X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=6e3024d7f0df99ad535d96128c74642e47beb042;hb=c0aaf84826ff25d510846bd1099e10809c4df711;hp=235deda5d217a3e2a5144cda02c964ba8f9e74f9;hpb=616890cfe05fa81f90835e426ff7b6207f05b64b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 235deda..6e3024d 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1076,10 +1076,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 .lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      success = new Jalview2XML().SaveAlignment(this, file, shortName);
+      /*
+       * First save any linked Chimera session.
+       */
+      Desktop.instance.saveChimeraSessions(file);
+
+      success = new Jalview2XML().saveAlignment(this, file, shortName);
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.successfully_saved_to_file_in_format", new String[]
+              "label.successfully_saved_to_file_in_format", new Object[]
               { fileName, format }));
 
     }