You are right that the Segment Map showed the segmentation regions in the wrong place if the original map has been moved in the scene. I fixed the underlying Segger code (from Greg Piintilie) to align them correctly in tonight's ChimeraX build. Details here https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19767

You can avoid the problem in your current ChimeraX by not changing the map's scene coordinates, or you can fix the segmentation model position with ChimeraX command "view position #5 sameAs #4".

Tom

On Jan 22, 2026, at 2:44 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

I'm seeing unexpected behavior when I do the following:
- open PDB A and corresponding MRC map A (models #1 and #2)
- open PDB B and corresponding MRC map B (models #3 and #4)
- match #3 to #1 bring #4
- use the "Segment Map" GUI tool to perform segmentation on #4 with default parameters except "Display at most" set to 160 and "Group by selectivity" selected instead of "Group by smoothing"

The unexpected behavior is that the segmentation surfaces are all offset from the map. It looks to me like the segmentation was performed on the map as though it had never been shifted/rotated by the match command.

This is with ChimeraX-1.10. My apologies - I've not had time to test whether the same happens with the latest version of ChimeraX, nor to come up with an open-source, sharable example.

Cheers,
Alexis

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