JAL-1333 more superposition debugging and deadlock avoidance

[jalview.git] / src / jalview / gui / ChimeraViewFrame.java

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 815957f..10082eb 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -586,7 +586,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     {
       command = "";
     }
-    jmb.evalStateCommand(command);
+    jmb.evalStateCommand(command, false);
     jmb.setFinishedInit(true);
   }
 
@@ -845,13 +845,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
       // do superposition if asked to
       if (alignAddedStructures)
       {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        new Thread(new Runnable()
         {
           public void run()
           {
             alignStructs_withAllAlignPanels();
           }
-        });
+        }).start();
         alignAddedStructures = false;
       }
       addingStructures = false;