\subsection{Recalculating coordinates}
\label{sec:recalc}

Molecules specified in \texttt{SMILES} format don't have any coordinates attached to them, so \mcf needs to calculate them; this is performed automatically. Input in \texttt{molfile} format comes with coordinates attached, and \mcf uses these by default. However, we can explicitly request \mcf to discard these coordinates and calculate new ones with the \lstinline!--recalculate-coordinates! or \lstinline!-u! option. When applied to the daptomycin example from section \ref{sec:example}, 
\lstinputlisting{daptomycin-u.sh}

this gives us

\cfpic{daptomycin-u.tex}

