<div dir="ltr"><div dir="ltr">Good to know!<div><br></div><div>On the same note, I was wondering if RELION could output similar IMOD folders but just from the tomogram.star, notably the IMOD .xf files.<br>It would be particularly useful after particle polishing. I found myself reconstructing "polished" tomograms and using them to repick and it has been working quite well. <br>However, I am not really happy with the CTF correction performed by RELION, that's why it would be useful to get these IMOD files to reconstruct the tomos outside of RELION. </div><div>Notably, we have seen that accurate CTF correction (not just simple phase flipping) does improve template matching results, so this would really be useful (as long as no other CTF correction option is not provided directly within RELION).</div><div><br></div><div>Best,</div><div><br></div><div>Florent</div></div><br><div class="gmail_quote gmail_quote_container"><div dir="ltr" class="gmail_attr">Le mar. 25 févr. 2025 à 13:53, Ioannis Skalidis via 3dem <<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>> a écrit :<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>Dear Andriko, Dear Sjors,</div><div><br></div><div>Thank you very much for your input! I was still working with the pre-release version, so in my case Relion 5 works still with AreTomo 1 and there is no option to include "Other AreTomo2 arguments". I will update my version and proceed as you suggested.</div><div><br></div><div>Thanks again,</div><div>Ioannis.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Στις Τρί 25 Φεβ 2025 στις 11:56 π.μ., ο/η Andriko von Kügelgen <<a href="mailto:andrikovk@mrc-lmb.cam.ac.uk" target="_blank">andrikovk@mrc-lmb.cam.ac.uk</a>> έγραψε:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u></u>
<div>
<p>Hi Ioannis,</p>
<p><br>
</p>
<p>the latest RELION 5.0 version should be able to do that by using
the option "Other AreTomo2 arguments" in the GUI or
"--other_wrappers_args" in the CLI. I just tested it internally at
the LMB and you should be able to add " -OutImod 1 ". That will
create a sub-directory called "$rlnTomoName_Imod" for each
tomogram inside of AlignTiltSeries/jobXXX/external/$rlnTomoName/
where $rlnTomoName corresponds to the name of the tomogram in the
input starfile. </p>
<p>I added an example command below:</p>
<p>/public/EM/RELION/relion-devel/build/bin/relion_align_tiltseries_mpi
--i CtfFind/job003/tilt_series_ctf.star --o
AlignTiltSeries/job004/ --tomogram_thickness 300 --aretomo2
--aretomo_exe /public/EM/AreTomo/AreTomo2/AreTomo2 --aretomo_ctf
--other_wrapper_args " -OutImod 1 " --gpu 0:1:2:3
--only_do_unfinished --pipeline_control AlignTiltSeries/job004/</p>
<p><br>
</p>
<p>Cheers,</p>
<p>Andriko<br>
</p>
<div>On 25/02/2025 09:49, Ioannis Skalidis
via 3dem wrote:<br>
</div>
<blockquote type="cite">
<div style="background-color:rgb(255,235,156);width:100%;padding:2pt;font-size:10pt;line-height:12pt;font-family:Calibri;color:black;text-align:left;border:1pt solid rgb(156,101,0)"><span style="color:rgb(156,101,0)">CAUTION:</span> This email originated
from outside of the LMB:<br>
<b>.-3dem-bounces@ncmir.ucsd.edu-.</b><br>
Do not click links or open attachments unless you recognize the
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If you think this is a phishing email, please forward it to
<a href="mailto:phishing@mrc-lmb.cam.ac.uk" target="_blank">phishing@mrc-lmb.cam.ac.uk</a></div>
<p>
<br>
--<br>
</p>
<div dir="ltr">
<div>Dear 3DEM,</div>
<div><br>
</div>
<div>I was wondering if anyone has an idea on how I would be
able to generate the Imod folder necessary to move to other
software for tomogram reconstruction, after I do tilt series
alignment with AreTomo in Relion 5. The standalone version of
AreTomo has the -OutImod command, but this cannot be included
as an additional argument when running it from within Relion
5. <br>
</div>
<div>Does anyone have a suggestion?</div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div>Ioannis.</div>
<div><br>
</div>
<div>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:10pt"><span style="color:rgb(102,102,102)">Dr. Ioannis Skalidis</span><span style="color:gray"> </span><span style="color:rgb(192,0,0)">| </span><span style="color:rgb(102,102,102)">Structural Biochemist</span><span style="color:gray"> </span><span style="color:rgb(192,0,0)">| </span><span style="color:rgb(102,102,102)">Twitter: <a href="https://urldefense.com/v3/__https://twitter.com/imjohnskal__;!!Mih3wA!HtjwqhxZbS8vtn7LLqtm2t3KwOWyGyG32KIylQvFo4XVUlTcFtJfEAfEzuyeGAGyd82FJWXhUZbnxg8isLWhzDXA$" target="_blank">@imjohnskal</a></span><span style="color:rgb(192,0,0)"> </span><span style="color:rgb(192,0,0)">| </span><span style="color:rgb(102,102,102)">Mobile: +30 698 807
7306</span><span style="color:gray"> </span><span style="color:rgb(192,0,0)">| </span><font color="#666666"><a href="mailto:johnskalidis@gmail.com" target="_blank">johnskalidis@gmail.com</a></font><span style="color:rgb(192,0,0)"><span style="background-color:rgb(204,204,204)"></span></span><span style="color:rgb(192,0,0)"></span><span style="color:rgb(192,0,0)"></span></div>
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