Ahh. But what I'm saying is that Rmeas is not a replacement for
Rmerge because Rmeas is _always_ lower than Rmerge. It is even less
useful that a low-multiplicity Rmerge for evaluating the
diffractometer.
I fully realize that Rmeas does have the desirable property of being
"flatter" with respect to multiplicity, but being equally "too low"
for all multiplicity is not better than being "too low" for some
multiplicities. IMHO. Yes, I know, we all like R statistics that are
lower. Indeed, by using the mean absolute deviation |I-<I>|, Uli was
able to come up with a definition of Rmerge that will always be lower
than the RMS error (for infinite multiplicity and RMS 5% error you
actually get Rmerge=3.99%). No doubt, this must have contributed to
the acceptance of Rmerge at the time. But we can't just keep
re-defining our metric of "error" every ~20 years so that the same
crappy data keeps looking better and better. That's a slippery slope
I'd rather not be on. I think it is important to remember what it is
we are trying to measure, and to be honest and consistent about what
the error bars really are.
But that's just my opinion. I could be wrong.
-James Holton
MAD Scientist
On Fri, Mar 29, 2013 at 10:28 AM, Tim Gruene <[log in to unmask]> 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 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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