Atom[] atomSet1 = listLeft.toArray(new Atom[listLeft.size()]);
Atom[] atomSet2 = listRight.toArray(new Atom[listRight.size()]);
SVDSuperimposer superimposer = new SVDSuperimposer(atomSet1, atomSet2);
Calc.rotate(right, superimposer.getRotation());
Calc.shift(right, superimposer.getTranslation());

// proceed with regular RMSD calculation from now on