super_imposer.rms
is indeed the root-mean-square deviation.
If you consult the source of Bio.PDB.Superimposer
, you'll see that the rms
attribute is the result of a call to get_rms()
. The docstring for get_rms()
reads:
Root mean square deviation of superimposed coordinates.
The Tutorial does say that "The RMSD is stored in the rmsd
attribute," however. No idea why this discrepancy exists.