Dear Jyotheeswaran Panapakam, In Chimera, you can calculate the RMSD between two sets of atoms (opened from two different input files) using command "match" or "rmsd" - the difference between these two commands is that "match" will rigidly move one model to best-fit it onto the other model and then give you the resulting best-fit RMSD, whereas "rmsd" will just calculate the RMSD in the current position without trying fit first. In the commands, you have to specify exactly which atoms you want to use for the command. So if you want to compare the protein part only, you should specify the protein residues in the command. See the command help pages including examples: match <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> rmsd <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> There is also a Matchmaker tool and command that will calculate RMSDs between two proteins but it will only use the CA atoms, and by default only the CA atoms that are sequence-aligned and also in the well-fitting parts (omitting loops that are in different conformations). <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 17, 2023, at 9:42 AM, Panapakam, Jyotheeswaran via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Officail,

This is Jyo writing from UNT biological sciences at Denton, TX, USA. I have been using your software for my research project for about an year. I was looking for a help/instructions about how to find out the configuration change in the protein after docking with a ligand. I have heard about RMSD docking value, that will be given in Amstrong units, could you kindly instruct me the process to perform it.

It would be more glad if you are able to answer me withing a week from now : )

Sincerely, Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.