X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ef8767128db8fca4832a3fac584f3c66a88b25bd;hb=0b0b3d3687479204da2d199042c7bc90f3a6fd43;hp=676d3cf048bc246fd602a2b59b753913bead4883;hpb=106a3890f956e2aa7780b2985f4326655912a558;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 676d3cf..ef87671 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1603,10 +1603,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       System.exit(0);
     }
-    else
+
+    viewport = null;
+    if (alignPanel != null && alignPanel.overviewPanel != null)
     {
+      alignPanel.overviewPanel.dispose();
     }
-    viewport = null;
     alignPanel = null;
     this.dispose();
   }
@@ -4147,7 +4149,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // register the association(s) and quit, don't create any windows.
       if (StructureSelectionManager.getStructureSelectionManager(applet)
-              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+              .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
       {
         System.err.println("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");