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.gru...@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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
