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diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index e8c87e1..5100c6b 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -1,61 +1,96 @@
-Annotation Colouring
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+
+Annotation Colouring
+
- Annotation Colouring
-Jalview allows the columns of an alignment to be coloured using any
- numerical annotation rows added to that alignment.
-Select "Colour" → "..
- by Annotation" to bring up the Colour by Annotation settings window.
-
-
- - Select which annotation to base the colouring scheme on using the top left
- selection box.
- - If the "Use Original Colours" box is selected, the colouring
- scheme will use the colouring scheme present on the alignment before the Annotation
- Colour Settings window was displayed.
+
+ Annotation Colouring
+
+ Jalview allows the columns of an alignment to be coloured using
+ any numerical annotation rows added to that alignment.
+ Select "Colour"
+ → ".. by Annotation" to bring up the
+ Colour by Annotation settings window.
+
+
+
+
+
+ - Select which annotation to base the colouring scheme on using
+ the top left selection box.
If the Per-sequence
+ only tick box is not greyed out, then ticking it will limit the
+ available annotation rows to just those that are sequence associated
+ (e.g. T-COFFEE scores and protein disorder
+ predictions), which will colour each sequence according to its own
+ per-residue scores.
+ Per-sequence associated annotation colouring was introduced
+ in Jalview 2.8
+
+ - If the "Use Original Colours" box is selected, the
+ colouring scheme will use the colouring scheme present on the
+ alignment before the Annotation Colour Settings window was displayed.
+
Please Note: If no colour scheme was
+ applied previously, then the colours for lines and labels at each
+ position in the annotation row will be used, for secondary structure
+ symbols and graphs, this may be black by default, so your alignment
+ will be coloured black.
+
+ - Secondary structure annotation colouring
By
+ default, Jalview will employ the helix or sheet colours to shade
+ sequences and columns by available secondary structure annotation
+ tracks. In the case of RNA, each structure is processed to identify
+ distinct RNA helices and rendered in the same way as the RNA Helices shading scheme. Structure based sequence shading was added in Jalview 2.8.2
- The colour scheme can display a colour gradient from a colour
representing the minimum value in the selected annotation to a colour
representing the maximum value in the selected annotation. Use the
"Min Colour" and "Max Colour" to set the colour
gradient range.
- - Select whether to colour the alignment above or below an adjustable threshold
- with the selection box center left of the window.
+ - Select whether to colour the alignment above or below an
+ adjustable threshold with the selection box center left of the
+ window.
- Change the threshold value with the slider, or enter the
- exact value in the text box.
-
+ exact value in the text box.
- Select the "Threshold is Min/Max" checkbox to
assign colours using the thresholded range's minimum and maximum
values, otherwise the scale will be defined by the range of values in
the annotation row.
-
+
+ 
+