Hi Abhilash, My way of doing it is to run the mm command for each chain separately. This assigns the rmsd score for each alpha-carbon in the selected chains and updates it after each new mm. The command look something like that: matchmaker #2/A to #1 show true matchmaker #2/B to #1 show true matchmaker #2/C to #1 show true color byattribute seq_rmsd #1 palette rainbow Best Rémi R. ----- Mail original ----- De: "Abhilash Padvannil via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> À: chimerax-users@cgl.ucsf.edu Envoyé: Mardi 29 Août 2023 03:15:55 Objet: [chimerax-users] Coloring by Ca-RMSD Hello, I am working with a multi-subunit protein. I aligned current structure with a previously determined structure using mm command. I am trying to color my protein using RMSD. Chimerax is however, coloring only one-subunit by RMSD, the other chains have default colors. Is there a way to color the whole molecule with RMSD attribute. Thanks Abhilash. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/