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To me, it almost looks like there is currently no good way to
describe, or even assess, the information content of diffraction data.
Something else seems to be needed. If we, for example, accept the
notion that there is information in data with I/sigma(I) of 1 and
below, we will have to learn to live with Rmerges of 100% and greater.
Also, some phenomena, such as radiation damage, aren't properly
modeled yet, making things look worse than they probably are. As Bart
rightfully says, people are throwing away perfectly useful data, just
because the numbers don't look too good.
I think the various cutoffs that are in use are primarily there to
satisfy reviewers. Nobody-knows-who came up with these thresholds,
when that was and - most importantly - what the rationale behind them
is. They seemed to have been passed down through the generations
without too much contemplation. I, for one, am often surprised at what
reviewers come up with, and I am getting more and more frustrated with
arguing with them. Many reviewers are not even structural biologists,
so who knows where they got their wisdom from.
It sure looks it's our own fault. We got to correct that.
One could just as well be pragmatic and use all data one can get, even
if the completeness in the highest resolution shell is only 20%, the
Rmerges approach 100%, and the I/sigma(I) is "only" 1.5. Current
maximum-likelihood methods seem to be very good at making proper use
of the information in the data. As long as the electron density
improves, use the data.
Of course, this would lead to the problem of how to assess the quality
of the electron density and, finally, the resolution of a structure. I
think this is where the real issue is. We need tools to determine the
effective resolution of an electron density in various regions. There
should not be just a single resolution value, because one portion of
the electron density may have a "resolution" of 1.8Å, whereas another
one may have 3.0Å, etc. Such a statistic would be much more useful for
scientists who are using our models than some esoteric way of
calculating Rmerges. Of course, the quality of the electron density
depends on the correctness of the model, which in turn is quite
subjective and brings a whole set of other problems with it. So, it
seems we are still having a way to go to come up with reasonable
guidelines that make the best out of our data.
On Apr 17, 2006, at 9:08 AM, Bart Hazes wrote:
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Hi Ashima,
With these statistics you shouldn't have to worry about reviewers,
it looks perfectly sensible. Actually I'm much more concerned about
the recent epidemic of overly pessimistic resolution cutoffs. In our
journal club at least half the papers have I/SigI in the highest
resolution bin in the 3-6 range which means they could have gotten
significantly higher resolution. There are situations where data
quality is more important than resolution, for instance
(anomalous) phasing, but I see the same with many native data sets.
It is not clear to me if people are placing the detector too far
from the crystal and thus not even measure the highest resolution
data or that they just elect not to process those data. Why??? To
get nicer looking statistics???? That would be VERY bad practice!!!
A kinder view is that the detector distance is set based on the
apparent resolution of the first image(s) which underestimates the
true resolution of a high redundancy data set. If you don't need a
long detector distance to resolve spots I prefer to select a
distance where my visible diffraction uses the central 80-90% of the
detector allowing mosflm to try to extract some sensible information
from beyond what the eye can see.
This looks like something James Holton may have looked at. If so I'd
be interested to hear if he or the elves have come up with a magic
rule.
Bart
Ashima Bagaria wrote:
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HI all,
In regards to my CCP4 question about the acceptable Rmerge values
in last resolution shell..various other parameters pertaining to
the protein data at 3.5 A are I/sigmaI = 13.1 (2.3) %completeness =
95.7(96.8) multiplicity = 3.8 All suggestions are welcome Regards
ashima
----------------------------------------------------------------------
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--------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
