+\subsection{Customising Structure Display}
+
+Structure display can be modified using the {\sl Colour} and {\sl View} menus
+in the structure viewer. The background colour can be modified by selecting the
+{\sl Colours $\Rightarrow$ Background Colour\ldots} option.
+
+By default, the structure will be coloured in the same way as the associated
+sequence(s) in the alignment view from which it was launched. The structure can
+be coloured independently of the sequence by selecting an appropriate colour
+scheme from the {\sl Colours} menu. It can be coloured according to the
+alignment using the {\sl Colours $\Rightarrow$ By Sequence } option. The image
+in the structure viewer can be saved as an EPS or PNG with the {\sl File
+$\Rightarrow$ Save As $\Rightarrow$ \ldots} submenu, which also allows the raw
+data to be saved as PDB format. The mapping between the structure and the
+sequence (How well and which parts of the structure relate to the sequence) can
+be viewed with the {\sl File $\Rightarrow$ View Mapping} menu option.
+
+\subsubsection{Using the Jmol Visualization Interface }
+
+Jmol has a comprehensive set of selection and visualization functions that are
+accessed from the Jmol popup menu (by right-clicking in the Jmol window or by
+clicking the Jmol logo). Molecule colour and rendering style can be manipulated,
+and distance measurements and molecular surfaces can be added to the view. It
+also has its own ``Rasmol\footnote{See \url{http://www.rasmol.org}}-like'' scripting
+language, which is described elsewhere\footnote{Jmol Wiki:
+\url{http://wiki.jmol.org/index.php/Scripting}
+
+Jmol Scripting reference:
+\url{http://www.stolaf.edu/academics/chemapps/jmol/docs/}}. Jalview utilises the
+scripting language to interact with Jmol and to store the state of a Jmol
+visualization within Jalview archives, in addition to the PDB data file
+originally loaded or retrieved by Jalview. To access the Jmol scripting
+environment directly, use the {\sl Jmol $\Rightarrow$ Console} menu option.
+
+If you would prefer to use Jmol to manage structure colours, then select the
+{\sl Colours $\Rightarrow$ Colour with Jmol} option. This will disable any
+automatic application of colour schemes when new structure data is added, or
+when associated alignment views are modified.
+
+\exercise{Viewing Structures in Jmol viewer}{\label{viewingstructex}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/examples/exampleFile.jar}.}
+\exstep{Right-click on the
+sequence ID label of {\sl FER1\_SPIOL} to open
+the context menu. Select {\sl 3D Structure}, this
+opens a Structure Chooser window, select { \sl 1A70} and click {\sl OK}.
+
+{\sl Note: the Structure Chooser interface
+provides a smart technique for selecting PDB structures by queryingthe meta-data
+of structures. Extra information can be including in this window by checking boxes
+in the ``Configure Displayed Columns'' tab}.
+% JBP Note: Bug JAL-1238 needs to be fixed ASAP
+}
+\exstep{By default the Jmol
+structure viewer opens in the Jalview desktop. Rotate the molecule by clicking
+and dragging in the structure viewing box.
+Zoom with the mouse scroll wheel. }
+\exstep{Roll the
+mouse cursor along the {\sl FER1\_SPIOL} sequence in the alignment.
+Note that if a residue in the sequence maps to one in the structure, a label
+will appear next to that residue in the structure viewer.}
+\exstep{Move the mouse over the structure. In the Jmol viewer, placing the mouse over a
+part of the structure will bring up a tool tip indicating the name and number of that residue.
+In the alignment window, the corresponding residue in the sequence is
+highlighted in black.}
+\exstep{Clicking the alpha carbon toggles the highlight and residue label on and
+off.
+Try this by clicking on a set of three or four adjacent residues so that the labels are persistent, then finding where they are in the sequence. }
+\exstep{In the structure viewer menu, select {\sl Colours $\Rightarrow$ Background
+Colour\ldots} and choose a suitable colour.
+Press {\sl OK} to apply this.}
+\exstep{Select {\sl File $\Rightarrow$ Save As $\Rightarrow$ PNG} and save the
+image. On your computer, view this with a suitable program. }
+\exstep{Select
+{\sl File $\Rightarrow$ View Mapping} from the structure viewer menu.
+A new window opens showing the residue by residue alignment between the sequence and the structure.}
+\exstep{Select {\sl File $\Rightarrow$ Save $\Rightarrow$ PDB file} and choose a new filename to save the PDB file.
+Once the file is saved, open the location in your file browser (or explorer
+window) and drag the PDB file that you just saved on to the Jalview desktop (or load it from the {\sl Jalview Desktop $\Rightarrow$ Input Alignment $\Rightarrow$ From File } menu).
+Verify that you can open and view the associated structure from the sequence ID
+context menu's {\sl 3D Structure } submenu in the new alignment window.}
+
+\exstep{In the Jmol window, right click on the structure window and explore the
+menu options. Try to change the style of molecular display - for example by
+using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {\sl n} is the number of residues selected), and then the {\sl Jmol $\Rightarrow$ Style $\Rightarrow$ Scheme $\Rightarrow$ Ball and Stick} command.}
+\exstep{In the alignment window, use the {\sl File $\Rightarrow$ Save As.. }
+function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
+Verify that the Jmol display is as it was when you just saved the file.}
+{\bf A video about this exercise is available on the Jalview website at at
+\url{http://www.jalview.org/training/Training-Videos}.}
+}
+
+\exercise{Setting Chimera as the default 3D Structure Viewer}{\label{viewingchimera}
+Jalview supports molecular structure
+visualization using both Jmol and Chimera 3D viewers. Jmol is the default
+viewer, however Chimera can be set up as the default choice from Preferences.
+
+\exstep{First, Chimera must be downloaded and installed on the computer.
+Chimera program is available on the UCSF web site \textsf{https://www.cgl.ucsf.edu/chimera/download.html}.}
+\exstep{In the desktop menu, select {\sl Tool $\Rightarrow$ Preferences}. In
+the ``{\sl
+Structure}'' tab set {\sl Default structure viewer} as {\sl
+Chimera}; then click {\sl OK}.}
+\exstep{Close the Jalview program, from the
+{\sl Desktop menu} select {\sl Jalview $\Rightarrow$ Quit Jalview}. Then reopen
+Jalview, Chimera should open as the default viewer.}
+{\sl Note: The Jmol structure viewer sits within the Jalview desktop. However
+the Chimera structure viewer sits outside the Jalview desktop and a Chimera
+view window sits inside the Jalview desktop.}
+
+{\bf A video about this exercise is available on the Jalview website at at
+\url{http://www.jalview.org/training/Training-Videos}.} }
+
+\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 superposition
+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 outputted 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}
+
+\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}
+
+\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 one of the PDB file associated with
+FER1\_MAIZE (eg. 3B2F). 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 {\sl 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
+(The easiest way to achieve this is to select column 121-132, and in the View
+menu selected ``All but selected region'' from the Hide options).
+
+{\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.}
+\exstep{The RMSD report can be
+viewed by right clicking the mouse on Jmol window, and select ``Show" and
+``Measurements". Which view do you think give the best 3D
+superposition, and why ?} }
+
+\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}}