<div dir="ltr">
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif">Dear All,<span></span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif">To be honest, I already
expected that my message on <b><i>Linearity and Resolution</i></b> would not be
well understood by especially the younger generation of researchers in the X-ray
crystallography (<b><i>XRC</i></b>) community. I intend to make a special entry
in my <b><i>Why-o-Why</i></b> series (moved from Twitter to LinkedIn) to explain,
using simple visual examples, why XRC is <b>not a linear technique</b> and why
such criteria like <b>Abbe's resolution metric</b> for microscopes simply does
not apply to <b><i>XRC</i></b>. In <b><i>XRC</i></b> there is no such thing as an
“<b><i>instrumental resolution</i></b>” that applies to <b><i>any sample</i></b>
one mounts in the diffractometer. Therefore the “<b><i>results resolution</i></b>”
cannot be directly coupled to <b><i>measured data</i></b>.<span></span></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif">Much of what is covered
in our review ( <a href="https://urldefense.com/v3/__https://osf.io/preprints/osf/5empt__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67ZZPZow0w$" style="color:rgb(5,99,193);text-decoration:underline">https://osf.io/preprints/osf/5empt</a>
) was presented at a meeting in the “<b><i>Flat Iron Institute</i></b>” in New
York in 2019 but the lecture got a bit lost because of the Pandemic. It is 5
years old but little has changed and issues like “<b><i>instrumental resolution</i></b>”
and “<b><i>results resolution</i></b>” are covered extensively:<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-family:"Times New Roman",serif"><a href="https://urldefense.com/v3/__https://www.youtube.com/watch?v=ElWsgWfxp8I__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67aX55KhcQ$" style="color:rgb(5,99,193);text-decoration:underline">https://www.youtube.com/watch?v=ElWsgWfxp8I</a><span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-family:"Times New Roman",serif">Why-O-why link:<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-family:"Times New Roman",serif"><a href="https://urldefense.com/v3/__https://www.linkedin.com/posts/marin-van-heel-5845b422b_whyowhyarchive-activity-7149738255154946048-Oc93?utm_source=share&utm_medium=member_desktop__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67aG-3lCZg$" style="color:rgb(5,99,193);text-decoration:underline">https://www.linkedin.com/posts/marin-van-heel-5845b422b_whyowhyarchive-activity-7149738255154946048-Oc93?utm_source=share&utm_medium=member_desktop</a><span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif">Have fun, <span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif">Marin<span></span></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><b><span style="font-size:12pt;line-height:107%;font-family:"Times New Roman",serif">PS:<i> I had an excellent teacher in understanding
imaging</i>:</span></b></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><b><span style="font-size:12pt;line-height:107%;font-family:"Times New Roman",serif"><i>(Sir William Bragg's book from my dad’s library I still use for teaching
and is sometimes still available in second-hand sites)</i></span></b></p><img src="cid:ii_m29g8xk80" alt="image.png" width="495" height="378" style="margin-right: 0px;"><br><br><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"></p>
<p class="MsoNormal" align="center" style="text-align:center;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif"></span><span style="font-size:14pt;line-height:107%;font-family:"Times New Roman",serif"><span></span></span></p>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 7, 2024 at 8:02 PM Marin van Heel <<a href="mailto:marin.vanheel@gmail.com">marin.vanheel@gmail.com</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"><div dir="ltr">
<div>Dear Marius Schmidt<br>
</div>
<div><br>
</div>
<div>In my (our) <b><i>original FRC/FSC papers</i></b> (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 <b><i>XRC resolution metrics</i></b> (
like phase residuals and R-factors) were also appropriate as <b><i>resolution metrics for EM</i></b>. However, in XRC the measurables are <b><i>diffraction patterns</i></b> for which <i><b>amplitudes </b></i>corresponding <b><i>phases </i></b>had to be derived <b><i>iteratively</i></b>. In EM and in imagining in general, the measurables are the images themselves, that contain both the <b><i>amplitude
information
</i></b>and the <b><i>phase information</i></b>. To revert to the then already established
<b><i>XRC resolution metrics</i></b> like phase residuals or R-factors, implied <b><i>discarding </i></b>the most important part of the available information (see the Why-O-Why ). </div><div>(<a href="https://urldefense.com/v3/__https://www.linkedin.com/posts/marin-van-heel-5845b422b_whyowhyarchive-activity-7149738255154946048-Oc93/?utm_source=share&utm_medium=member_desktop__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67Zz9YEvEw$" target="_blank">https://www.linkedin.com/posts/marin-van-heel-5845b422b_whyowhyarchive-activity-7149738255154946048-Oc93/?utm_source=share&utm_medium=member_desktop</a>).</div><div>That problem was realized soon and the mentioned <b><i>FRC and FSC metrics</i></b> were thus suggested which exploit all the available information. Thus, the <b><i>XRC atomic resolution</i></b> <b><i>technique </i></b>of the 1980s came with a <b><i>low-quality resolution metric</i></b> whereas the <b><i>Cryo-EM low-resolution blobology </i></b>approach of the 1980s came with a <b><i>high-quality resolution metric</i></b>.</div><div>Thus, in summary, <b><i>all resolution criteria
in XRC</i></b> are <b><i>ad-hoc non-linear metrics</i></b> that have no general validity outside of <b><i>XRC</i></b>.
