Dear Marius Schmidt In my (our) *original FRC/FSC papers* (1982; 1986 ; 2000; 2004; 2017; 2020; 2024) the linearity of these correlation functions/metrics have been extensively discussed. Historically, EM started at a low resolution "blobology" level whereas X-ray crystallography (XRC) at that time, already had reached atomic resolution. This led to the belief that the *XRC resolution metrics* ( like phase residuals and R-factors) were also appropriate as *resolution metrics for EM*. However, in XRC the measurables are *diffraction patterns* for which *amplitudes *corresponding *phases *had to be derived *iteratively*. In EM and in imagining in general, the measurables are the images themselves, that contain both the *amplitude information *and the *phase information*. To revert to the then already established *XRC resolution metrics* like phase residuals or R-factors, implied *discarding *the most important part of the available information (see the Why-O-Why ). ( https://www.linkedin.com/posts/marin-van-heel-5845b422b_whyowhyarchive-activity-7149738255154946048-Oc93/?utm_source=share&utm_medium=member_desktop ). That problem was realized soon and the mentioned *FRC and FSC metrics* were thus suggested which exploit all the available information. Thus, the *XRC atomic resolution* *technique *of the 1980s came with a *low-quality resolution metric* whereas the *Cryo-EM low-resolution blobology *approach of the 1980s came with a *high-quality resolution metric*. Thus, in summary, *all resolution criteria in XRC* are *ad-hoc non-linear metrics* that have no general validity outside of *XRC*. Looking at only the amplitudes of a diffraction pattern is like finding the highest resolution spot in a diffraction pattern, where, even if the spot is clearly visible, that does not mean one would be able to find its phase. We need a more comprehensive metric that has a wide range of applicability. In other words, where a CC1-2 metric cannot be applied to assess the 3D brain scan of a brain-tumor patient, the FRC / FSC, and the newest FRI / FSI metrics can be applied in all cases where 2D and 3D data are dealt with!
Hope this helps, Marin van Heel On Mon, Oct 7, 2024 at 3:04 PM Marius Schmidt <smar...@uwm.edu> wrote: > I think this is taken care of: > The CC1/2 and the CC1/2* are appropriate metrics for the resolution limit. > They are all spit out by newer data processing software. > The CC1/2 is directly comparable to the FSC. Many people use CC1/2 = 1/e as > the resolution limit. > In many cases of data the CC1/2 = 1/e is equivalent to I/sigI of 1, which > is used sometimes as a metric for the resolution limit (some use I/sigI = > 2), > and in more cases the CC1/2 corresponds to Rmerge in the range of 40%. > For serial crystallography, the R-split goes through the roof at CC1/2 = > 1/e, > so the CC1/2 is the better metric. > > Best > Marius > > > > > > Marius Schmidt, Dr. rer. Nat. (habil.) > Professor > University of Wisconsin-Milwaukee > Kenwood Interdisciplinary Research Complex > Physics Department, Room 3087 > 3135 North Maryland Avenue > Milwaukee, Wi 53211 > phone (office): 1-414-229-4338 > phone (lab): 414-229-3946 > email: smar...@uwm.edu > https://uwm.edu/physics/people/schmidt-marius/ > https://sites.uwm.edu/smarius/ > https://www.bioxfel.org/ > Nature News and Views: https://www.nature.com/articles/d41586-023-00504-4 > > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Marin > van Heel <marin.vanh...@gmail.com> > *Sent:* Monday, October 7, 2024 11:24 AM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* [ccp4bb] Review: Linearity and Resolution in X-Ray > Crystallography and Electron Microscopy > > > Dear All, > > Sayan Bhakta and I have recently posted the preprint of a review on > resolution and linearity which will appear in a book to be launched on the > 16th of October 2024. > ( https://doi.org/10.1201/9781003326106 ). > It is the first Cryo-EM review that I have been involved in for 25 years. > In our preparation, I was quite amazed about what other authors wrote (or > did not write) in their many reviews on these matters. > For example, I missed any serious discussion about resolution metrics in > X-ray crystallography, which technique is fundamentally non-linear. > Linearity is a prerequisite for defining the resolution of any instrument. > The iterative refinements applied in X-ray crystallography (and sometimes > Cryo-EM) makes that all Phase-residuals and R-factors or fixed threshold > values cannot be used to compare the results of independently conducted > experiments. What is an obvious consequence of the lack of universality of > such metrics like phase-residuals and R-factors, is that they cannot be > used outside of the immediate context in which they were defined, like > X-ray crystallography or structural biology. In contrast, the > Fourier-Ring-Correlation (FRC); Fourier-Shell-Correlation (FSC) and their > recent successors: the Fourier-Ring-Information (FRI) and the > Fourier-Shell-Information (FSI), plus their integrated versions, are > universal metrics that are applicable to all fields of science where 2D and > 3D data are dealt with! > > https://doi.org/10.31219/osf.io/5empt > > Have fun reading it! > > Marin > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
