Hi, just a quick question. In TM_Align, is the reported RMSD value the average angstrom distance between the alpha carbons in the backbones of the two structures? Thanks.
RMSD is not the average of Ca distance error. It is the square root of the Ca distance between the two structures divided by the sequence length after the superposition. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321859/