+\subsection{Superimposing structures}
+\label{superposestructs}
+Many comparative biomolecular analysis investigations aim to determine if the
+biochemical properties of a given molecule are significantly different to its
+homologues. When structure data is available, comparing the shapes of molecules
+by superimposing them enables substructure that may impart different behaviour
+to be quickly identified. The identification of optimal 3D superpositions
+involves aligning 3D data rather than sequence symbols, but the result can
+still be represented as a sequence alignment, where columns indicate positions
+in each molecule that should be superposed to recreate the optimal 3D alignment.
+
+Jalview can employ Jmol's 3D fitting routines\footnote{See
+\href{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}{http://chemapps.stolaf.edu/jmol/docs/?ver=12.2$\#$compare}
+for more information.} to recreate 3D structure superpositions based on the
+correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view happens automatically if a
+structure is added to an existing Jmol display using the {\sl Structure
+$\Rightarrow$ View PDB Structure $\Rightarrow$ ..}. A new Jmol view containing
+superposed structures can also be created using the {\sl Structure
+$\Rightarrow$ View all {\bf N} PDB Structures} option (when {\bf {\sl N}}
+$>$ 1) if the current selection contains two or more sequences with associated
+structures.
+
+\subsubsection{Obtaining the RMSD for a superposition}
+The RMSD (Root Mean Square Deviation) is a measure of how similar the structures
+are when they are superimposed. Figure \ref{mstrucsuperposition} shows a
+superposition created during the course of Exercise \ref{superpositionex}. The
+parts of each molecule used to construct the superposition are rendered using
+the cartoon style, with other parts of the molecule drawn in wireframe. The Jmol
+console, which has been opened after the superposition was performed, shows the
+RMSD report for the superposition.
+Full information about the superposition is also output to the Jalview
+console.\footnote{The Jalview Java Console is opened from {\sl Tools
+$\Rightarrow$ Java Console} option in the Desktop's menu bar} This output also
+includes the precise atom pairs used to superpose structures.
+
+\subsubsection{Choosing which part of the alignment is used for structural
+superposition} Jalview uses the visible part of each alignment view to define
+which parts of each molecule are to be superimposed. Hiding a column in a view
+used for superposition will remove that correspondence from the set, and will
+exclude it from the superposition and RMSD calculation.
+This allows the selection of specific parts of the alignment to be used for
+superposition. Only columns that define a complete set of correspondences for
+all structures will be used for structural superposition, and as a consequence,
+the RMSD values generated for each pair of structures superimposed can be
+directly compared.
+
+In order to recompute a superposition after changing a view or editing the
+alignment, select the {\sl Jmol $\Rightarrow$ Align sequences } menu option. The {\sl
+Jmol $\Rightarrow$ Superpose with ..} submenu allows you to choose which of the
+associated alignments and views are to be used to create the set of
+correspondences. This menu is useful when composing complex superpositions
+involving multi-domain and multi-chain complexes, when correspondences may be
+defined by more than one alignment.
+
+Note that these menu options appear when you have two or more structures in one Jmol viewer.
+
+
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/fdxsuperposition.pdf}
+\caption{{\bf Superposition of two ferredoxin structures.} The alignment on the
+left was used by jalview to superpose structures associated with the
+FER1\_SPIOL and FER1\_MAIZE sequences in the alignment. Parts of each structure
+used for superposition are rendered as a cartoon, the remainder rendered in
+wireframe. The RMSD between corresponding positions in the structures before and
+after the superposition is shown in the Jmol console.}
+\label{mstrucsuperposition}
+\end{center}
+\end{figure}
+
+\exercise{Aligning structures using the ferredoxin
+sequence alignment.}{\label{superpositionex}
+
+\exstep{Continue with the Jalview project created in exercise
+\ref{viewingstructex}. Use the {\sl Discover PDB IDs} function to retrieve PDB
+IDs associated with the FER1\_MAIZE sequence.}
+\exstep{Once discovery has completed, use the {\sl
+View PDB Structure} submenu to view the PDB file associated with FER1\_MAIZE.
+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 the {\bf Yes} button.
+
+{\sl The Jmol view will 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.}
+\exstep{Use the {\sl Jmol} submenu to
+recompute the superposition using just columns 121-132 of the alignment.
+
+{\sl Note how the molecules shift position when superposed using a short part of
+the two structures.}}
+\exstep{Compare the initial and final RMSDs for superimposing molecules with
+the small section and with the whole alignment. Which view do you think give the
+best 3D superposition, and why ?} }
+
+\subsection{Colouring structure data associated with multiple alignments and views}
+Normally, the original view from which a particular structure view was
+opened will be the one used to colour structure data. If alignments involving
+sequences associated with structure data shown in a Jmol have multiple views, Jalview gives you full control
+over which alignment, or alignment view, is used to colour the structure
+display. Sequence-structure colouring associations are
+changed {\sl via} the {\sl View $\Rightarrow$ Colour by ..} menu, which lists all
+views associated with data shown in the embedded Jmol view. A tick is shown beside
+views currently used as colouring source, and moving the
+mouse over each view will bring it to the front of the alignment display,
+allowing you to browse available colour sources prior to selecting one. If the
+{\sl Select many views} option is selected, then multiple views can be selected as sources for colouring the
+structure data. {\sl Invert selection} and {\sl Select all views} options are also provided to quickly change between multi-view selections.
