X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FabovePID.html;h=8adacc9ab34d32083239fde7c76fa32525cc56a4;hb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;hp=570640ceb4812752b7c2a5463930b487eb481a8c;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index 570640c..8adacc9 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -35,10 +35,10 @@ td {
     <strong>Colouring above a percentage identity threshold</strong>
   </p>
   <p>Selecting this option causes the colour scheme to be applied to
-    only those residues that occur in that column more than a certain
-    percentage of the time. For instance selecting the threshold to be
-    100 will only colour those columns with 100 % identity. This
-    threshold option can be applied to the Zappo, Taylor, Hydrophobicity
-    and User colour schemes.</p>
+    only those residues that occur in that column at least a certain
+    percentage of the time. For instance, selecting the threshold to be
+    100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column.</p>
+   <p>The percentage calculation may include or exclude gaps in the column, depending on the option selected for the <a href="../calculations/consensus.html">consensus calculation</a>.</p>
+   <p>With a threshold of 0, colouring is unchanged.</p>
 </body>
 </html>
