[3dem] Output Imod folders from Relion 5 Tomo

[Ioannis Skalidis]

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> 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
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