<div dir="ltr"><div dir="ltr"><div class="gmail_default" style="font-size:small">Hi Mat,</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Here are some options, mileage may vary:</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">- If you want to use Fourier Cropping, you could use the CLI program "resample" that comes with cisTEM. <br></div><div class="gmail_default" style="font-size:small">- At your resolution, you could probably just use real-space resampling via IMOD's "newstack -shrink [shrinkFactor]", double check the man page, but I think you would want a shrinkFactor > 1 applied to your stack with the higher pixel sampling rate (lower pixel size.) e.g. newstack -shrink 1.035 stack_in.mrc stack_out.mrc. The header should confirm the correct pixel size (header stack_out.mrc)</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"> * * * Both of these would change the imod alignments, which are in pixels. You might just scale the 5/6 column which are x/y shifts from your imod.xf file, or alternatively, just update your tilt-series automatically by using "emClarity autoAlign" which will do an automatic tilt-series alignment for you. If you have more questions about that option, please post them on the emClarity mailing list.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">- Finally, if you are feeling spunky, I think you could get away with scaling the first 4 columns in your imod.xf files, which are a transformation matrix that includes magnification. emClarity uses this matrix in Fourier Space when resampling the tilt-series. Using awk or something, you would just scale those 4 values by your wanted mag change. Off the top of my head, I can't remember which you would want, so as a control, you could take a stack, scale by either 1/2 or 2, and then run "emClarity ctf estimate" which outputs the resampled stack in your "aliStacks" directory. It should be clear which direction you need to go then. Same advice for further questions on this option, as it is emC specific, please post over that way.</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">HTH</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small">Ben<br></div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br clear="all"></div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr">------------------------<br><font size="2" face="Tahoma" color="black"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial">Benjamin Himes</font><font face="Arial">, PhD<br>
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cryoEM methods development </font><font face="Arial"><br></font><font face="Arial">HHMI</font><font face="Arial">, RNA Therapeutics Institute, University of Massachusetts Medical School<br></font></span></font></span></font></div><div dir="ltr"><font size="2" face="Tahoma" color="black"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial"><br></font></span></font></span></font></div><div dir="ltr"><font size="2" face="Tahoma" color="black"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial">
cryo-STA development @ </font><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bHimes_emClarity&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=M_dZB06pzOavKuuu783BOvjiGtUd5r50ihEbVPhfzzs&s=2khunCSL7vOwJCK-LNA1OaAvRBPVrwGQQwF16ZK_tP8&e=" target="_blank"><font face="Arial">emClarity</font></a></span></font></span></font></div><div><font size="2" face="Tahoma" color="black"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial">Visual Proteomics @ <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_timothygrant80_cisTEM&d=DwMFaQ&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=M_dZB06pzOavKuuu783BOvjiGtUd5r50ihEbVPhfzzs&s=SID-lccuQDLpb6fqKdcvafXXzAdEn5hAnWY5zeOJdU0&e=" target="_blank">cisTEM</a><br></font></span></font></span></font></div><div dir="ltr"><font size="2" face="Tahoma" color="black"><span style="font-size:10pt" dir="ltr"><font size="1"><span style="font-size:13px"><font face="Arial">-------------------------</font></span></font></span></font></div></div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 8, 2021 at 3:00 PM <<a href="mailto:3dem-request@ncmir.ucsd.edu">3dem-request@ncmir.ucsd.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">Send 3dem mailing list submissions to<br>
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Message: 1<br>
Date: Wed, 8 Sep 2021 11:11:16 +0000<br>
From: "McLaren, Mathew" <<a href="mailto:M.McLaren@exeter.ac.uk" target="_blank">M.McLaren@exeter.ac.uk</a>><br>
To: "<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>><br>
Subject: [3dem] Fourier cropping to merge tomography datasets<br>
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Dear all,<br>
<br>
I am working with two tomogram datasets collected using two separate Krios microscopes and I've been picking particles to perform STA. I have somewhat successfully processed these using Relion to a resolution of 20 A but I've been experimenting with emClarity in an attempt to improve it further. There is a small pixel size difference (<span class="gmail_default" style="font-size:small"></span>4.377 A and <span class="gmail_default" style="font-size:small"></span>4.53 A), which I've previously accounted for by resizing the processed tomogram with the smaller pixel size through IMOD to match the larger one. I was looking for a different approach to this as I realise that this is probably a terrible way to combine two datasets!<br>
<br>
For emClarity I need to work with the tilt series, so I was thinking that I should do a (non-integer) fourier crop the tilts from one dataset so they match with the other, and I was wondering if anyone has any experience of the best way to do this? Also, would this invalidate the alignments performed in IMOD and require me to reprocess the tilt series?<br>
<br>
Cheers,<br>
<br>
Mat<br>
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----------<br>
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Dr Mathew McLaren<br>
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TEM Experimental Officer<br>
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Living Systems Institute<br>
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University of Exeter<br>
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T: +44(0)1392 727468<br>
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E: <a href="mailto:m.mclaren@exeter.ac.uk" target="_blank">m.mclaren@exeter.ac.uk</a><br>
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My pronouns are he / him / his.<br>
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