X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=518d27195e8eeec1aeca06e839eafcd8b71ff70b;hb=refs%2Fheads%2Fbug%2FJAL-3201groupClustal;hp=e57dd0166ac1b25d705648f8788dbb57f5319724;hpb=928017f8d5b3b70273b62ac83a9015fe2e785ff3;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index e57dd01..518d271 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -4971,21 +4971,22 @@ public class Jalview2XML
       }
     }
 
+    /*
+     * turn off 'alignment colour applies to all groups'
+     * while restoring global colour scheme
+     */
+    viewport.setColourAppliesToAllGroups(false);
     viewport.setGlobalColourScheme(cs);
     viewport.getResidueShading().setThreshold(pidThreshold,
             view.isIgnoreGapsinConsensus());
     viewport.getResidueShading()
             .setConsensus(viewport.getSequenceConsensusHash());
-    viewport.setColourAppliesToAllGroups(false);
-
     if (safeBoolean(view.isConservationSelected()) && cs != null)
     {
       viewport.getResidueShading()
               .setConservationInc(safeInt(view.getConsThreshold()));
     }
-
     af.changeColour(cs);
-
     viewport.setColourAppliesToAllGroups(true);
 
     viewport