Hi again, I was wondering if the mmaker command had an option (or if there is some other way within chimera) of reporting the RMSD (as calculated by mmaker) of an alignment without actually superimposing one structure on the other. The reason that I am doing this that for a group of structures I can see with mmaker that they superimpose very well, but I want to show that when you compute the RMSD of those same structures when each is bound to a partner they are not quite as well aligned. In essence, what I want mmaker to do is not really realign the structures for me, but to calculated the RMSD of an alignment that I provide it. I looked at the mmaker command page but I couldn't seem to find an option for this. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html Thanks again, and Chimera is a wonderful piece of software! Sincerely, Joshua Broyde