Hi Jim, of course the issue of crystallographic data quality indicators deserves a somewhat more appropriate (or at least more permanent, and peer-reviewed) means of dissemination than CCP4BB. Nevertheless I'll sum up some of the most important points I can think of:
A) all data quality indicators measure precision, not accuracy B) there are those data quality indicators that measure the precision of unmerged data: (Rsym=)Rmerge, Rmeas, (I/sigma)_unmerged and those that measure the precision of merged data: Rpim, Rsplit (the FEL community uses this; same as R_mrgd_I - see Diederichs&Karplus 1997), CC1/2, (I/sigma)_merged The merged indicators usually differ by a factor of sqrt(m) from their unmerged counterparts, where m is multiplicity. Rsplit (~R_mrgd_I) and CC1/2 compare random half-datasets which may be more robust than just hoping that the explicit sqrt(m) law holds (it only holds for unrelated errors). There is no unmerged counterpart of CC1/2. C) Since downstream steps use intensities, it is preferable to use a data quality indicator that does not require sigma to be estimated, because the authors of the different data processing programs/algorithms have different ideas how this should be done. This rules out I/sigma as a useful quality indicator - at least as soon as different programs look at the same data. D) Merged data quality indicators are more useful because we are using merged data for downstream steps (phasing, molecular replacement, refinement), so we need to know _their_ precision, not that of the unmerged data. E) Rpim and Rsplit are calculated from intensities and have a different asymptotic behaviour than model R-values (Rwork, Rfree), so they cannot be meaningfully be compared with model R-values (i.e. their numerical value tells you nothing about the Rwork/Rfree your model can be refined to). This is very different from CC1/2 - it can be used to calculate CC*, a quantity that is the upper limit of what the CC of the model intensities against the experimental intensities can reach. I'll stop here. Most of this may be at variance with what we were all brought up with, but it's time for a change! best, Kay On Tue, 19 Nov 2013 13:18:19 +0000, Jim Pflugrath <[email protected]> wrote: >Graeme wrote: >"... Rpim is much more instructive. ... as each of these tells something >different." > >I have to ask: >"Why is Rpim much more instructive? I'm trying to figure this out still. Can >one please summarize what are best practices with all these numbers and how >each of these tells something different?" > >Another problem that I see is that folks can adjust their sigmas many >different ways without knowing they have adjusted their sigmas. And they can >be adjusted incorrectly when they are adjusted. > >BTW, Graeme is correct about lots of multiple low I/sigI observations for each >Bragg reflection in a resolution shell will lead to 100% (or higher) Rmerge >with <I/sigI> of 3. This assumes no systematic errors and only randomly >distributed random errors (a rare if not impossible situation, I would think). > I will defer to others about what the relevance of that is. > >Thanks for any insights, Jim > > >________________________________ >From: CCP4 bulletin board [[email protected]] on behalf of Graeme Winter >[[email protected]] >Sent: Tuesday, November 19, 2013 2:02 AM >To: [email protected] >Subject: Re: [ccp4bb] 100% Rmerge in high resolution shell > >Usually this means that you have relatively high multiplicity, which >give-or-take improves the I/sig(I) by sqrt(m) where m is the multiplicity, but >also increases the Rmerge. > >For any given narrow shell of reflections, > >Rmerge ~ 0.8 / unmerged(I/sig(I)) > >merged(I/sig(I)) ~ sqrt(m) * unmerged(I/sig(I)) > >So it is perfectly possible to have unmerged I/sig(I) of 0.8 which will give >you an Rmerge of around 1.0, and have I/sig(I) (merged) around 3, by having >multiplciity 14 or so. I suggest that this is the case: if it is much lower >than this there is something odd going on. > >For the merged I/sig(I) Rpim is much more instructive. I'd love it if people >reported merged and unmerged I/sig(I), Rmerge, Rmeas, Rpim, CC1/2, ... as each >of these tells something different. > >Best wishes, > >Graeme > >Possibly useful papers: > >http://www.nature.com/nsmb/journal/v4/n4/abs/nsb0497-269.html >http://scripts.iucr.org/cgi-bin/paper?he0191 >http://scripts.iucr.org/cgi-bin/paper?he0268 > > > > >On 19 November 2013 06:43, Shanti Pal Gangwar ><[email protected]<mailto:[email protected]>> wrote: >Dear All > > >Can anyone explain the meaning and relevance of data when the Rmerge is 100% >in high resolution shell and I/sig(I) is 3. > > > >Thanks > > > >-- >******************** >regards >Shanti Pal Gangwar >School of Life Sciences >Jawaharlal Nehru University >New Delhi-110067 >India >Email:[email protected]<mailto:email%[email protected]> > > > >
