Hi Francisco, Your map is probably a unit cell with your atomic model stradling the boundary. Coot replicates X-ray unit cell maps while ChimeraX (which is focused on cryoEM) does not. In ChimeraX if your atomic model is #1 and your unit cell map is #2 you can use the ChimeraX volume cover command to use the symmetry to produce a new map that covers your atomic model volume cover #2 atom #1 and you could save that covering map with save mydiffmap.mrc model #3 Tom

On Mar 10, 2026, at 1:33 PM, Francisco Murphy Pérez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I generated a difference map using MatchMaps (https://github.com/rs-station/matchmaps). However, when I load the map in ChimeraX, the density appears split into two distinct regions.

Interestingly, this does not occur when the same map is opened in Coot, where it displays as expected.

I have attached a screenshot for reference. Any ideas on how to “unsplit” the map or what might be causing this behavior?

Thanks in advance.

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