I would like to support Graeme in his wish to retain Rmerge in Table 1, essentially for exactly the same reasons.
I also strongly support Francis Reyes comment about the usefulness of Rmerge at low resolution, and I would add to his list that it can also, in some circumstances, be more indicative of the wrong choice of symmetry (too high) than the statistics that come from POINTLESS (excellent though that program is!). Andrew > On 5 Jul 2017, at 05:44, Graeme Winter <[email protected]> wrote: > > HI Jacob > > Yes, I got this - and I appreciate the benefit of Rmeas for dealing with > measuring agreement for small-multiplicity observations. Having this *as > well* is very useful and I agree Rmeas / Rpim / CC-half should be the primary > “quality” statistics. > > However, you asked if there is any reason to *keep* rather than *eliminate* > Rmerge, and I offered one :o) > > I do not see what harm there is reporting Rmerge, even if it is just used in > the inner shell or just used to capture a flavour of the data set overall. I > also appreciate that Rmeas converges to the same value for large multiplicity > i.e.: > > Overall InnerShell OuterShell > Low resolution limit 39.02 39.02 1.39 > High resolution limit 1.35 6.04 1.35 > > Rmerge (within I+/I-) 0.080 0.057 2.871 > Rmerge (all I+ and I-) 0.081 0.059 2.922 > Rmeas (within I+/I-) 0.081 0.058 2.940 > Rmeas (all I+ & I-) 0.082 0.059 2.958 > Rpim (within I+/I-) 0.013 0.009 0.628 > Rpim (all I+ & I-) 0.009 0.007 0.453 > Rmerge in top intensity bin 0.050 - - > Total number of observations 1265512 16212 53490 > Total number unique 17515 224 1280 > Mean((I)/sd(I)) 29.7 104.3 1.5 > Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.778 > Completeness 100.0 99.7 100.0 > Multiplicity 72.3 72.4 41.8 > > Anomalous completeness 100.0 100.0 100.0 > Anomalous multiplicity 37.2 42.7 21.0 > DelAnom correlation between half-sets 0.497 0.766 -0.026 > Mid-Slope of Anom Normal Probability 1.039 - - > > (this is a good case for Rpim & CC-half as resolution limit criteria) > > If the statistics you want to use are there & some others also, what is the > pressure to remove them? Surely we want to educate on how best to interpret > the entire table above to get a fuller picture of the overall quality of the > data? My 0th-order request would be to publish the three shells as above ;o) > > Cheers Graeme > > > >> On 4 Jul 2017, at 22:09, Keller, Jacob <[email protected] >> <mailto:[email protected]>> wrote: >> >> I suggested replacing Rmerge/sym/cryst with Rmeas, not Rpim. Rmeas is simply >> (Rmerge * sqrt(n/n-1)) where n is the number of measurements of that >> reflection. It's merely a way of correcting for the multiplicity-related >> artifact of Rmerge, which is becoming even more of a problem with data sets >> of increasing variability in multiplicity. Consider the case of comparing a >> data set with a multiplicity of 2 versus one of 100: equivalent data quality >> would yield Rmerges diverging by a factor of ~1.4. But this has all been >> covered before in several papers. It can be and is reported in resolution >> bins, so can used exactly as you say. So, why not "disappear" Rmerge from >> the software? >> >> The only reason I could come up with for keeping it is historical reasons or >> comparisons to previous datasets, but anyway those comparisons would be >> confounded by variabities in multiplicity and a hundred other things, so >> come on, developers, just comment it out! >> >> JPK >> >> >> >> >> -----Original Message----- >> From: [email protected] <mailto:[email protected]> >> [mailto:[email protected] <mailto:[email protected]>] >> Sent: Tuesday, July 04, 2017 4:37 PM >> To: Keller, Jacob <[email protected] >> <mailto:[email protected]>> >> Cc: [email protected] <mailto:[email protected]> >> Subject: Re: [ccp4bb] Rmergicide Through Programming >> >> HI Jacob >> >> Unbiased estimate of the true unmerged I/sig(I) of your data (I find this >> particularly useful at low resolution) i.e. if your inner shell Rmerge is >> 10% your data agree very poorly; if 2% says your data agree very well >> provided you have sensible multiplicity… obviously depends on sensible >> interpretation. Rpim hides this (though tells you more about the quality of >> average measurement) >> >> Essentially, for I/sig(I) you can (by and large) adjust your sig(I) values >> however you like if you were so inclined. You can only adjust Rmerge by >> excluding measurements. >> >> I would therefore defend that - amongst the other stats you enumerate below >> - it still has a place >> >> Cheers Graeme >> >>> On 4 Jul 2017, at 14:10, Keller, Jacob <[email protected] >>> <mailto:[email protected]>> wrote: >>> >>>> Rmerge does contain information which complements the others. >>> >>> What information? I was trying to think of a counterargument to what I >>> proposed, but could not think of a reason in the world to keep reporting it. >>> >>> JPK >>> >>> >>> On 4 Jul 2017, at 12:00, Keller, Jacob <[email protected] >>> <mailto:[email protected]><mailto:[email protected] >>> <mailto:[email protected]>>> wrote: >>> >>> Dear Crystallographers, >>> >>> Having been repeatedly chagrinned about the continued use and reporting of >>> Rmerge rather than Rmeas or similar, I thought of a potential way to >>> promote the change: what if merging programs would completely omit >>> Rmerge/cryst/sym? Is there some reason to continue to report these stats, >>> or are they just grandfathered into the software? I doubt that any journal >>> or crystallographer would insist on reporting Rmerge per se. So, I wonder >>> what developers would think about commenting out a few lines of their code, >>> seeing what happens? Maybe a comment to the effect of "Rmerge is now >>> deprecated; use Rmeas" would be useful as well. Would something >>> catastrophic happen? >>> >>> All the best, >>> >>> Jacob Keller >>> >>> ******************************************* >>> Jacob Pearson Keller, PhD >>> Research Scientist >>> HHMI Janelia Research Campus / Looger lab >>> Phone: (571)209-4000 x3159 >>> Email: [email protected] >>> <mailto:[email protected]><mailto:[email protected] >>> <mailto:[email protected]>> >>> ******************************************* >>> >>> >>> -- >>> This e-mail and any attachments may contain confidential, copyright and or >>> privileged material, and are for the use of the intended addressee only. If >>> you are not the intended addressee or an authorised recipient of the >>> addressee please notify us of receipt by returning the e-mail and do not >>> use, copy, retain, distribute or disclose the information in or attached to >>> the e-mail. >>> Any opinions expressed within this e-mail are those of the individual and >>> not necessarily of Diamond Light Source Ltd. >>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >>> attachments are free from viruses and we cannot accept liability for any >>> damage which you may sustain as a result of software viruses which may be >>> transmitted in or with the message. >>> Diamond Light Source Limited (company no. 4375679). Registered in England >>> and Wales with its registered office at Diamond House, Harwell Science and >>> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >>> >> >
