X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f3927df1af24bcd16df63d27ee8340fecdaeef42;hp=ffa8b9c60d67a6b5e188e08fcdf281b55f820e03;hb=67ba2560892f47d848754a97c7a809c7b8f8b3fb;hpb=8b55eedb9d76a8c65b80f756c4412bf029906bf7

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ffa8b9c..f3927df 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -423,9 +423,16 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
       ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
 
-      if (sg.cs != null && sg.cs.conservationApplied())
+      if (sg.cs != null)
       {
-        conservationMenuItem.setSelected(true);
+        if (sg.cs.conservationApplied())
+        {
+          conservationMenuItem.setSelected(true);
+        }
+        if (sg.cs.getThreshold() > 0)
+        {
+          abovePIDColour.setSelected(true);
+        }
       }
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());