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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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