\begin{Verbatim}[commandchars=\\\{\}]
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{sup} \PYG{o}{=} \PYG{n}{Superimposer}\PYG{p}{()}
\PYG{g+go}{\PYGZsh{} Specify the atom lists}
\PYG{g+go}{\PYGZsh{} \PYGZsq{}fixed\PYGZsq{} and \PYGZsq{}moving\PYGZsq{} are lists of Atom objects}
\PYG{g+go}{\PYGZsh{} The moving atoms will be put on the fixed atoms}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{sup}\PYG{o}{.}\PYG{n}{set\PYGZus{}atoms}\PYG{p}{(}\PYG{n}{fixed}\PYG{p}{,} \PYG{n}{moving}\PYG{p}{)}
\PYG{g+go}{\PYGZsh{} Print rotation/translation/rmsd}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{sup}\PYG{o}{.}\PYG{n}{rotran}\PYG{p}{)}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n+nb}{print}\PYG{p}{(}\PYG{n}{sup}\PYG{o}{.}\PYG{n}{rms}\PYG{p}{)}
\PYG{g+go}{\PYGZsh{} Apply rotation/translation to the moving atoms}
\PYG{g+gp}{\PYGZgt{}\PYGZgt{}\PYGZgt{} }\PYG{n}{sup}\PYG{o}{.}\PYG{n}{apply}\PYG{p}{(}\PYG{n}{moving}\PYG{p}{)}
\end{Verbatim}
