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<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Dear Colin<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Great that you mention the Rose equation and
its consequences for cryo-EM! I have actually written a paper on that topic some
40 years ago [Marin van Heel: Detection of object in quantum-noise limited images.
Ultramicroscopy 8 (1982) 331-342]. <span> </span>I honestly
have not thought about it for a long time but I have recently been thinking
about revisiting the topic. It remains one of the very first particle-picking papers
ever, and certainly still one of the very best (and reference free) ones [Afanasyev
2017].<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">I remember I was very pleased when I realised one
could calculate local variances rapidly using fast convolutions! I remember the
very moment in December 1979, while visiting my parents in their house in Spain
and catching a bit of winter sunshine, leaning against the wall of their house
with my eyes half closed, that the “Aha-Erlebnis” struck.<span> </span>Thank you for reminding me to go back to that
issue! <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Cheers<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Marin<span></span></p>
<span></span>
</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Feb 17, 2020 at 2:36 PM <a href="mailto:colin.nave@diamond.ac.uk">colin.nave@diamond.ac.uk</a> <<a href="mailto:colin.nave@diamond.ac.uk">colin.nave@diamond.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:black">Dear Marin<u></u><u></u></span></p>
<p class="gmail-m_5024405669271467559IUCrreferences" style="line-height:normal"><span style="font-family:"Calibri",sans-serif;color:black">For electron microscopy, the Rose criterion (a measure of contrast/noise) is sometime used to distinguish low contrast features within polymers (see
for example <span style="background:white none repeat scroll 0% 0%">Libera, M. & Egerton, R. (2010). <i>Polymer Reviews</i>.
<b>50</b>, 321-339.). A particular value of the Rose criterion implies a particular information content.
<u></u><u></u></span></span></p>
<p class="gmail-m_5024405669271467559IUCrreferences" style="line-height:normal"><span style="font-family:"Calibri",sans-serif;color:black;background:white none repeat scroll 0% 0%">I think this can be directly related to a particular threshold for FSC or FRC. If you can comment on this in your
</span><i><span style="font-family:"Calibri",sans-serif;font-style:normal">Why-o-Why didactical crusade, I might even register for a twitter account!</span></i><i><span style="font-style:normal"><u></u><u></u></span></i></p>
<p class="gmail-m_5024405669271467559IUCrreferences" style="line-height:normal"><i><span style="font-family:"Calibri",sans-serif;font-style:normal">Regards<u></u><u></u></span></i></p>
<p class="gmail-m_5024405669271467559IUCrreferences" style="line-height:normal"><i><span style="font-family:"Calibri",sans-serif;font-style:normal">Colin</span></i><span style="color:rgb(31,73,125)"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri",sans-serif;color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11pt;font-family:"Calibri",sans-serif" lang="EN-US">From:</span></b><span style="font-size:11pt;font-family:"Calibri",sans-serif" lang="EN-US"> CCP4 bulletin board <<a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a>>
<b>On Behalf Of </b>Marin van Heel<br>
<b>Sent:</b> 17 February 2020 13:29<br>
<b>To:</b> <a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a><br>
<b>Subject:</b> Re: [ccp4bb] [3dem] Which resolution?<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Resolution in the sense of the Abbe <span class="gmail-m_5024405669271467559gmail-st">Diffraction Limit or the Rayleigh
</span><i><span style="font-style:normal">Criterion are part of what we would now call the theory of linear systems, and are described by a “transfer function”. “Fourier Optics” covers the theory of linear systems in Optics. These two (essentially identical)
resolution criteria state that the smallest details (let us call that “A(r)” for “Airy”) you can possible observe in real-space is inversely proportional to the size of the maximum aperture in Fourier space, i.e., the extent of the transfer function in Fourier
space “T(f)”. This defines what “Instrumental Resolution” one could possibly achieve in an experiment, “instrumental” to differentiate it from the “Results Resolution” you actually managed achieve in your data collection/processing experiment [#Why-o-Why #10].
What a linear imaging system will do the image of the object (under the best of circumstances) is described by a (Fourier-space) multiplication of the Fourier transform of the object O(r) [= O(f)] with the (Fourier-space) transfer function T(f) of the instrument,
yielding O’(f), which you need to transfer back to real space to obtain the exit wave in the image plane; that is: {O’(f)=T(f)·O(f)}.
</span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal"> </span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal">Note, however, that the properties of the sample, that is, of O(r), does nowhere appear in the transfer function T(f) or in its real-space version A(r)! The very concept of (instrumental) resolution
is exactly that it does NOT depend on the object O(r)! The “results resolution” [#Why-o-Why #10], on the other hand, obviously depends on the sample; the illumination; on the radiation dose; the pH of the solvent; the air humidity; and the mood of the person
doing the work on the day of preparation… </span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal"> </span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal">The FRC/FSC “results resolution” measures we introduced in 1982/1986, fit perfectly in the abstract framework of linear systems and Fourier optics. The X-ray metrics like R-factor and phase-residuals
and FOMs do NOT fit into that clean mathematical framework. Unfortunately, my EM colleagues started using X-ray metrics like “Differential Phase Residual” and “FOMs” in EM based on some gut feeling that the X-ray scientists know it better because they achieve
a higher resolution than us EM blobologists. How wrong my EM colleagues were: the quality of the resolution metric is totally unrelated to the numerical resolution levels we operate at! Seeing 3mm kidney stones in a patient’s tomogram can be equally important
as seeing </span></i>some hydrogen bond length in a cryo-EM density. The FRC/FSC actually make more sense than the indirect and hybrid X-ray ones. <i><span style="font-style:normal">This misconception has introduced a very tainted – and still ongoing –
discussion in cryo-EM. Now that the fields of X-ray crystallography and cryo-EM are merging it is time to get things right!
