X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FannotationColouring.html;h=ed0ab3feaf095959753e40e983a0c02b2df56755;hb=3a5e7da51af0166273109f98bdf942e733105233;hp=30b63960b6ab3cea715744183421e42447f7e867;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html
index 30b6396..ed0ab3f 100755
--- a/help/html/colourSchemes/annotationColouring.html
+++ b/help/html/colourSchemes/annotationColouring.html
@@ -39,14 +39,17 @@
   </div>
   <ul>
     <li>Select which annotation to base the colouring scheme on
-      using the top left selection box.<br />If the <strong>Per-sequence
-        only</strong> 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 <a
-      href="../webServices/proteinDisorder.html"
-    >protein disorder predictions</a>), which will colour each sequence
-      according to its own per-residue scores.<br /> <em>Per-sequence
-        associated annotation colouring was introduced in Jalview 2.8</em>
+      using the top left selection box. Sequence associated alignment
+      annotation are shown with the seuqence's name appended.<br />If
+      the <strong>Per-sequence only</strong> tick box is not greyed out,
+      then ticking it will limit the list of available annotation rows
+      to just the labels for those that are sequence associated.
+      Annotation rows on each sequence with the same label (e.g.
+      T-COFFEE scores and <a href="../webServices/proteinDisorder.html">protein
+        disorder predictions</a>) will then be used to colour its
+      corresponding positions in the alignment.<br /> <em>Per-sequence
+        associated annotation colouring is currently only available in
+        the Desktop.</em>
     </li>
     <li>If the &quot;Use Original Colours&quot; box is selected,
       the colouring scheme will use the colouring scheme present on the