+\exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{
+\label{superpositionex}
+
+\exstep{Continue with the Jalview project created in exercise
+\ref{viewingstructex}}
+
+\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL
+by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$
+3D Structure Data \ldots } }
+
+\exstep{Pick 1A70 from the Structure Chooser dialog, and click the {\bf View}
+button. Jalview will give you the option of aligning the
+structure to the one already open. To superimpose the structure associated with
+FER1\_MAIZE with the one associated with FER1\_SPIOL, press {\sl Yes}.
+
+{\sl The Jmol view should update to show both structures, and one will be
+moved on to the other. If this doesn't happen, use the Align function in the
+Jmol submenu}.
+}
+
+\exstep{Create a new view on the alignment, and hide all but columns 121
+through to 132 (you can do this via {\sl View $\Rightarrow$ Hide $\Rightarrow$
+All but selected region}).}
+\exstep{Select the newly created view in the {\sl Jmol $\Rightarrow$ Superpose
+With } submenu, and then recompute the superposition with {\sl Jmol
+$\Rightarrow$ Align Structures}.
+
+{\sl Note how the molecules shift position when superposed with only a small
+region of the alignment.}}
+
+\exstep{Compare RMSDs obtained when superimposing molecules with
+columns 121-132 and with the whole alignment.}
+
+\exstep{The RMSD report can be
+viewed by right clicking the mouse on Jmol window, and select {\sl
+Console} from the menu (if nothing is shown, recompute the superposition after
+displaying the console).
+
+Which view do you think give the best 3D superposition, and why ?} }
+
+\exercise{Setting Chimera as the default 3D Structure Viewer}{
+\label{viewingchimera}