There are three places in a pdb file where resolution is defined.
Unfortunately by current conventions I believe they are all required
to show the same value. If one of them could be redefined to be
"effective resolution", with a comment to explain how that was
arrived at, it would take the pressure off of resolution cuttoff
to serve double duty as the principal indicator of quality.
I guess you can entitle your paper "2.2 A structure of XYZ" even if
the pdb file shows the resolution to be 1.92 with 22% completeness
in the last shell, which could appease some reviewers but make
problems with others.
eab
DUFF, Anthony wrote:
I thought... we had a definition for reportable resolution: The resolution at which
<I/sig(I)> = 2, and completeness > 50%
This reported resolution is not to be confused with data cutoff. We give the
software all the scaled and merged data and let it down-weight the weak data. At the
edge, we might happily have Rmerge=50%, multiplicity = 1.1, <I/sig(I)> = 1.
The resolution of the edge data should not be reported as the resolution of the data.
This reportable resolution is actually useful in refinement. Very very
roughly, you are done when the R-factor equals reportable resolution divided by
10. 25% for 2.5A data. 15% for 1.5A data.
Anthony Duff
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: Saturday, 19 April 2014 6:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallographic confusion
As has been alluded to, people (and not just crystallographers) are looking for
a simple number to indicate the quality of a structure.
Unfortunately this doesn't exist, but it doesn't keep people from wanting such
a number.
Most crystallographers (I think) now agree that throwing data away is a bad
idea and will make maps worse.
The real question is not whether to throw data away, but what to call the
resolution of a map/ structure.
A structure that has been refined with data that is ~90% complete at 3.6
Angstrom resolution but that has 2% completeness at 2.8 Angstrom would be
considered to be ? (Just to pull one instance from the PDB).
If we as crystallographers could agree to some definition as to what our
arbitrary resolution number is, life would probably be easier for the
non-crystallographers (as well as for the crystallographers in some instances-
particularly in the process of reviewing papers).
cheers, tom
Tom Peat
Biophysics Group
CSIRO, CMSE
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of William G. Scott
[wgsc...@ucsc.edu]
Sent: Saturday, April 19, 2014 11:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] crystallographic confusion
Dear Arnon et al:
My understanding of the Shannon/Nyquist sampling theorem is admittedly
extremely rudimentary, but I think aliasing can result if an arbitrary
brick-wall resolution cut-off to the data is applied.
So let's say there are real data are to 2.0 Å resolution. Applying the 2.2 Å
cutoff will result in aliasing artifacts in the electron density map
corresponding to an outer shell reciprocal space volume equal but opposite to
the cut out data.
The alternative, which is to process and keep all the measured reflections,
should help to minimize this. An effective resolution can be calculated and
quoted. This becomes a significant problem with nucleic acids and their
complexes, which often diffract with significant anisotropy.
The idea that 85% completeness in the outer shell should dictate its rejection
seems rather surprising and arbitrary. The aliasing artifacts in that case
would probably be significant. The map image quality, after all, is what we
are after, not beautiful Table 1 statistics.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry and The Center for the Molecular
Biology of RNA University of California at Santa Cruz Santa Cruz, California
95064 USA http://scottlab.ucsc.edu/scottlab/
On Apr 18, 2014, at 5:22 PM, Lavie, Arnon <la...@uic.edu> wrote:
Dear Kay.
Arguably, the resolution of a structure is the most important number
to look at; it is definitely the first to be examined, and often the
only one examined by non-structural biologists.
Since this number conveys so much concerning the quality/reliability
of the the structure, it is not surprising that we need to get this
one parameter right.
Let us examine a hypothetical situation, in which a data set at the
2.2-2.0 resolution shell has 20% completeness. Is this a 2.0 A
resolution structure? While you make a sound argument that including
that data may result in a better refined model (more observations,
more restraints), I would not consider that model the same quality as
one refined against a data set that has >90% completeness at that resolution
shell.
As I see it, there are two issues here: one, is whether to include
such data in refinement? I am not sure if low completeness
(especially if not
random) can be detrimental to a correct model, but I will let other
weigh in on that.
The second question is where to declare the resolution limit of a
particular data set? To my mind, here high completeness (the term "high"
needs a precise definition) better describes the true resolution limit
of the diffraction, and with this what I can conclude about the
quality of the refined model.
My two cents.
Arnon Lavie
On Fri, April 18, 2014 6:51 pm, Kay Diederichs wrote:
Hi everybody,
since we seem to have a little Easter discussion about
crystallographic statistics anyway, I would like to bring up one more topic.
A recent email sent to me said: "Another referee complained that the
completeness in that bin was too low at 85%" - my answer was that I
consider the referee's assertion as indicating a (unfortunately not
untypical case of) severe statistical confusion. Actually, there is
no reason at all to discard a resolution shell just because it is not
complete, and what would be a cutoff, if there were one? What
constitutes "too low"?
The benefit of including also incomplete resolution shells is that
every reflection constitutes a restraint in refinement (and thus
reduces overfitting), and contributes its little bit of detail to the
electron density map. Some people may be mis-lead by a wrong
understanding of the "cats and ducks" examples by Kevin Cowtan:
omitting further data from maps makes Fourier ripples/artifacts worse, not
better.
The unfortunate consequence of the referee's opinion (and its
enforcement and implementation in papers) is that the structures that
result from the enforced re-refinement against truncated data are
_worse_ than the original data that included the "incomplete"
resolution shells.
So could we as a community please abandon this inappropriate and
un-justified practice - of course after proper discussion here?
Kay