Intra rms cur
intra_rms_cur calculates rms values for all states of an object over an atom selection relative to the indicated state without performing any fitting. The rms values are returned as a python array.
cmd.intra_rms_cur( string selection, int state)
from pymol import cmd rms = cmd.intra_rms_cur("(name ca)",1)
See Rms for selection caveats for this group of commands.