+<html>
+<head>
+<title>Sequence Feature Settings Dialog Box</title>
+</head>
+<body>
+<p><strong>Sequence Feature Settings Dialog Box</strong></p>
+<p>Select <strong>View→Feature Settings...</strong> menu entry in
+an alignment window to open the feature settings dialog box, which
+allows you to precisely control the presence and appearance of
+sequence features for the current alignment.</p>
+<center><img src="appFeatureSettings.gif" align="center"><br>Sequence Feature
+ Settings for the Jalview Application</img></center>
+<p>The top section of the dialog box lists all the sequence feature
+ groups, along with a tickbox for each that controls whether its
+ features are displayed. The table in the middle lists all the
+ features in the currently selected groups, along with their display
+ colour and whether they are currently being displayed (only the
+ ticked features and groups are displayed). <strong><em>You can change the
+ colour used for a feature in the associated alignment by clicking on
+ its colour box.</em></strong></p>
+<p><strong>Transparency and Feature Ordering</strong></p><p>
+ It is important to realise that sequence features are often not
+ distinct and often overlap (for example, a metal binding site
+ feature may be attached to one position along a stretch of sequence
+ marked with a secondary structure feature).</p>
+<p>The ordering of the sequence features in the dialog box list is the
+ order used by jalview for rendering sequence features. A feature at
+ the bottom of the list is rendered <em>below</em> a feature higher
+ up in the list.<br><em><strong>You can change the order of a feature
+ by dragging it up and down the list with the
+ mouse</strong></em>.</p>
+<p>
+ The <strong><em>transparency slider setting</em></strong> (currently only available
+ in the application version) controls the visibility of features
+ rendered below other features. Reducing the transparency will mean
+ that features at the top of the list can obscure features lower
+ down, and increasing it allows the user to 'see through' the upper
+ layers of a set of features.</p>
+<p><strong><em>You can save all features, with their current colours and visibility
+ in a Jalview format file. </em></strong>
+</p>
+</body>
+</html>