[3dem] Output Imod folders from Relion 5 Tomo

[Mohamad HARASTANI]

Hello

@Florent Waltz: I asked this question a while ago on the Github page of Relion https://urldefense.com/v3/__https://github.com/3dem/relion/issues/1213__;!!Mih3wA!DGF3VRKpLmEwj7p886noSY87wTRjBMcVbY2sOViFVg18f0X8aRI-a9VP5pUjjGJnBwg9zGDu38h6MytKG_3BoGH8_q1o0QPJ$ 
I ended up scripting the conversion for per tomogram star files to xf files. I'm attaching my script in case it helps you.

Cheers
Mohamad


________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Florent Waltz via 3dem <3dem at ncmir.ucsd.edu>
Sent: Tuesday, February 25, 2025 3:53 PM
To: Ioannis Skalidis
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Output Imod folders from Relion 5 Tomo

Good to know!

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.
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.
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.
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).

Best,

Florent

Le mar. 25 févr. 2025 à 13:53, Ioannis Skalidis via 3dem <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>> a écrit :
Dear Andriko, Dear Sjors,

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.

Thanks again,
Ioannis.

Στις Τρί 25 Φεβ 2025 στις 11:56 π.μ., ο/η Andriko von Kügelgen <andrikovk at mrc-lmb.cam.ac.uk<mailto:andrikovk at mrc-lmb.cam.ac.uk>> έγραψε:

Hi Ioannis,


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.

I added an example command below:

/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/


Cheers,

Andriko

On 25/02/2025 09:49, Ioannis Skalidis via 3dem wrote:
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Dear 3DEM,

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.
Does anyone have a suggestion?

Thanks in advance,
Ioannis.

Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal<https://urldefense.com/v3/__https://twitter.com/imjohnskal__;!!Mih3wA!HtjwqhxZbS8vtn7LLqtm2t3KwOWyGyG32KIylQvFo4XVUlTcFtJfEAfEzuyeGAGyd82FJWXhUZbnxg8isLWhzDXA$> | Mobile: +30 698 807 7306 | johnskalidis at gmail.com<mailto:johnskalidis at gmail.com>



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--
Florent WALTZ
Ambizione Project Leader,
Biozentrum, Basel



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