+\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 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
+pop-up 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.}}
+
+\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.}
+{\s 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.} }