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
>> <[log in to unmask]> 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 ÷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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