Nothing should be different about the alignment of maps in ChimeraX 1.4 versus older versions. ChimeraX uses the map origin and voxel size that is in the map file header. You can see and change the origin and voxel size using menu Tools / Volume Data / Map Coordinates. If there really is a different behavior in ChimeraX 1.4 versus 1.3 in the alignment then use ChimeraX menu entry Help / Report a Bug... and we can investigate it further.

On Aug 4, 2022, at 11:53 AM, Moritz, Michelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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Hello,
I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen?
Thanks for your help,
Michelle
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