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CCP4BB  July 2017

CCP4BB July 2017

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Subject:

Re: Rmergicide Through Programming

From:

Graeme Winter <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Wed, 5 Jul 2017 15:04:05 +0000

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Dear Frank, 
 
You are forcefully arguing essentially that others are wrong if we feel an existing statistic continues to be useful, and instead insist that it be outlawed so that we may not make use of it, just in case someone misinterprets it. 
 
Very well 
 
I do however express disquiet that we as software developers feel browbeaten to remove the output we find useful because “the community” feel that it is obsolete. 
 
I feel that Jacob’s short story on this thread illustrates that educating the next generation of crystallographers to understand what all of the numbers mean is critical, and that a numerological approach of trying to optimise any one statistic is essentially doomed. Precisely the same argument could be made for people cutting the “resolution” at the wrong place in order to improve the average I/sig(I) of the data set. 
 
Denying access to information is not a solution to misinterpretation, from where I am sat, however I acknowledge that other points of view exist. 
 
Best wishes Graeme 
 
 
On 5 Jul 2017, at 12:11, Frank von Delft <[log in to unmask]<mailto:[log in to unmask]>> wrote: 
 
 
Graeme, Andrew 
 
Jacob is not arguing against an R-based statistic;  he's pointing out that leaving out the multiplicity-weighting is prehistoric (Diederichs & Karplus published it 20 years ago!). 
 
So indeed:   Rmerge, Rpim and I/sigI give different information.  As you say. 
 
But no:   Rmerge and Rmeas and Rcryst do NOT give different information.  Except: 
 
  * Rmerge is a (potentially) misleading version of Rmeas. 
 
  * Rcryst and Rmerge and Rsym are terms that no longer have significance in the single cryo-dataset world. 
 
phx. 
 
 
 
On 05/07/2017 09:43, Andrew Leslie wrote: 
 
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 <[log in to unmask]<mailto:[log in to unmask]>> 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 <[log in to unmask]<mailto:[log in to unmask]>> 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: [log in to unmask]<mailto:[log in to unmask]> [mailto:[log in to unmask]] 
Sent: Tuesday, July 04, 2017 4:37 PM 
To: Keller, Jacob <[log in to unmask]<mailto:[log in to unmask]>> 
Cc: [log in to unmask]<mailto:[log in to unmask]> 
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 <[log in to unmask]<mailto:[log in to unmask]>> 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 <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]>> 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: [log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]> 
******************************************* 
 
 
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