Chimera Alignments

I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form.

I want to superpose the N-terminal subunits (A), note the root mean square of the atomic deviations (RMSD), then apply the resulting matrix to the superposition of both subunits of the molecule with both subunits of the other (B), then I want to superpose on the C-terminal subunits (C), and then measure the RMSD between (C) and the C-terminal subunits from (B).

Do you know how can I do this in Chimera? I know how to superpose molecules and calculate the RMSD in Chimera, but I do not know how to apply the resulting matrix from (A) to (B). I tried to save the aligned structures from (A) as a PDB file to check and see if there was a matrix in the file, but an error message came up saying that I needed to save the file as $name or $number. I tried to save the file with $ in front of the name, but it didn't work. How can I do this correctly? 1 Answer Answer from @terdon converted from comment: The $ are often used to signify that something is a variable. So I guess they mean you need to use a name that you've already used. I mean, the same name as used for something else in your pipeline, so that then the program will see the file with the same name and know to apply it. Sorry, I don't have any experience with chimera, so I have no idea if what I'm suggesting is reasonable. It's just what I get from the \$ you mentioned.

Answer from @marcin converted from comment:

this question was answered on chimera-users:

http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/014045.html

Answer from @joe-healey converted from comment:

You are probably looking for the “Morph Conformations” function within Chimera. It’ll move and superimpose 2 structures on to one another.