From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 7 Nov 2016 12:23:40 +0000 (+0000)
Subject: JAL-2318 updated help text
X-Git-Tag: Release_2_10_1^2~8^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0350dbbb4ab895c253162de8a108984826b9cb22;p=jalview.git

JAL-2318 updated help text
---

diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index 614764b..ad47dae 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -36,9 +36,10 @@ td {
   </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>
+    percentage of the time. For instance, selecting the threshold to be
+    100 will only colour those columns with 100% identity.</p>
+   <p>To be coloured, a residue must match the consensus (most commonly occurring) residue for the column (or joint equal consensus).</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 (including non-consensus residues).</p>
 </body>
 </html>