From 157385223801346ee6800b5eb1e0cecc33b12701 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 17 Sep 2024 16:56:03 +0100
Subject: [PATCH] JAL-4418 documentation for ss annotation row preference and
 auto show (JAL-4425 JAL-4392)

---
 help/help/html/calculations/protssconsensus.html |    9 ++++++---
 help/help/html/features/preferences.html         |    7 ++++++-
 2 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/help/help/html/calculations/protssconsensus.html b/help/help/html/calculations/protssconsensus.html
index b98fb14..76619db 100755
--- a/help/help/html/calculations/protssconsensus.html
+++ b/help/help/html/calculations/protssconsensus.html
@@ -31,9 +31,12 @@
   secondary structure for an alignment of protein sequences where one or 
   more sequences have secondary structure annotation, in the same way
   as is done with the <a href="consensus.html">sequence consensus</a>.</p>
-  <p>Secondary structure consensus rows will only be shown if 
-  there are secondary structure data available for two or more 
-  sequences in the alignment.</p>
+  <p>To view secondary structure consensus rows, you should first 
+  enable the <em>Secondary Structure</em> checkbox in 
+  <a href="../features/preferences.html#secondarystructure">Jalview 
+  Preferences</a>. Once this option is checked, a consensus row will 
+  be shown if secondary structure annotations are available for 
+  two or more sequences in the alignment.</p>
   <p>
   <em>Sources of secondary structure data</em></p>
   <p>Sequences can have several different secondary structure 
diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 6708c57..943118e 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -95,7 +95,12 @@
     standard annotations <em>Conservation</em>, <em>Quality</em>, 
     <em>Occupancy</em> and <em>Consensus</em> for the alignment may 
     be shown or hidden by default using the checkboxes adjacent and
-    below.
+    below.<br/><em><a name="secondarystructure">Secondary Structure</a>
+    </em> consensus annotation rows can also be enabled 
+    (since version 2.11.4.0). When enabled, 
+    <a href="../calculations/protssconsensus.html">secondary 
+    structure consensus rows</a> only be shown if there are secondary 
+    structure annotions on the alignment.
   </p>
   <p>
     <em>Show group: Conservation and Consensus</em> controls the display
-- 
1.7.10.2