From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 16 Nov 2016 14:35:07 +0000 (+0000)
Subject: JAL-2318 revised documentation for above PID Threshold
X-Git-Tag: Release_2_10_1~11^2^2~5^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=acd1da77644c3144730cc6e737f75dda036d02ca;p=jalview.git

JAL-2318 revised documentation for above PID Threshold
---

diff --git a/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index ad47dae..8adacc9 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -35,11 +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
+    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.</p>
-   <p>To be coloured, a residue must match the consensus (most commonly occurring) residue for the column (or joint equal consensus).</p>
+    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 (including non-consensus residues).</p>
+   <p>With a threshold of 0, colouring is unchanged.</p>
 </body>
 </html>