diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/BaseToolPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/BaseToolPanel.java
index ce85b687e..667a1e0bd 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/BaseToolPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/BaseToolPanel.java
@@ -67,187 +67,232 @@
 import org.opensim.view.pub.OpenSimDB;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
+import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 public abstract class BaseToolPanel extends JPanel implements ActionListener, Observer {
-  
-   private FileFilter settingsFilter = null;
-
-   protected JButton loadSettingsButton = new JButton("Load...");
-   protected JButton saveSettingsButton = new JButton("Save...");
-   protected JButton applyButton = new JButton("Run");
-   protected JButton okButton = new JButton("Close");
-   //protected JButton cancelButton = new JButton("Cancel");
-   protected JButton helpButton = new JButton("Help");
-   protected Dialog ownerDialog = null;
-   protected boolean cleanupAfterExecuting = false;  // Keep track if cleaning up needs to be done on execution finish vs. dialog close
-
-   static String stripOuterTags(String nmsmFilename) {
-       try {
-           DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
-           DocumentBuilder builder = dbf.newDocumentBuilder();
-           FileInputStream fis = new FileInputStream(nmsmFilename);
-           
-           Document doc = builder.parse(new File(nmsmFilename));
-           InputSource is = new InputSource(fis);
-           // get the first element
-           Element element = doc.getDocumentElement();
-           
-           // get all child nodes
-           NodeList nodes = element.getChildNodes();
-           int lastDotLocation  = nmsmFilename.lastIndexOf(".");
-           String extension="";
-           if (lastDotLocation!=-1)
-                extension = nmsmFilename.substring(lastDotLocation);
-           String osimFile = nmsmFilename.replace(extension, "osim"+extension);
-           TransformerFactory transformerFactory = TransformerFactory.newInstance();
-           Transformer transformer = transformerFactory.newTransformer();
-           DOMSource source = new DOMSource(nodes.item(1));
-           FileWriter writer = new FileWriter(new File(osimFile));
-           StreamResult result = new StreamResult(writer);
-           transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
-           transformer.transform(source, result);
-           writer.flush();
-           writer.close();
-           
-           return osimFile;
-       } catch (ParserConfigurationException ex) {
-           Exceptions.printStackTrace(ex);
-       } catch (FileNotFoundException ex) {
-           Exceptions.printStackTrace(ex);
-       } catch (SAXException ex) {
-           Exceptions.printStackTrace(ex);
-       } catch (IOException ex) {
-           Exceptions.printStackTrace(ex);
-       } catch (TransformerConfigurationException ex) {
-           Exceptions.printStackTrace(ex);
-       } catch (TransformerException ex) {
-           Exceptions.printStackTrace(ex);
-       }
-       return "";
-    }
-
-   //------------------------------------------------------------------------
-   // Load/Save Settings Actions
-   //------------------------------------------------------------------------
-   class LoadSettingsAction extends AbstractAction {
-      public LoadSettingsAction() { super("Load Settings..."); }
-      public void actionPerformed(ActionEvent evt) {
-         String fileName = FileUtils.getInstance().browseForFilename(settingsFilter);
-         if(fileName!=null) loadSettings(fileName);
-      }
-   }
-   class SaveSettingsAction extends AbstractAction {
-      public SaveSettingsAction() { super("Save Settings..."); }
-      public void actionPerformed(ActionEvent evt) {
-         String fileName = FileUtils.getInstance().browseForFilenameToSave(settingsFilter, true, "", null);
-         if(fileName!=null) saveSettings(fileName, getToolXML());
-      }
-   }
-
-   public BaseToolPanel() {
-
-      loadSettingsButton.addActionListener(new LoadSettingsAction());
-      saveSettingsButton.addActionListener(new SaveSettingsAction());
-      applyButton.setEnabled(false);
-      OpenSimDB.getInstance().addObserver(this);
-   }
-
-   public void setSettingsFileDescription(String description) {
-      settingsFilter = FileUtils.getFileFilter(".xml", description);
-   }
-
-   //------------------------------------------------------------------------
-   // Override in derived classes
-   //------------------------------------------------------------------------
-   public void loadSettings(String fileName) {
-   
-   }
-   public void saveSettings(String fileName, String contents) {
-         String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
-         OpenSimObject.setSerializeAllDefaults(true);
-         //String toolFileContent = jointPersonalizationToolModel.getToolAsObject().dump();
-         BufferedWriter writer;
+
+    private FileFilter settingsFilter = null;
+
+    protected JButton loadSettingsButton = new JButton("Load...");
+    protected JButton saveSettingsButton = new JButton("Save...");
+    protected JButton applyButton = new JButton("Run");
+    protected JButton okButton = new JButton("Close");
+    //protected JButton cancelButton = new JButton("Cancel");
+    protected JButton helpButton = new JButton("Help");
+    protected Dialog ownerDialog = null;
+    protected boolean cleanupAfterExecuting = false;  // Keep track if cleaning up needs to be done on execution finish vs. dialog close
+
+    static String stripOuterTags(String nmsmFilename) {
         try {
-            writer = new BufferedWriter(new FileWriter(fullFilename));
-            writer.write("<NMSMPipelineDocument Version=\"1.0.0\">\n");
-            writer.write(contents);
-            writer.write("</NMSMPipelineDocument>");
+            DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
+            DocumentBuilder builder = dbf.newDocumentBuilder();
+            FileInputStream fis = new FileInputStream(nmsmFilename);
+
+            Document doc = builder.parse(new File(nmsmFilename));
+            InputSource is = new InputSource(fis);
+            // get the first element
+            Element element = doc.getDocumentElement();
+
+            // get all child nodes
