The RMS Alignment menu fits molecules based on selected groups of atoms. Whereas the RMSD Calculator finds the RMS distance between molecules without disturbing their coordinates, the RMS Alignment menu actually moves molecules to new positions.
This menu is quite simple: Enter an atom selection in the input field, and press Align to align the molecules based on the atoms in that selection. If you recompute the RMSD between molecules in the RMSD Calculator menu, you will probably find that the values are different; this is because the calculation is made based on the current positions of the atoms.
