Hello, Fiitting uses one point per residue: CA atoms in amino acids and C4' atoms in nucleic acids. You can click the Help button on the dialog to see this and other information about the tool. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 1, 2016, at 8:00 AM, sdimicco <sdimicco@unisa.it> wrote:

Dear Developer,

I am using MatchMaker to compare some peptides. I would like to know if the RMSD value is referenced to the backbone atoms or to whole atom structure.

Thank you in advamce.

All the best.