I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command.

The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely.

The two structures I am trying to align are 3U7Q and 5N6Y.

Thanks in advance for any assistance you can offer!