Tilt angle offset being undone when aligning TS with IMOD

[rdrighetto]

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 even know this was possible, but I like it. If i proceed with the tomogram reconstruction in Etomo I get a nicely flattened lamella in the XZ plane:

However, upon proceeding to the "Reconstruct tomograms" step in RELION, I see that the lamella is tilted as if the tilt angle offset had not been applied:

This is confirmed by inspecting the _rlnTomoYTilt field in the respective tilt series STAR file.

Upon inspecting the code of the align tilt-series job, I found that the tilt angle offset is being undone by these lines:
https://github.com/3dem/relion/blob/6331fe600cca7683ecf7c1011ce676701faf1e97/src/tomography_python_programs/align_tilt_series/imod/_utils.py#L28C1-L29C41

Is this a bug, or is it meant to be this way? Or did the IMOD behavior in this regard has changed across versions?

Environment:

• OS: Ubuntu 22.04.3 LTS
• RELION version: RELION-5.0-beta-3-commit-63311fe

Job options:

• Type of job: Align tilt-series
• IMOD version: 4.12.61

Thank you!