<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 gmail_quote_container"><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">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
sender and know the content is safe.<br>
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>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
3dem mailing list
<a href="mailto:3dem@ncmir.ucsd.edu" target="_blank">3dem@ncmir.ucsd.edu</a>
<a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem" target="_blank">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a>
</pre>
</blockquote>
</div>
</blockquote></div>