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 <br>
</div>
<div>
<span><span dir="ltr">where 2D and 3D data are dealt with!</span></span>
</div>
<div><br></div><div>Hope this helps, <br>
</div>
<div><br>
</div>
<div>Marin van Heel</div>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 7, 2024 at 3:04 PM Marius Schmidt <<a href="mailto:smarius@uwm.edu" target="_blank">smarius@uwm.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>
<div dir="ltr">
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I think this is taken care of:</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
The CC1/2 and the CC1/2* are appropriate metrics for the resolution limit.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
They are all spit out by newer data processing software.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
The CC1/2 is directly comparable to the FSC. Many people use CC1/2 = 1/e as</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
the resolution limit.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
In many cases of data the CC1/2 = 1/e is equivalent to I/sigI of 1, which</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
is used sometimes as a metric for the resolution limit (some use I/sigI = 2),</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
and in more cases the CC1/2 corresponds to Rmerge in the range of 40%.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
For serial crystallography, the R-split goes through the roof at CC1/2 = 1/e,</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
so the CC1/2 is the better metric.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Best</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Marius</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div id="m_2016212617228391247m_-4964509200517277593Signature">
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<br>
</div>
<div style="background-color:rgb(255,255,255);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div style="direction:ltr;margin:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">
<span style="color:rgb(0,0,0)">Marius Schmidt, Dr. rer. Nat. (habil.)<br>
Professor<br>
University of Wisconsin-Milwaukee<br>
Kenwood Interdisciplinary Research Complex<br>
Physics Department, Room 3087<br>
3135 North Maryland Avenue<br>
Milwaukee, Wi 53211<br>
phone (office): 1-414-229-4338<br>
phone (lab): 414-229-3946<br>
email: <a href="mailto:smarius@uwm.edu" target="_blank">smarius@uwm.edu</a><br>
<a href="https://urldefense.com/v3/__https://uwm.edu/physics/people/schmidt-marius/__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67bNpWhOEw$" target="_blank">https://uwm.edu/physics/people/schmidt-marius/</a><br>
<a href="https://urldefense.com/v3/__https://sites.uwm.edu/smarius/__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67ZOMxAY2Q$" target="_blank">https://sites.uwm.edu/smarius/</a><br>
</span><span style="color:rgb(0,111,201)"><a href="https://urldefense.com/v3/__https://www.bioxfel.org/__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67ZRzp61sQ$" style="color:rgb(0,111,201)" target="_blank">https://www.bioxfel.org/</a></span></div>
</div>
<div style="background-color:rgb(255,255,255);color:rgb(0,0,0)"><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt">Nature News and Views:
</span><span style="font-family:"Calibri",sans-serif;font-size:11pt"><a href="https://urldefense.com/v3/__https://www.nature.com/articles/d41586-023-00504-4__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67YIuM-jzg$" title="Original URL: https://www.nature.com/articles/d41586-023-00504-4. Click or tap if you trust this link." target="_blank">https://www.nature.com/articles/d41586-023-00504-4</a></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
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<div id="m_2016212617228391247m_-4964509200517277593appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="m_2016212617228391247m_-4964509200517277593divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> CCP4 bulletin board <<a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a>> on behalf of Marin van Heel <<a href="mailto:marin.vanheel@GMAIL.COM" target="_blank">marin.vanheel@GMAIL.COM</a>><br>
<b>Sent:</b> Monday, October 7, 2024 11:24 AM<br>
<b>To:</b> <a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a> <<a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a>><br>
<b>Subject:</b> [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div><br>
</div>
<div>Dear All,</div>
<div><br>
</div>
<div><span><span dir="ltr">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<span>
</span><span>2024. </span></span></span></div>
<div><span><span dir="ltr"><span>(</span></span></span>
<a href="https://urldefense.com/v3/__https://doi.org/10.1201/9781003326106__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67aqgSDLLw$" target="_blank">
https://doi.org/10.1201/9781003326106</a> <span>
<span dir="ltr"><span>)</span>.<span></span> </span></span></div>
<div><span><span dir="ltr">It is the first Cryo-EM review that I have been involved in for 25 years. </span></span></div>
<div><span><span dir="ltr">In our preparation, I was quite amazed about what other authors wrote (or did not write) in their many reviews on these matters.</span></span></div>
<div><span><span dir="ltr">For example, I missed any serious discussion about resolution metrics in X-ray crystallography, which technique is fundamentally non-linear. </span></span></div>
<div><span><span dir="ltr">Linearity is a prerequisite for defining the resolution of any instrument. The iterative refinements applied in X-ray crystallography (and sometimes Cryo-EM) makes that all
Phase-residuals and R-factors or fixed threshold values cannot be used to compare the results of independently conducted experiments. What is an obvious consequence of the lack of universality of such metrics like phase-residuals and R-factors, is that they
cannot be used outside of the immediate context in which they were defined, like X-ray crystallography or structural biology. In contrast, the Fourier-Ring-Correlation (FRC); Fourier-Shell-Correlation (FSC) and their recent successors: the Fourier-Ring-Information
(FRI) and the Fourier-Shell-Information (FSI), plus their integrated versions, are universal metrics that are applicable to all fields of science where 2D and 3D data are dealt with!<br>
</span></span></div>
<div><span><span dir="ltr"><br>
</span></span></div>
<div><a href="https://urldefense.com/v3/__https://doi.org/10.31219/osf.io/5empt__;!!Mih3wA!FVNU4WysI0Eg7Ul5pEBJ8Z92lOWymfr05kCOZkOrOAKkWmdr13GZ-lkp2RkBzGFal7c-nFviBe_ziO1L67Yy7wSwrA$" target="_blank">https://doi.org/10.31219/osf.io/5empt</a></div>
<div><br>
</div>
<div><span><span dir="ltr">Have fun reading it!<span><br>
</span><span><br>
</span>Marin<span> <br>
</span><span></span><br>
</span></span></div>
<div><br>
</div>
<div><br>
<br>
</div>
</div>
<br>
<hr>
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