X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolBindingModel.java;fp=src%2Fjalview%2Fgui%2FPymolBindingModel.java;h=538b101b22015f22a4099e08915eab15924fd132;hb=2fb924ec0d110eb3ca6c3fb06efa27acd34b2750;hp=264a49cf564fe4fce0f887fdea775035efe5ccf2;hpb=8939be9b96e7e3f7e836037b972ddce75fa4a17e;p=jalview.git

diff --git a/src/jalview/gui/PymolBindingModel.java b/src/jalview/gui/PymolBindingModel.java
index 264a49c..538b101 100644
--- a/src/jalview/gui/PymolBindingModel.java
+++ b/src/jalview/gui/PymolBindingModel.java
@@ -6,6 +6,7 @@ import java.util.List;
 import java.util.Map;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.pymol.PymolCommands;
@@ -29,8 +30,6 @@ public class PymolBindingModel extends AAStructureBindingModel
 
   private PymolManager pymolManager;
 
-  private Thread pymolMonitor;
-
   /*
    * full paths to structure files opened in PyMOL
    */
@@ -139,16 +138,7 @@ public class PymolBindingModel extends AAStructureBindingModel
   public void closeViewer(boolean closePymol)
   {
     super.closeViewer(closePymol);
-    if (closePymol)
-    {
-      pymolManager.exitPymol();
-    }
     pymolManager = null;
-
-    if (pymolMonitor != null)
-    {
-      pymolMonitor.interrupt();
-    }
   }
 
   public boolean launchPymol()
@@ -158,16 +148,17 @@ public class PymolBindingModel extends AAStructureBindingModel
       return true;
     }
 
-    boolean launched = pymolManager.launchPymol();
-    if (launched)
+    Process pymol = pymolManager.launchPymol();
+    if (pymol != null)
     {
       // start listening for PyMOL selections - how??
+      startExternalViewerMonitor(pymol);
     }
     else
     {
-      System.err.println("Failed to launch PyMOL!");
+      Cache.log.error("Failed to launch PyMOL!");
     }
-    return launched;
+    return pymol != null;
   }
 
   public void openFile(PDBEntry pe)