-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 > <[email protected]> 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 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRVc8mUxlJ7aRr7hoRAg8aAKDMxBrbHy0chAnnZasHZyQHjwfysgCgu+dv wEgawnqMAPQQh7wjgUv+27Y= =1veF -----END PGP SIGNATURE-----