+
+Note that the {\sl Select many views} option is useful if you have different
+views that colour different areas or domains of the alignment. This option is
+further explored in Section \ref{complexstructurecolours}.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=5.5in]{images/mviewstructurecol.pdf}
+\caption{{\bf Choosing a different view for colouring a structure display}
+Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control
+of which alignment view is used to colour structures when the {\sl Colours
+$\Rightarrow$ By Sequence} option is selected.}
+\label{mviewstructurecol}
+\end{center}
+\end{figure}
+
+\subsubsection{Colouring complexes}
+\label{complexstructurecolours}
+The ability to control which multiple alignment view is used to colour
+structural data is essential when working with data relating to
+multidomain biomolecules and complexes.
+
+In these situations, each chain identified in the structure may have a different
+evolutionary history, and a complete picture of functional variation can
+only be gained by integrating data from different alignments on the same
+structure view. An example of this is shown in Figure
+\ref{mviewalcomplex}, based on data from Song et. al\footnote{Structure of
+DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation. Jikui Song, Olga Rechkoblit, Timothy H. Bestor, and Dinshaw J. Patel.
+{\sl Science} 2011 {\bf 331} 1036-1040
+\href{http://www.sciencemag.org/content/331/6020/1036}{DOI:10.1126/science.1195380}}
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[]{images/mchainstructureview.pdf}
+\caption{{\bf The biological assembly of Mouse DNA Methyltransferase-1 coloured
+by Pfam alignments for its major domains} Alignments for each domain within the
+Uniprot sequence DNMT1\_MOUSE have been used to visualise sequence conservation
+in each component of this protein-DNA complex. Instructions for recreating this figure are given in exercise \ref{dnmtcomplexex}. }
+\label{mviewalcomplex}
+\end{center}
+\end{figure}
+
+\exercise{Colouring a protein complex to explore domain-domain interfaces}{\label{dnmtcomplexex}
+
+\exstep{Download the PDB file at
+\textsf{\url{http://www.jalview.org/tutorial/DNMT1\_MOUSE.pdb}} to your desktop. This
+is the biological unit for PDB ID 3pt6, as identified by the PDBe's PISA server.}
+
+\exstep{Launch the Jalview desktop and ensure you have at least 256MB of
+free memory available.
+
+{\sl Use the following webstart link:
+\href{http://www.jalview.org/webstart/jalview_1G.jnlp}{http://www.jalview.org/webstart/jalview\_1G.jnlp}}.}
+\exstep{Retrieve the following
+{\bf full} PFAM alignments: PF02008, PF00145, PF01426 (make sure you select the {\sl PFAM {\bf (Full)}} source). These will each be retrieved into their own alignment window.}
+\exstep{Drag the structure you downloaded in
+step 1 onto one of the alignments to associate it with the mouse sequence in
+that Pfam domain family.}
+\exstep{For every DNMT1\_MOUSE sequence in the alignment, use the sequence
+ID popup menu's {\sl Structure} submenu to view the DNMT1\_MOUSE structure for the associated mouse sequence. When given the option, {\bf view all of the structures in the same Jmol viewer}. Check the contents of the {\sl View $\Rightarrow$ Colour by ..} submenu to see what alignments can be used to
+colour the sequence.}
+\exstep{Repeat the previous two steps for each of
+the other alignments. In each case, when performing the `View DNMT1\_MOUSE.pdb'
+step, Jalview will ask if you wish to create a new Jmol view. You should
+respond `No', {\bf ensuring that each sequence fragment is associated with the same Jmol view}.}
+\exstep{Pick a different colourscheme for each alignment, and use the {\sl
+Colour by ..} submenu to ensure they are all used to colour the complex shown
+in the Jmol window.}
+\exstep{The final step needed to reproduce the shading in Figure
+\ref{mviewalcomplex} is to use the {\sl Colour $\Rightarrow$ By
+Annotation } option in each alignment window to shade the alignment by the
+{\bf Conservation} annotation row. This function was described in section
+\ref{colourbyannotation}.
+
+Ensure that you first disable the {\sl View $\Rightarrow$ Show Features} menu option, or you may not see any colour changes in the associated structure.
+
+{\sl Note: Choose a different shading scheme for each
+alignment so that the regions of strong physicochemical conservation are highlighted. This
+kind of shading will reveal conserved regions of interaction between domains
+in the structure.}}
+\exstep{Save your work as a Jalview project and verify that it can be opened again by starting another Jalview Desktop instance, and dragging the saved project into the desktop window.}
+
+{\sl Note: This exercise relies on new features introduced in Jalview 2.7. If
+you notice any strange behaviour when trying out this exercise, it may be a
+bug (see
+\href{http://issues.jalview.org/browse/JAL-1008}{http://issues.jalview.org/browse/JAL-1008}
+for one relating to highlighting of positions in the alignment window).} }
+