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: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: ccp4bb@jiscmail.ac.uk 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 <kell...@janelia.hhmi.org> 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 > <kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> 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: kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org> > ******************************************* > > > -- > 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 >
