+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 and annotation added to associated sequences.
+<p><em>Use RNAView for secondary structure</em> - if selected, the pyRNA RNAView service (<a href="https://github.com/fjossinet/PyRNA">https://github.com/fjossinet/PyRNA</a>) will be
+called to derive secondary structure information for RNA chains.
+<p><em>Add secondary structure annotation to alignment</em> - if selected, <a href="http://swift.cmbi.ru.nl/gv/dssp/">Jmol's implementation DSSP</a> will be used to add annotation to polypeptide chains in the structure.
+<p><em>Add Temperature Factor annotation to alignment</em> - if selected, values extracted from the Temperature Factor
+column for the backbone atoms in the PDB file will be extracted as annotation lines shown on the alignment.
+<p><em>Default structure viewer</em> - choose JMOL or CHIMERA for viewing 3D structures.
+<p><em>Path to Chimera program</em> - Optional, as Jalview will search standard installation paths for Windows, Linux or MacOS.
+If you have installed Chimera in a non-standard location, you can specify it here, by entering the full path to the Chimera executable program.
+Double-click this field to open a file chooser dialog.
+