ChimeraX has a "morph" command.  Here's an example using it

open 2vaa

open 2vab

matchmaker #2 to #1

morph #1,2

save morph.pdb model #3 allCoordsets true

Morphing of course only contains the atoms that are in both structures.  So if you have an unbound and a bound state, and the bound tapasin is only in one structure then it will not be included in the morph since there is nothing to morph it to in the unbound state.  You can delete chains that the two structures do not have in common before morphing, or you can use the same true option to the morph command "morph #1,2 same true" which will ignore chains which do not appear in both structures.

Tom