I must disagree with Tim on the statement "Rmerge should not be
published anymore".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 <[log in to unmask]> wrote:
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> 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 ÷2 0.94 (1.01)
>>
>> Average I/ó(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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