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 <[email protected]
<mailto:[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]]
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]>>
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]>
*******************************************
--
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
