-vbersion of the font to sequence labels.</p>
-<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster rendering
- of the alignment.</p>
-<p><em>Wrap Alignment</em> - Select whether to open new alignment windows in wrapped
- mode or not.</p>
-<p><em>Gap Symbol</em> - The default gap symbol may be set to either "-" or "."</p>
-<p><em>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>Sort by</em> - When the alignment is loaded in, it will can be sorted by
- Id or pairwise identity.</p>
-<p><em>Open file</em> - If this is selected then the default alignment file will
- be opened when Jalview is started. You can change the default file by clicking
- on file name and either typing in the file path or selecting it from the file
- chooser window. </p>
-<p><a name="connections"><strong>"Connections" Preferences tab</strong></a></p>
+version of the font to sequence labels.</p>
+<p><em>Smooth Font</em> - Toggles anti-aliasing on / off for faster
+rendering of the alignment.</p>
+<p><em>Gap Symbol</em> - The default gap symbol may be set to either
+"-" or "."</p>
+<p><em>Wrap Alignment</em> - Select whether to open new alignment
+windows in wrapped mode or not.</p>
+<p><em>Sort alignment by</em> - When the alignment is loaded in, it can
+be ordered as read (No sort), or sorted by Id or pairwise identity.</p>
+<p><em>Sort annotations by</em> - Annotations can be unsorted, sorted by the order of the related sequences in
+the alignment, or by label. Autocalculated annotations (e.g. Consensus) can be shown either last (below sequence
+annotations) or first (above sequence annotations). <em>Since Jalview 2.8.2.</em></p>
+<p><em>Open file</em> - If this is selected then the default
+alignment file will be opened when Jalview is started. You can change
+the default file by clicking on file name and either typing in the file
+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.
+
+<p><a name="connections"><strong>"Connections"
+Preferences tab</strong></a></p>