[Chimera-users] Quantify the movement between two domains

Hi, I'm looking for a way to quantify the movement between two domains in my structure. I know I can calculate an RMSD between the same domains in different conformations. I can also generate a distance matrix between the two chains in different conformations. I tried to measure the distance between the two centers of mass of my domains, but the change doesn't really capture the magnitude of the movement, also the same domains are not identical in the two conformations in the sense that one domain is missing so many loops, which will affect the com calculation. What other ways to quantify the distance between two different domains? Thank you.