Map is split

[frmupe]

But this seems to be a chimerax thing

[dennisbrookner]

Wow that is very strange! You might be the first person to ever try and open a matchmaps map in chimeraX, so I wasn't aware of this behavior. I don't know how soon I will be able to get to this, but I will leave you with a few thoughts if you're interested in debugging more yourself.

As I note in the documentation here, orthorhombic matchmaps outputs have a weird hack where alpha is to 90.006. If have found that this is sufficient to signal to coot that the map is a crystallographic map, rather than a cryoEM map, and thus that periodic boundary conditions are appropriate. Otherwise, when alpha=beta=gamma=90 and the spacegroup is P1, coot assumes that the map is a cryoEM map.

I suspect that what's going on here is that chimeraX is still treating your map as a cryoEM map (and thus is not rendering periodic boundary conditions). I would recommend playing around with the chimeraX settings to see if there's any way to override this. If you figure this out, let me know, and I can update the documentation to reflect what you learn. If that doesn't work, you could also try using gemmi to edit your map files and increase the unit cell angles a tiny bit more, and see if that does the trick.