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Hi Tim,</div>
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We have done something like what you describe with Z-scores:</div>
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<a href="https://www.ncbi.nlm.nih.gov/pubmed/30144506" style="margin: 0px">https://www.ncbi.nlm.nih.gov/pubmed/30144506</a><br>
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and now Q-scores which look at each atom:</div>
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<a title="https://rdcu.be/b1tNg" href="https://t.co/C9rchvTT6Z?amp=1" target="_blank" dir="ltr" rel=" noopener noreferrer" style="margin: 0px; border: 0px solid black; font-size: 15px; line-height: 1.3125; font-family: system-ui, -apple-system, system-ui, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; background-color: rgb(245, 248, 250); color: rgb(27, 149, 224); list-style: none; cursor: pointer; box-sizing: border-box; display: inline; overflow-wrap: break-word; min-width: 0px; outline: none"><span style="margin: 0px; border: 0px solid black; font-size: 0px; font-family: system-ui, -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, "Helvetica Neue", sans-serif; box-sizing: border-box; overflow-wrap: break-word; min-width: 0px">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</span></a><a href="https://www.nature.com/articles/s41592-020-0731-1" style="margin: 0px">https://www.nature.com/articles/s41592-020-0731-1</a><br>
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<span style="margin: 0px">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. </span><br>
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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.</div>
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Regards,</div>
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Greg</div>
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PS. free full text preview link for the above: <span style="margin: 0px"><a href="https://rdcu.be/b1tNg" style="margin: 0px">https://rdcu.be/b1tNg</a><br>
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<span style="margin: 0px">and bioRxiv version: </span><a href="https://www.biorxiv.org/content/10.1101/722991v2" style="margin: 0px">https://www.biorxiv.org/content/10.1101/722991v2</a><span style="margin: 0px"><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Tim Gruene <tim.gruene@univie.ac.at><br>
<b>Sent:</b> Wednesday, February 12, 2020 9:22 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Cc:</b> Marin van Heel <marin.vanheel@googlemail.com>; CCPEM@jiscmail.ac.uk <CCPEM@jiscmail.ac.uk>; Laurence Pearl <Laurence.Pearl@sussex.ac.uk><br>
<b>Subject:</b> Re: [3dem] [ccpem] Which resolution?</font>
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<div class="PlainText">Dear Marin,<br>
<br>
I did not read the enire thread, nor the manuscript you point at - apologize <br>
in case this has been discussed before.<br>
<br>
What about a practical approach to determine the resolution of a cryoEM map: <br>
one could take a feature with scales of interest, e.g. an alpha-helix, and <br>
shift and/or rotate it in steps of, say, 0.3A in several directions to see, at <br>
which magnitude (degree / distance) refinement does not take the helix back to <br>
its original position (within error margins).<br>
<br>
One could also take a Monte-Carlo approach and do an arbitrary number of <br>
random re-orientations of such a helix, refine, and calculate the variation in <br>
position and rotation.<br>
<br>
This would reflect my understanding of resolution, much more than any <br>
statistical descriptor.<br>
<br>
Best regards,<br>
Tim<br>
<br>
On Wednesday, February 12, 2020 1:46:48 PM CET Marin van Heel wrote:<br>
> Hi Laurence,<br>
> <br>
> One thing is certain: the 0.143 threshold is RUBBISH and all CC50 etc are<br>
> also based on the same SLOPPY STATISTICS as are all fixed-valued FSC<br>
> thresholds. This controversy has been ragings for a long long time and the<br>
> errors made were extensively described (again) in our most recent paper<br>
> (Van Heel & Schatz 2017 BioRxiv:<br>
> <a href="https://www.biorxiv.org/content/10.1101/224402v1">https://www.biorxiv.org/content/10.1101/224402v1</a>) which has been downloaded<br>
> more than 3000 times. Further papers on the issue are in the pipeline. The<br>
> math BLUNDER behind this controversy is simple: the inner product between<br>
> a signal vector and a noise vector is NOT zero (but rather proportional to<br>
> SQRT(N) where N is the length of the vectors) and cannot be left out of the<br>
> equations. This error goes back to a paper published in Nature in 1975 and<br>
> has since been repeated frequently, including in the first paper promoting<br>
> the erroneous 0.143 FSC threshold. The consequences of this blunder in<br>
> current processing are serious especially when these erroneous metrics are<br>
> used as an optimisation criterion in iterative refinements at resolutions<br>
> close to Nyquist. I get tired of facing this systematic misuse of the FSC<br>
> function, which I myself have introduced into the literature in 1982/1986,<br>
> and people nevertheless feel they know better (with no scientific arguments<br>
> to support!) and they feel justified to use it beyond its definition range,<br>
> and to continue to ignore the correct math. To counter this systematic<br>
> abuse of my brain child - over decades - I feel the need to use CLEAR<br>
> LANGUAGE!<br>
> Have fun!<br>
> Marin<br>
<br>
-- <br>
--<br>
Tim Gruene<br>
Head of the Centre for X-ray Structure Analysis<br>
Faculty of Chemistry<br>
University of Vienna<br>
<br>
Phone: +43-1-4277-70202<br>
<br>
GPG Key ID = A46BEE1A<br>
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