From: Jim Procter
Secondary structure consensus rows will only be shown if - there are secondary structure data available for two or more - sequences in the alignment.
+To view secondary structure consensus rows, you should first + enable the Secondary Structure checkbox in + Jalview + Preferences. 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.
Sources of secondary structure data
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 Conservation, Quality,
Occupancy and Consensus for the alignment may
be shown or hidden by default using the checkboxes adjacent and
- below.
+ below.
Secondary Structure
+ consensus annotation rows can also be enabled
+ (since version 2.11.4.0). When enabled,
+ secondary
+ structure consensus rows only be shown if there are secondary
+ structure annotions on the alignment.
Show group: Conservation and Consensus controls the display