<div dir="ltr"><p>Hi Yuejiao,</p><div><br></div><div>I'm not sure what you mean by many datasets have a distortion above 1.5%? You mean data taken on the same microscope? The drifting can complicate the analysis, but looking at your images, I'm pretty sure it isn't causing an issue for you, and you just don't have much distortion in them.</div><div><br></div><div>You can use mag_distortion_estimate to work with water rings, as it asks for a resolution range to use for the analysis. Simply change your resolution to match the ring that you would like. You will have to provide a stack of images which provide strong water / ice rings if you want to do this.</div><div><br></div><div>Thanks,</div><div><br></div><div>Tim</div><div class="gmail-yj6qo gmail-ajU" style="outline:none;padding:10px 0px;width:22px;margin:2px 0px 0px"><br class="gmail-Apple-interchange-newline"></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 14 Aug 2020 at 15:43, 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 style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hello, Tim, </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Thank you for your quick feedback. I did compare the rings and find that the change is very minor as you pointed out. However, I find it hard to believe that the distortion is so minor because many datasets were shown had distortion above 1.5%. I am wondering
if the drifting would affect the estimation, as you can see that the ring is much brighter in the horizontal direction?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I am also wondering if the mag_distortion_estimate can work with the water rings Marin mentioned in his email? The water ring appears at 3.6Å, 2.2Å and 1.8Å. If I was right, the mag_distortion_estimate only consider the area encapsulating the gold rings (2.4Å-2.0Å),
then I should be able to perform estimation on the 2.2Å water ring? </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Many thanks again for your time. </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Yuejiao</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div id="gmail-m_5101930065781580963appendonsend"></div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_5101930065781580963divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tim Grant <<a href="mailto:timothy.r.grant@gmail.com" target="_blank">timothy.r.grant@gmail.com</a>><br>
<b>Sent:</b> Friday, August 14, 2020 12:53 PM<br>
<b>To:</b> Xian, Yuejiao <<a href="mailto:yxian@miners.utep.edu" target="_blank">yxian@miners.utep.edu</a>><br>
<b>Cc:</b> <a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>>; Yuejiao Xian <<a href="mailto:xianyuejiao@gmail.com" target="_blank">xianyuejiao@gmail.com</a>><br>
<b>Subject:</b> Re: [3dem] anisotropic magnification distortion correction with mag_distortion_estimate/correct</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div dir="ltr">Hi Yuejiao,
<div><br>
</div>
<div>0.15% is not a significant result, as it changes the rings so little, so the angle changing is likely to be a random effect. Both results are essentially telling you that there is very little to no magnification distortion. A good way to confirm this
is to overlay the rotationally averaged ring with the original ring and flick between them. If there is appreciable distortion you should see a directional difference in the rings (it will look like they are being squashed in one direction). In your case,
as far as I can tell your rings line up well.</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Tim </div>
</div>
<br>
<div>
<div dir="ltr">On Fri, 14 Aug 2020 at 12:50, Xian, Yuejiao <<a href="mailto:yxian@miners.utep.edu" target="_blank">yxian@miners.utep.edu</a>> wrote:<br>
</div>
<blockquote 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 face="Arial" style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;font-weight:normal"><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 color="#000000" face="Calibri, Arial, Helvetica, sans-serif"><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 face="Arial" 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)"><span style="margin:0px;font-size:11pt">the
one in the middle is the<span style="margin:0px"> </span></span></font><font color="#000000" face="Arial" 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)"><span style="margin:0px;font-size:14.6667px">rotational</span></font><font face="Arial" 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)"><span style="margin:0px;font-size:11pt"> averaged
ring, </span></font><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif"><span style="font-size:11pt">the one in the right is the ring after distortion correction</span></font></span></font><font face="Arial" 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"><span style="margin:0px;font-size:11pt">. </span></font></div>
<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif"><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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