[3dem] [ccpem] Which resolution?

[Pintilie, Greg]

Hi Tim,

We have done something like what you describe with Z-scores:
https://www.ncbi.nlm.nih.gov/pubmed/30144506

and now Q-scores which look at each atom:
https://http://em.rdcu.be/ls/click?upn=1VX9wGiUV7k-2FG8imEHteF4DkoRWJEqlBHutCP3gIiGI-3DeaVt_QxsRAMBCpXQk28bNMeZkwxn0MTz-2BYbTSOpGuDTqhH11Dwky7HCow3vVx2cxeQ1DYLL0wZNXzCJgP7Krk-2B5teet37Cd-2FVbS85rRO-2BJpHIu8Y8zK2C2YxDdH-2FEatpR6IPcjQ8GzK7VBgbQjqUB63D4-2Fu-2BhyaJMF1rIMokALnhN3NQMw0U3E-2FYwi3jPB8OPcQj8Fa5MIVznmvqkEDJRbMZ1KsRclA5mEXZMoFQPssFmJ1OJ-2BzqmUr6ELj8V5554mJonhn4pbFQb0og72UNmHVxdM-2F5IZ99w7dPBkwb1KawS2RHx1UfMZDT1nm46SLlwMn8Lhttps://rdcu.be/b1tNghttp://em.rdcu.be/ls/click?upn=1VX9wGiUV7k-2FG8imEHteF4DkoRWJEqlBHutCP3gIiGI-3DeaVt_QxsRAMBCpXQk28bNMeZkwxn0MTz-2BYbTSOpGuDTqhH11Dwky7HCow3vVx2cxeQ1DYLL0wZNXzCJgP7Krk-2B5teet37Cd-2FVbS85rRO-2BJpHIu8Y8zK2C2YxDdH-2FEatpR6IPcjQ8GzK7VBgbQjqUB63D4-2Fu-2BhyaJMF1rIMokALnhN3NQMw0U3E-2FYwi3jPB8OPcQj8Fa5MIVznmvqkEDJRbMZ1KsRclA5mEXZMoFQPssFmJ1OJ-2BzqmUr6ELj8V5554mJonhn4pbFQb0og72UNmHVxdM-2F5IZ99w7dPBkwb1KawS2RHx1UfMZDT1nm46SLlwMn8L<https://t.co/C9rchvTT6Z?amp=1>https://www.nature.com/articles/s41592-020-0731-1

These scores correlate very well to how well features are visually resolved and also the FSC-estimated resolution, though they do require that you have a properly-fitted /built model first.

It is an interesting idea to do it with refinement, but the test on whether it comes back to it's position may be complicated depending on how far you've moved it and if it clashed any other atoms close by.

Regards,

Greg

PS. free full text preview link for the above: https://rdcu.be/b1tNg
and bioRxiv version: https://www.biorxiv.org/content/10.1101/722991v2




________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Tim Gruene <tim.gruene at univie.ac.at>
Sent: Wednesday, February 12, 2020 9:22 AM
To: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Cc: Marin van Heel <marin.vanheel at googlemail.com>; CCPEM at jiscmail.ac.uk <CCPEM at jiscmail.ac.uk>; Laurence Pearl <Laurence.Pearl at sussex.ac.uk>
Subject: Re: [3dem] [ccpem] Which resolution?

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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