</span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal"> </span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal">I guess I cannot yet terminate my #Why-o-Why didactical crusade: I will need at least one more on just this linear-transfer theory issue alone…</span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal"> </span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal">Marin van Heel, CNPEM/LNNano, Campinas, Brazil </span></i><u></u><u></u></p>
<p class="MsoNormal"><i><span style="font-style:normal"> </span></i><u></u><u></u></p>
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<p class="MsoNormal">On Sun, Feb 16, 2020 at 6:51 PM Petrus Zwart <<a href="mailto:phzwart@lbl.gov" target="_blank">phzwart@lbl.gov</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi All,<u></u><u></u></p>
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<p class="MsoNormal">How is the 'correct' resolution estimation related to the estimated error on some observed hydrogen bond length of interest, or an error on the estimated occupancy of a ligand or conformation or anything else that has structural significance?<u></u><u></u></p>
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<p class="MsoNormal">In crystallography, it isn't really (only in some very approximate fashion), and I doubt that in EM there is something to that effect. If you want to use the resolution to get a gut feeling on how your maps look and how your data behaves,
it doesn't really matter what standard you use, as long as you are consistent in the use of the metric you use. If you want to use this estimate to get to uncertainties of model parameters, you better try something else.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Regards<u></u><u></u></p>
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<p class="MsoNormal">Peter Zwart<u></u><u></u></p>
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<p class="MsoNormal">On Sun, Feb 16, 2020 at 8:38 AM Marin van Heel <<a href="mailto:0000057a89ab08a1-dmarc-request@jiscmail.ac.uk" target="_blank">0000057a89ab08a1-dmarc-request@jiscmail.ac.uk</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Dear Pawel and All others .... <u></u><u></u></p>
<p class="MsoNormal" style="margin-bottom:8pt;line-height:105%">This 2010 review is - unfortunately - largely based on the flawed statistics I mentioned before, namely on the a priori assumption that the inner product of a signal vector and a noise vector
are ZERO (an orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted on a number of occasions (for example in 2005, and most recently in our BioRxiv paper) but you still take that as the correct relation between SNR and FRC (and you never
cite the criticism...). <u></u><u></u></p>
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<p class="MsoNormal">Sorry<u></u><u></u></p>
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<p class="MsoNormal">Marin<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A <<a href="mailto:Pawel.A.Penczek@uth.tmc.edu" target="_blank">Pawel.A.Penczek@uth.tmc.edu</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif"></span>Dear Teige,
<u></u><u></u></p>
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<p class="MsoNormal">I am wondering whether you are familiar with<u></u><u></u></p>
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<span style="font-size:15pt;font-family:"Helvetica",sans-serif"><u></u> <u></u></span></h2>
<h2 style="margin-right:0cm;margin-bottom:6pt;margin-left:0cm;line-height:18pt;box-sizing:border-box">
<span style="font-size:15pt;font-family:"Helvetica",sans-serif">Resolution measures in molecular electron microscopy.<u></u><u></u></span></h2>
<div id="gmail-m_5024405669271467559gmail-m_-3796767887894287704gmail-m_8609787314343393747gmail-m_-8079088879635535655gmail-m_4473107327319981263gmail-m_-4642610284911275282cit_summary">
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:rgb(39,39,39)">Penczek PA. Methods Enzymol. 2010.<u></u><u></u></span></p>
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<div id="gmail-m_5024405669271467559gmail-m_-3796767887894287704gmail-m_8609787314343393747gmail-m_-8079088879635535655gmail-m_4473107327319981263gmail-m_-4642610284911275282cit_full">
<h3 style="margin-bottom:0.0001pt"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:black">Citation<u></u><u></u></span></h3>
<p style="margin-right:0cm;margin-bottom:1.5pt;margin-left:0cm;box-sizing:border-box">
<span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:rgb(39,39,39)">Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8.<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">You will find there answers to all questions you asked and much more. <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Regards, <u></u><u></u></p>
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<p class="MsoNormal">Pawel Penczek<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><u></u> <u></u></p>
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<p class="MsoNormal">Regards, <u></u><u></u></p>
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<p class="MsoNormal">Pawel<u></u><u></u></p>
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<p class="MsoNormal">_______________________________________________<br>
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<p class="MsoNormal">-- <u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:10pt">------------------------------------------------------------------------</span><br>
<span style="font-size:7.5pt">P.H. Zwart<br>
Staff Scientist</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:7.5pt">Molecular Biophysics and Integrated Bioimaging &</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:7.5pt">Center for Advanced Mathematics for Energy Research Applications</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:7.5pt">Lawrence Berkeley National Laboratories<br>
1 Cyclotron Road, Berkeley, CA-94703, USA<br>
Cell: 510 289 9246</span><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><span style="font-size:7.5pt">PHENIX: <a href="http://www.phenix-online.org/" target="_blank"><span style="color:rgb(17,85,204)">http://www.phenix-online.org</span></a></span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:7.5pt">CAMERA: <a href="http://camera.lbl.gov/" target="_blank">http://camera.lbl.gov/</a></span><u></u><u></u></p>
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