<div dir="ltr">Hi Kyle,<div><br></div><div>I'm sorry you didn't find the tutorial beginner friendly enough - it looks like reading the helptexts for the commands you have been using might be useful, these are also available on our <a href="https://urldefense.com/v3/__https://warpem.github.io/warp/reference/warptools/api/general/__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42Isv3weM$">API docs pages</a></div><div><br></div><div>re: AreTomo, we provide an AreTomo wrapper similar to the IMOD wrappers called ts_aretomo (<a href="https://urldefense.com/v3/__https://warpem.github.io/warp/reference/warptools/api/tilt_series/*ts_aretomo__;Iw!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi421ZgGrYE$">docs</a>) which is compatible with AreTomo 1.3.4<br>If you want to run any external tilt series alignment program you can follow <a href="https://urldefense.com/v3/__https://warpem.github.io/warp/reference/warptools/custom_tilt_series_alignments/__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42jiRRIJI$">this guide</a>, we require IMOD format results for import into Warp</div><div><br></div><div>re: EER file processing you can add `--eer_ngroups` or `--eer_groupexposure` to your create_settings command, I've added a note about this to the tutorial</div><div><br></div><div>Any problems that come up don't hesitate to reach out, I'm more likely to see questions asked on the <a href="https://urldefense.com/v3/__https://groups.google.com/u/1/g/warp-em__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42Xx_IpOw$">Warp google group</a> or our <a href="https://urldefense.com/v3/__https://github.com/warpem/warp/issues__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42jdZqteo$">GitHub issues</a>.</div><div><br></div><div>Cheers,</div><div><br></div><div>Alister</div></div><br><div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">On Wed, 22 Jan 2025 at 12:00, <<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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1. Anyone have a detailed tutorial for Warptools? (Kyle Messina)<br>
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Message: 1<br>
Date: Wed, 22 Jan 2025 11:37:47 -0600<br>
From: Kyle Messina <<a href="mailto:messi144@umn.edu" target="_blank">messi144@umn.edu</a>><br>
To: <a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a><br>
Subject: [3dem] Anyone have a detailed tutorial for Warptools?<br>
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<<a href="mailto:CA%2B1M%2BbBXSVQBqRB5p3A%2BwgCSsGk573MxfYJiNOV9Jz5U2BC3kA@mail.gmail.com" target="_blank">CA+1M+bBXSVQBqRB5p3A+wgCSsGk573MxfYJiNOV9Jz5U2BC3kA@mail.gmail.com</a>><br>
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<br>
Hello All,<br>
<br>
I've been trying to learn both Warp and Warptools for subtomo averaging but<br>
I've had issues learning Warptools. The Quick Start: Tilt Series tutorial<br>
on the website only focuses on the example dataset but does not go into<br>
details for other potential options such as processing data with AreTomo2<br>
instead of IMOD or working with EER files. I have been running into issues<br>
due to user error and (probably) lack of general knowledge about Warp<br>
inputs, outputs and how/why different settings affect your results or are<br>
needed.<br>
<br>
Does anyone have a written tutorial that is beginner friendly? The more<br>
detailed it is for the various steps and commands the better!<br>
<br>
Thank you,<br>
Kyle Messina<br>
<a href="mailto:messi144@umn.edu" target="_blank">messi144@umn.edu</a><br>
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