Interesting conversation! I see the 2017 paper is on bioRxiv. I wonder if it ever made into a peer reviewed journal (couldn't find quickly)? @Tim Gruene <tim.gru...@psi.ch> : have a look at d_model in https://www.ncbi.nlm.nih.gov/pubmed/30198894 which is sort of along similar lines of what you are hinting here. Pavel
On Wed, Feb 12, 2020 at 3:07 PM Marin van Heel < 0000057a89ab08a1-dmarc-requ...@jiscmail.ac.uk> 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.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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
