Ricardo Righetto

Allow custom activation commands

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This PR implements custom activation commands (for example a non-default conda environment outside of Scipion) and updates README for explaining how to use `ISONET_HOME` and `ISONET_ACTIVATION_CMD` config variables.

relion_tomo_reconstruct_tomogram_mpi requiring more memory than before and then crashing

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**Describe your problem** Reconstructing tomograms, which worked fine in a previous version (RELION-5.0-beta-3-commit-63311fe) now seems to be broken. The first issue I see is that it now requires more RAM....

Tilt angle offset being undone when aligning TS with IMOD

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Hi, I noticed that when aligning TS using patch-tracking in IMOD from RELION-5, a tilt angle offset is estimated in the "Fine Alignment" step equivalent of Etomo:  I didn't...

**Describe your problem** I wasn't able to start napari from the conda environment installed by RELION-5 following the instructions (see error message below). However, a clean installation of a conda...

IsoNet generates lots of subtomogram files from the extraction, which could be cleaned up at the end of the network training.

Feature request: allow flexibility in rlnTomoName

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(I have a vague remembrance of discussing this in the past, so apologies if this is redundant) Currently, for reading RELION STAR files, ArtiaX expects `rlnTomoName` to follow the format...

Bug in saving Relion-5 STAR file: rlnTomoVisibleFrames not saved in output

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When saving particle lists in RELION-5 format, it seems the `rlnTomoVisibleFrames` column is ignored, which gives an error in downstream processing in Relion-5. Maybe it is not even being read...

Does DynaMight work for tomography?

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Hi, I tried to run DynaMight on a dataset I processed with `relion --tomo` (v5.0) where particles are stored as 2D tilt stacks. I tried: ``` dynamight optimize-deformations --refinement-star-file Refine3D/ribo_tm2_bin1_ref3d5_ctfref2_polish2/run_data.star...