[3dem] [ccpem] Which resolution?

[Tim Gruene]

Hi Marin,

crystallography has long moved away from the term 'resolution', see e.g. 
https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2. It is merely a 
ballpark number, and it is good to know whether crystallographic data were cut 
at 1, 2, or 3 Angstrom, but not very important.

What counts is the interpretation of the model and conclusion that can be 
drawn on the system under study. It requires a broader understanding of 
crystallography in order to understand whether the conclusions are justified. 
Resolution plays only a minor role in this. It is more useful to take a look 
at the crystallographic map itself in order to understand.

EM is totally different from crystallography, and why would one mix concepts 
between the fields?

Best,
Tim

On Thursday, February 13, 2020 12:07:15 AM CET Marin van Heel wrote:
> Hi Tim,
> Good to hear from you!  No longer at PSI??
> See... You are already touching upon one of the logical breaking points in
> the resolutiton story...!  X-ray crystallography resolution criteria like
> R-factors make absolutely no sense outside the field of crystallography and
> of structural biology.  It is the result of a hybrid iterative optimisation
> process between the phases of a model structure and the measured amplitudes
> of a diffraction experiment!  The FRC/FSC resolution criteria, in contrast,
> are universal quality metrics not at all coupled to Cryo-EM or structural
> biology.  Using structural biology arguments like how well I see an alpha
> helix or how well I see the hole in an aromatic ring as an assessment
> criterion of whether a metric is good or not is a waste of time!  (Moreover
> filtering a map can completley change its appearance without changing its
> information contents). Even some my own (ex-)students and (ex-)postdocs
> sometimes completely miss this fundamental point. The FRC and FSC criteria
> are now used as quality metrics in all walks of image science like X-ray
> tomography and super-resolution light microscopy, fields of science where
> atomic coordinates of proteins are not an issue. The FRC / FSC functions
> are universal and very direct metrics that compare both the amplitudes and
> the phases of two independent measurements of images or 3D-densities of the
> same object. For more details, see the 2017 bioRxiv paper and references
> therein (https://www.biorxiv.org/content/10.1101/224402v1) and check my
> #WhyOWhy tweets (@marin_van_heel). See also: van Heel - Unveiling ribosomal
> structures: the final phases - Current opinion in structural biology 10
> (2000) 259-264.
> 
> Cheers,
> Marin
> 
> On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene <tim.gruene at univie.ac.at> wrote:
> > Dear Marin,
> > 
> > I did not read the enire thread, nor the manuscript you point at -
> > apologize
> > in case this has been discussed before.
> > 
> > What about a practical approach to determine the resolution of a cryoEM
> > map:
> > one could take a feature with scales of interest, e.g. an alpha-helix, and
> > shift and/or rotate it in steps of, say, 0.3A in several directions to
> > see, at
> > which magnitude (degree / distance) refinement does not take the helix
> > back to
> > its original position (within error margins).
> > 
> > One could also take a Monte-Carlo approach and do an arbitrary number of
> > random re-orientations of such a helix, refine, and calculate the
> > variation in
> > position and rotation.
> > 
> > This would reflect my understanding of resolution, much more than any
> > statistical descriptor.
> > 
> > Best regards,
> > Tim
> > 
> > On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:
> > > Hi Laurence,
> > > 
> > > One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc
> > > are
> > > also based on the same SLOPPY STATISTICS  as are all  fixed-valued  FSC
> > > thresholds. This controversy has been ragings for a long long time and
> > 
> > the
> > 
> > > errors made were extensively described (again) in our most recent paper
> > > (Van Heel & Schatz 2017 BioRxiv:
> > > https://www.biorxiv.org/content/10.1101/224402v1) which has been
> > 
> > downloaded
> > 
> > > more than 3000 times. Further papers on the issue are in the pipeline.
> > 
> > The
> > 
> > > math BLUNDER behind this controversy is simple:  the inner product
> > 
> > between
> > 
> > > a signal vector and a noise vector is NOT zero (but rather proportional
> > 
> > to
> > 
> > > SQRT(N) where N is the length of the vectors) and cannot be left out of
> > 
> > the
> > 
> > > equations. This error goes back to a paper published in Nature in 1975
> > 
> > and
> > 
> > > has since been repeated frequently, including in the first paper
> > 
> > promoting
> > 
> > > the erroneous 0.143 FSC threshold. The consequences of this blunder in
> > > current processing are serious especially when these erroneous metrics
> > 
> > are
> > 
> > > used as an optimisation criterion in iterative refinements at
> > > resolutions
> > > close to Nyquist.  I get tired of facing this systematic misuse of the
> > 
> > FSC
> > 
> > > function, which I myself have introduced into the literature in
> > 
> > 1982/1986,
> > 
> > > and people nevertheless feel they know better (with no scientific
> > 
> > arguments
> > 
> > > to support!) and they feel justified to use it beyond its definition
> > 
> > range,
> > 
> > > and to continue to ignore the correct math. To counter this systematic
> > > abuse of my brain child - over decades - I feel the need to use CLEAR
> > > LANGUAGE!
> > > Have fun!
> > > Marin
> > 
> > --
> > --
> > Tim Gruene
> > Head of the Centre for X-ray Structure Analysis
> > Faculty of Chemistry
> > University of Vienna
> > 
> > Phone: +43-1-4277-70202
> > 
> > GPG Key ID = A46BEE1A

-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A
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