ChimeraX should show an IMOD model and map aligned if they align in IMOD. So in your case something is going wrong, and I have no way to know what that is without looking at the data. I believe the IMOD model has no positioning info, just coordinates for the surfaces. So trouble is most likely with the map alignment. You can try to adjust the map origin in ChimeraX using Tools / Volume Data / Map Coordinates and changing the origin, maybe try changing it to 0,0,0 if it is not set to that by default. I don't know if IMOD respects the origin in the map file. ChimeraX does, and if IMOD does not then that would cause misalignment.

On Jun 29, 2023, at 9:03 AM, Guilliams,Bradley via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi All,

I have been working with a tomogram and corresponding model in IMOD and when I load these files into ChimeraX the model and tomogram are offset (see included image). At the highest plane of the tomogram, it intersects roughly halfway up the model. Any advice on how to fix this would be much appreciated!

Cheers,
Bradley

Bradley Guilliams (he/him/his)
PhD Candidate
Ackerson Research Group
Analytical Resources Core – Imaging & Surface Science (ARC-ISS)
Department of Chemistry
Colorado State University

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