Hello, You should probably use command "rmsd" (not "match"). With either command, you also have to specify which atoms the command should use, such as the model number and residue name or number for both the docked ligand and the original ligand. It is impossible for me to tell what they are since I am not looking at your data. Here is the help on how to specify atoms in the command line: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> Here is the "rmsd" help with some examples: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.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 Oct 28, 2022, at 6:56 AM, Naima syed via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hello

I am trying to find the RMSD between docked ligand and original ligand but I am not able to do it. When i tried the command "match" it showed the error atom spec missing. Can you please tell me how to fix this problem?

Thank you