Hi Vani, If you already superimposed the structures the way you want, now you can use command “rmsd” to measure RMSDs between sets of atoms without moving them. See “rmsd” manual page for examples: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> In case you might be interested, different ways to superimpose structures are discussed here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> You can also search for help topics using menu: Help… Search Documentation, for example for “rmsd" I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 26, 2018, at 5:01 AM, Vani Pande <vani.pande@students.iiserpune.ac.in> wrote:

Hi, I am new to chimera. I want to superimpose a domain for the two protein molecules and get the rmsd for the non superimposed protein parts. How should i do it. Ihave superimposed domain of interest for my protein using match, but now i am not getting how to proceed further.