<div dir="ltr">
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Hi Jose-Maria,<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">I appreciate that you consider all our
contributions to be important (“Ed, Paul and Marin papers are very important”) and
that people need to “reconnect” to the resolution issue since that remains so
very important! I couldn’t agree more! <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">But then you go on to suggest that everyone who
does “feel like not sleeping at all today” read your 2017 review. The review you
are promoting, is the one we had refuted in our BioRxiv paper (see below), with
very serious criticism, which you never bothered to respond.<span> </span>I feel compelled to repeat what I have said
in my earlier reaction to Pawel’s response, above. <span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">“What I am criticising is the very foundation
you use to construct your science, namely the flawed Frank & Al-Ali (1975)
formula relating SNR and CCC! Agreed, their errors are not of your making and
not your responsibility! It is, however, your choice and your judgement
to build upon that flawed foundation. At the end of the day, your
construct, even when based on shaky foundations created by others, will remain
your responsibility!”<span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Sorry,<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>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">Our criticism (<a href="https://www.biorxiv.org/content/10.1101/224402v1">https://www.biorxiv.org/content/10.1101/224402v1</a>)
was:</p><div><img src="cid:ii_k6vc1hc10" alt="image.png" width="474" height="423"><br><br></div><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif"><br><span></span></p>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Feb 16, 2020 at 4:08 PM Jose Maria Carazo <<a href="mailto:carazo@cnb.csic.es">carazo@cnb.csic.es</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"><div dir="ltr">Dear Marin and colleagues,<div><br></div><div>As Ed, I have tried to stay away from these interchanges about resolution, simply because they go forever and I think that most people either get fed up, drop the attention, or -and this is the danger- end up thinking that we do not know what we are doing.</div><div><br></div><div>For all of you that have already "disconnected", please "reconnet", because it is an important topic, but think about it in the context of "validation" / "quality assessment". At the end of the day what we want to know is whether there are problems with a map and how much one can trust a structural model derived from it. Consider that if we know already that something is a simplification of what we really want to do, to keep going over it yet another time may not add too much to the discussion (perhaps this applies to the whole point on the FSC)</div><div> </div><div>Ed, Paul and Marin papers are very important because we must have sound theoretical and statistical bases..... but do not forget to contextualize the whole topic around "validation".</div><div> </div><div>If you want to have another quite deep view on the statistics of many things we do, Carlos and me we did a review a few years ago (as Ed said in his email, 2017 may be considered already "dated" in this fast evolving field). Still, it gives you an idea that statistics has been worked out a lot, that we know that a number of "common approaches " have intrinsic limitations, and that it is precisely because of that that we keep working on validation</div><div><br></div><div>If you feel like not sleeping at all today, another paper to add to your list could be:</div><div> </div><div><p style="margin:0px;font-size:1.108em;color:rgb(0,0,0);font-family:arial,helvetica,clean,sans-serif"><a href="https://www.ncbi.nlm.nih.gov/pubmed/27666962" style="color:rgb(100,42,143)" target="_blank">A review of resolution measures and related aspects in 3D Electron Microscopy.</a></p><div style="margin:0.1425em 0px;color:rgb(0,0,0);font-family:arial,helvetica,clean,sans-serif;font-size:13px"><p style="margin:0px;font-size:1.077em"><b>Sorzano</b> CO, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, <b>Carazo JM</b>.</p><p style="margin:0px;font-size:0.923em"><span title="Progress in biophysics and molecular biology">Prog Biophys Mol Biol</span>. 2017 Mar;124:1-30. doi: 10.1016/j.pbiomolbio.2016.09.005. </p></div></div><div><br></div><div>..... but may be you have already had your share of discussion about "resolution measures" ...</div><div><br></div><div>With best regards...JM</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Feb 16, 2020 at 5:59 PM Penczek, Pawel A <<a href="mailto:Pawel.A.Penczek@uth.tmc.edu" target="_blank">Pawel.A.Penczek@uth.tmc.edu</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">
<div dir="auto">
Marin,
<div><br>
</div>
<div>The statistics in 2010 review is fine. You may disagree with assumptions, but I can assure you the “statistics” (as you call it) is fine. Careful reading of the paper would reveal to you this much. <br>
<br>
<div dir="ltr">Regards,
<div>Pawel</div>
</div>
<div dir="ltr"><br>
<blockquote type="cite">On Feb 16, 2020, at 10:38 AM, Marin van Heel <<a href="mailto:marin.vanheel@googlemail.com" target="_blank">marin.vanheel@googlemail.com</a>> wrote:<br>
<br>
</blockquote>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>
<p><font size="3" face="arial, sans-serif" color="Red"><strong>**** EXTERNAL EMAIL ****</strong></font></p>
</div>
<div dir="ltr">
<div>Dear Pawel and All others ....
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">
</p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:12pt;font-family:"Times New Roman",serif">
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...).
<span></span></p>
<span></span></div>
<div></div>
<div></div>
<div></div>
<div>Sorry</div>
<div>Marin<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">
<div dir="ltr">Dear Teige,
<div><br>
</div>
<div>I am wondering whether you are familiar with</div>
<div>
<h2 style="box-sizing:border-box;font-family:"Lucida Grande","Helvetica Neue",Helvetica,Arial;font-size:20px;margin:8px auto;line-height:24px">
<br>
</h2>
<h2 style="box-sizing:border-box;font-family:"Lucida Grande","Helvetica Neue",Helvetica,Arial;font-size:20px;margin:8px auto;line-height:24px">
Resolution measures in molecular electron microscopy.</h2>
<div id="gmail-m_485648542627986468gmail-m_9159147229686973669gmail-m_4473107327319981263gmail-m_-4642610284911275282cit_summary" style="box-sizing:border-box;font-size:14px;color:rgb(39,39,39);font-family:Arial">
<div style="box-sizing:border-box">Penczek PA. Methods Enzymol. 2010.</div>
</div>
<div id="gmail-m_485648542627986468gmail-m_9159147229686973669gmail-m_4473107327319981263gmail-m_-4642610284911275282cit_full" style="box-sizing:border-box;font-size:14px;color:rgb(39,39,39);font-family:Arial">
<h3 style="box-sizing:border-box;font-family:"Lucida Grande","Helvetica Neue",Helvetica,Arial;color:rgb(0,0,0);margin-bottom:0px;font-size:14px">
Citation</h3>
<p style="box-sizing:border-box;margin:2px 0px">Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8.</p>
</div>
<div><br>
</div>
<div>You will find there answers to all questions you asked and much more. </div>
<br>
<div dir="ltr">Regards,
<div>Pawel Penczek</div>
</div>
</div>
</div>
<br>
<br>
<div dir="ltr">Regards,
<div>Pawel</div>
</div>
</div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div>Prof. Jose-Maria Carazo<br>Biocomputing Unit, Head, CNB-CSIC<br>Spanish National Center for Biotechnology</div><div>Darwin 3, Universidad Autonoma de Madrid</div><div>28049 Madrid, Spain</div><div><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif"><br></p>Cell: +34639197980<br></div></div></div>
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