useless for
this, especially the outermost bin, where you are basically
dividing by zero. The only useful Rmerge "bin" is actually the
lowest-angle one, where the spots tend to all be "strong".
Remember, Rmerge is defined as the _sum_ of all the variations in
spot intensity divided by the _sum_ of all the intensity. This
should never be much more than 5% for strong spots. If it is, then
something is wrong with either your detector, or your shutter, or
perhaps your assumptions about symmetry.
Yes, I know multiplicity makes Rmerge higher, but in actual fact
multiplicity makes Rmerge more "honest". It is better to say that
low multiplicity makes your Rmerge appear too low. Basically, if
you actually do have RMS 5% error per spot, and you only measure
each hkl twice, then you expect to see Rmerge=2.8%, even though the
actual error is 5%. And of course, if you measure 1e6 photons in
one spot you might fool yourself into thinking the error is only
0.1%. Its not. On the other hand, if all your spots are weak,
then you do expect the variation to be dominated by photon-counting
error, and you will get Rmerge values much greater than 5% on a
perfectly good detector. It is only at high multiplicities with
strong spots that Rmerge truly shows you how bad your equipment is.
This is why its always good to check Rmerge in your lowest-angle
bin.
Yes, I know we probably all take our local well-maintained and
finely-tuned beamline for granted, but that does not mean we
should stop using the only statistic that tells us something might
be wrong with the machine we used to measure our data. That is
definitely worth the ~20 extra bytes it takes up in your paper.
-James Holton MAD Scientist
On Fri, Mar 29, 2013 at 6:48 AM, Tim Gruene
<t...@shelx.uni-ac.gwdg.de> wrote: Dear Hamid,
the statistics for I/sigI and the R-value per resolution shell
would shed more light than the overall values.
Judging from the Rmerge in the high resolution shell the data may
have been processed by somebody who still thinks Rmerge <= 30% is a
good criterium for resolution cut-off.
The high overall Rmerge might indicate a wrong space-group was
picked with too high symmetry.
If you have a copy of the unmerged data, run it through pointless,
if you even have a copy of the frames, reprocess them in P1 and run
the data through pointless!
If these data are from an article you are refereeing please point
out that Rmerge should not be published anymore and be replaced by
Rmeas (alias Rrim)!
Best, Tim Gruene
On 03/29/2013 02:19 PM, hamid khan wrote:
Dear CCP4BB Members,
I am interested in your expert comments/opinions about two
values of a protein crystal diffraction data. Basically I am
new to this field and do not have much idea about diffraction
data interpretation and crystallography software’s use.
1) What could be the possible reasons for a high Rmerge
value, say like 0.185?
2) Value 6.2 for average I/sigma(I) for higher shell means
that the resolution of the diffraction data is much higher
than actually measured, what could be the possible reasons
for this?
For your ease I would like to past the table here;
Values in parentheses are for the last resolution shell
Space group P2221
Unit-cell parameters (A°)
a 58.08
b 101.32
c 103.47
Molecules in ASU 1
Resolution range 38.63 - 2.50 (2.59 - 2.50)
Total number of reflections 228902
Number of unique reflections 21600
Completeness (%) 99.1 (98.0)
Rmerge 0.185
(0.373)
Reduced χ2 0.94 (1.01)
Average I/σ(I) 9.8 (6.2)
Thanks for the tips..,
Hamid Khan
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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