[3dem] Output Imod folders from Relion 5 Tomo

[Florent Waltz]

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> 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> 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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>>
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-- 
*Florent WALTZ*

*Ambizione Project Leader,Biozentrum, Basel*
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