[3dem] [ccpem] Which resolution?

[Tim Gruene]

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

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