<div dir="ltr"><div>Dear
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Yuejiao Xian</span>
</div><div><br></div><div>I had a quick look at your data and I noticed that you have significant power anisotropy in your gold grating images. <br></div><div> It is a better idea in general to use the dataset itself rather than to get the anisotropy from a separate measurement! <br></div><div>Use the water-rings in the main eigenvectors of the amplitude spectra as per our paper. <br></div><div>(
<h3><a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Afanasyev,*20P.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkrPj9T7Aw$">Single-particle cryo-EM using alignment by classification (ABC): the structure of <span class="gmail-it"><i>Lumbricus terrestris</i></span> haemoglobin <br></a></h3><h3><a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Afanasyev,*20P.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkrPj9T7Aw$">P. Afanasyev</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Seer-Linnemayr,*20C.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkrQGJ5ULA$">C. Seer-Linnemayr</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Ravelli,*20R.B.G.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkr7a31vIg$">R. B. G. Ravelli</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Matadeen,*20R.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkrRgH4tSg$">R. Matadeen</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=De*20Carlo,*20S.__;JSU!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkohM39HwQ$">S. De Carlo</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Alewijnse,*20B.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkq6mlNsTQ$">B. Alewijnse</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Portugal,*20R.V.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkr0Qpwjtw$">R. V. Portugal</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Pannu,*20N.S.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkq5buCRyw$">N. S. Pannu</a>, <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Schatz,*20M.__;JQ!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkqYU9KTPQ$">M. Schatz</a> and <a href="https://urldefense.com/v3/__https://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=van*20Heel,*20M.__;JSU!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkrRHxmQFg$">M. van Heel</a></h3>
)<br></div><div><br></div><div>Cheers,</div><div>Marin<br></div><div><br></div><div><a href="https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html__;!!Mih3wA!TBMiKsb1NNawn9IDxSZR92a0zOZHKRiwZYQaariOIgLJ9V9oyGSldSAbzkoSJgSyZg$">https://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html</a></div><div><br></div><div><div><img src="cid:ii_kdukgx1l0" alt="image.png" width="494" height="244"><br><br></div></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 14, 2020 at 2:50 PM Xian, Yuejiao <<a href="mailto:yxian@miners.utep.edu">yxian@miners.utep.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="ltr">
<div>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Hello, all.</span></p>
<br>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">I am trying to estimate the anisotropic magnification distortion from a cryo-EM dataset, however, I am not sure if I got the accurate estimation. I appreciate any comments or suggestions.
Here is what I did: </span></p>
<br>
<p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><font style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:normal" face="Arial"><span style="font-size:11pt">I stacked about
70 gold grating images into one mrc file, which I used as the input of the mag_distortion_estimate program developed by Timothy Grant and Nikolaus Grigorieff. Here is the output parameter:</span></font></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">=====================================</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">The following distortion parameters were found :-</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:700">Distortion Angle = 112.6</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:700">Major Scale = 1.001</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:700">Minor Scale = 0.999</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> Stretch only parameters would be as follows :-</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Distortion Angle = 112.6</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Major Scale = 1.002</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Minor Scale = 1.000</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Corrected Pixel Size = 0.669</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">The Total Distortion = .15%</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">=========================================</span></p>
<font style="background-color:rgb(255,255,255)"><span style="margin:0px"><span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:11pt;font-weight:normal"> T</span><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="font-size:11pt">he
</span><span style="font-size:14.6667px">outputted</span><span style="font-size:11pt"> ring images are attached. The ring on the left is the combined ring before any distortion correction,</span></font><span style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:11pt;font-weight:normal"> </span><font style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:normal;background-color:rgb(255,255,255)" face="Arial"><span style="margin:0px;font-size:11pt">the
one in the middle is the<span style="margin:0px"> </span></span></font><font style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-weight:normal;background-color:rgb(255,255,255)" face="Arial" color="#000000"><span style="margin:0px;font-size:14.6667px">rotational</span></font><font style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:normal;background-color:rgb(255,255,255)" face="Arial"><span style="margin:0px;font-size:11pt"> averaged
ring, </span></font><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="font-size:11pt">the one in the right is the ring after distortion correction</span></font></span></font><font style="font-size:12pt;font-weight:normal;background-color:rgb(255,255,255);color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif" face="Arial"><span style="margin:0px;font-size:11pt">. </span></font></div>
<div><font face="Calibri, Arial, Helvetica, sans-serif" color="#000000"><span style="font-size:14.6667px"><br>
</span></font>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">To verify if the parameters are accurate, I then took the three parameters ( highlighted in bold) and the same stack file as an input for mag_distortion_correct to correct the
distortion. With the corrected stack file, I then estimated the distortion again, and it showed the images still have 0.15% distortion, with the following parameters:</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">=========================================</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:700">Distortion Angle = 21.0</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:700">Major Scale = 1.001</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:700">Minor Scale = 0.999.</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> Stretch only parameters would be as follows :-</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Distortion Angle = 21.0</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Major Scale = 1.002</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Minor Scale = 1.000</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Corrected Pixel Size = 0.669</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400"> </span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">The Total Distortion = .15%</span></p>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">=========================================</span></p>
<br>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Note that the values of both major and minor scale remind the same as before its corrected, but the distortion angle changed dramatically. Why could be the reason for this? If you
had experience with the mag_distortion_estimate/correct, would you please let me know if there is anything that I should specifically pay attention to in order to get the accurate estimation? </span></p>
<br>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Many thanks in advance.</span></p>
<br>
<p dir="ltr" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:bold;line-height:1.38;margin-top:0pt;margin-bottom:0pt">
<span style="font-size:11pt;font-family:Arial;color:rgb(0,0,0);font-weight:400">Yuejiao Xian</span></p>
Ph.D candidate,</div>
<div>Department of Chemistry and Biochemistry, </div>
<div>University of Texas at El Paso</div>
</div>
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