Hi Sasha, It is between (or among if >2) all structure chains associated with the sequence(s). Association is the only thing that matters, not whether the structure sequence is exactly same as the displayed sequence or not. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 17, 2026, at 1:11 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear All, I was not able to find out what is the formula for calculating RMSF in the commans Sequences-> Headers-> Calpha. Does it calculate the RMSD per residue of distance between C-alpha of each of the associated sequence and the displayed sequence, or RMSD per residue between all of the associated sequences? Thank you very much in advance for explanation. Best regards Sasha