<div dir="ltr">Marin,<div>What everyone wants is an Abbe criterion - when can I tell one point scattering center from two? FSC curves are very useful, but none of the measures of "resolution" derived from FSC curves are equivalent to the Abbe criterion.</div><div><br></div><div>To my knowledge, the closest thing is the Qscore measurement (made at each atom in a model) in recent versions of Phenix. Unfortunately it is still not straightforward to calibrate the scores to absolute units of distance; they are pure numbers. I suspect that arguments about resolution, and how it's measured, will continue in cryo-EM until a convincing method for determining something like an Abbe criterion is proposed.</div><div><br></div><div>Best,</div><div>-da</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 12, 2020 at 3:07 PM Marin van Heel <<a href="mailto:marin.vanheel@googlemail.com">marin.vanheel@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi Tim,</div><div>Good to hear from you! No longer at PSI??</div><div></div><div>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 (<a href="https://www.biorxiv.org/content/10.1101/224402v1" target="_blank">https://www.biorxiv.org/content/10.1101/224402v1</a>) and check my #WhyOWhy tweets (@marin_van_heel). See also: <span style="font-size:10pt;line-height:115%">van
Heel - Unveiling ribosomal structures: the final phases - Current opinion in
structural biology 10 (2000) 259-264.<span></span></span>
</div><div><br></div><div>Cheers,</div><div>Marin<br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 12, 2020 at 11:22 AM Tim Gruene <<a href="mailto:tim.gruene@univie.ac.at" target="_blank">tim.gruene@univie.ac.at</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Marin,<br>
<br>
I did not read the enire thread, nor the manuscript you point at - apologize <br>
in case this has been discussed before.<br>
<br>
What about a practical approach to determine the resolution of a cryoEM map: <br>
one could take a feature with scales of interest, e.g. an alpha-helix, and <br>
shift and/or rotate it in steps of, say, 0.3A in several directions to see, at <br>
which magnitude (degree / distance) refinement does not take the helix back to <br>
its original position (within error margins).<br>
<br>
One could also take a Monte-Carlo approach and do an arbitrary number of <br>
random re-orientations of such a helix, refine, and calculate the variation in <br>
position and rotation.<br>
<br>
This would reflect my understanding of resolution, much more than any <br>
statistical descriptor.<br>
<br>
Best regards,<br>
Tim<br>
<br>
On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:<br>
> Hi Laurence,<br>
> <br>
> One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc are<br>
> also based on the same SLOPPY STATISTICS as are all fixed-valued FSC<br>
> thresholds. This controversy has been ragings for a long long time and the<br>
> errors made were extensively described (again) in our most recent paper<br>
> (Van Heel & Schatz 2017 BioRxiv:<br>
> <a href="https://www.biorxiv.org/content/10.1101/224402v1" rel="noreferrer" target="_blank">https://www.biorxiv.org/content/10.1101/224402v1</a>) which has been downloaded<br>
> more than 3000 times. Further papers on the issue are in the pipeline. The<br>
> math BLUNDER behind this controversy is simple: the inner product between<br>
> a signal vector and a noise vector is NOT zero (but rather proportional to<br>
> SQRT(N) where N is the length of the vectors) and cannot be left out of the<br>
> equations. This error goes back to a paper published in Nature in 1975 and<br>
> has since been repeated frequently, including in the first paper promoting<br>
> the erroneous 0.143 FSC threshold. The consequences of this blunder in<br>
> current processing are serious especially when these erroneous metrics are<br>
> used as an optimisation criterion in iterative refinements at resolutions<br>
> close to Nyquist. I get tired of facing this systematic misuse of the FSC<br>
> function, which I myself have introduced into the literature in 1982/1986,<br>
> and people nevertheless feel they know better (with no scientific arguments<br>
> to support!) and they feel justified to use it beyond its definition range,<br>
> and to continue to ignore the correct math. To counter this systematic<br>
> abuse of my brain child - over decades - I feel the need to use CLEAR<br>
> LANGUAGE!<br>
> Have fun!<br>
> Marin<br>
<br>
-- <br>
--<br>
Tim Gruene<br>
Head of the Centre for X-ray Structure Analysis<br>
Faculty of Chemistry<br>
University of Vienna<br>
<br>
Phone: +43-1-4277-70202<br>
<br>
GPG Key ID = A46BEE1A<br>
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