+path or selecting it from the file chooser window.<br/><em>Note: The default example alignment is updated periodically to demonstrate new features in Jalview.</em></p>
+<p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
+<p><em>Alignment Colour</em> - The default colour scheme for a new alignment
+window. If the chosen option is "User Defined" then the last
+User Defined Colour loaded or saved via the User Defined Colours panel
+will be loaded.</p>
+ <p>
+ <em>Annotation Shading Default</em> - set the default minimum
+ and maximum colours used when <a
+ href="../colourSchemes/annotationColouring.html">Colour by
+ Annotation...</a> is selected from the alignment window's colours menu.
+ </p>
+<p><a name="structure"><strong>"Structure"
+Preferences tab</strong></a><em> added in Jalview 2.8.2</em></p>
+<p><em>Process secondary structure from PDB</em> - if selected, then structure information
+read from PDB will be processed to derive secondary structure annotation.
+<p><em>Use RNAView for secondary structure</em> - if selected, the RNAView service will be
+automatically called to derive secondary structure information.
+<p><em>Add secondary structure annotation to alignment</em> - if selected, PDB secondary structure
+annotation will be shown on the alignment when available.
+<p><em>Add Temperature Factor annotation to alignment</em> - if selected, PDB Temperature Factor
+annotation will be shown on the alignment when available.
+<p><em>Default structure viewer</em> - choose JMOL or CHIMERA for viewing 3D structures.
+