+            NodeList nodes = element.getChildNodes();
+            int lastDotLocation = nmsmFilename.lastIndexOf(".");
+            String extension = "";
+            if (lastDotLocation != -1) {
+                extension = nmsmFilename.substring(lastDotLocation);
+            }
+            String osimFile = nmsmFilename.replace(extension, "osim" + extension);
+            TransformerFactory transformerFactory = TransformerFactory.newInstance();
+            Transformer transformer = transformerFactory.newTransformer();
+            DOMSource source = new DOMSource(nodes.item(1));
+            FileWriter writer = new FileWriter(new File(osimFile));
+            StreamResult result = new StreamResult(writer);
+            transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+            transformer.transform(source, result);
+            writer.flush();
             writer.close();
+
+            return osimFile;
+        } catch (ParserConfigurationException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (FileNotFoundException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (SAXException ex) {
+            Exceptions.printStackTrace(ex);
         } catch (IOException ex) {
             Exceptions.printStackTrace(ex);
+        } catch (TransformerConfigurationException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (TransformerException ex) {
+            Exceptions.printStackTrace(ex);
         }
-   }
-   public void pressedCancel() {}
-   public void pressedClose() {}
-   public void pressedApply() {}
-
-   //------------------------------------------------------------------------
-   // Dialog Operations
-   //------------------------------------------------------------------------
-   public JButton[] getDialogOptions() {
-      return new JButton[]{loadSettingsButton, saveSettingsButton, okButton, helpButton};
-   }
-
-   public void setOwner(Dialog window) { ownerDialog = window; }
-
-   public void updateApplyButton(boolean applyEnabled) {
-      applyButton.setEnabled(applyEnabled);
-   }
-
-   public void actionPerformed(ActionEvent evt) {
-      if(evt.getSource() == okButton) {
-         pressedClose();
-         ownerDialog.dispose();
-      } else if(evt.getSource() == applyButton) {
-         pressedApply();
-      }
-   }
-
-   //------------------------------------------------------------------------
-   // Helper function to create dialog
-   //------------------------------------------------------------------------
-   public static void openToolDialog(final BaseToolPanel panel, String name) {
-      DialogDescriptor dlg = new DialogDescriptor(panel, name, false, panel);
-      dlg.setOptions(panel.getDialogOptions());
-      Dialog dialog = DialogDisplayer.getDefault().createDialog(dlg);
-      panel.setOwner(dialog);
-      dialog.setVisible(true);      
-      dialog.requestFocus();      
-      //JFrame toolFrame = DialogUtils.createFrameForPanel(panel, name);
-      //DialogUtils.addButtons(toolFrame, (JButton[]) panel.getDialogOptions(), panel);
-      //panel.setOwner(toolFrame);
-      //toolFrame.setVisible(true);      
-      dialog.requestFocus();
-      dialog.addWindowListener(new WindowAdapter(){
-         public void windowClosed(WindowEvent e) {
-            super.windowClosed(e);
-            panel.cleanup();
-            OpenSimDB.getInstance().deleteObserver(panel);
-         }
-
-         public void windowClosing(WindowEvent e) {
-            super.windowClosing(e);
-            panel.cleanup();
-            OpenSimDB.getInstance().deleteObserver(panel);
-         }
-      });
-   }
-   // Relinquish C++ resources by setting references to them to null
-   public void cleanup()
-   {
-      // If tool is still running don't do any cleanup until the tool is done otherwise cleanup now
-      // by freeing C++ allocated resources.
-   }
-
-   public void close()
-   {
-       pressedCancel();
-       OpenSimDB.getInstance().deleteObserver(this);
-       ownerDialog.dispose();
-   }
-   
-   abstract String getToolXML();
+        return "";
+    }
+
+    static void replaceOpenSimDocumentTags(String pathName) {
+        try {
+            File inputFile = new File(pathName);
+            DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
+            DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
+            Document doc = dBuilder.parse(inputFile);
+            //doc.getDocumentElement().normalize();
+            NodeList nodeList = doc.getElementsByTagName("OpenSimDocument");
+            for (int i = 0; i < nodeList.getLength(); i++) {
+                Node oldNode = nodeList.item(i);
+                Element element = (Element) oldNode; 
+                if (element != null) { element.setAttribute("Version", "1.0.0"); }
+                doc.renameNode(oldNode, oldNode.getNamespaceURI(), "NMSMPipelineDocument");
+            }
+            TransformerFactory transformerFactory = TransformerFactory.newInstance();
+            Transformer transformer = transformerFactory.newTransformer();
+            transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+            DOMSource source = new DOMSource(doc);
+            StreamResult result = new StreamResult(inputFile);
+            transformer.transform(source, result);
+        } catch (ParserConfigurationException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (TransformerConfigurationException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (TransformerException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (SAXException ex) {
+            Exceptions.printStackTrace(ex);
+        } catch (IOException ex) {
+            Exceptions.printStackTrace(ex);
+        }
+    }
+    //------------------------------------------------------------------------
+    // Load/Save Settings Actions
+    //------------------------------------------------------------------------
+    // Override this method to change behavior of writing properties only if different from default
+    // Per issue #40 https://github.com/aymanhab/opensim-gui-rcnl/issues/40
+    void forceWritableProperties(OpenSimObject dObject) {
+    }
+
+    class LoadSettingsAction extends AbstractAction {
+
+        public LoadSettingsAction() {
+            super("Load Settings...");
+        }
+
+        public void actionPerformed(ActionEvent evt) {
+            String fileName = FileUtils.getInstance().browseForFilename(settingsFilter);
+            if (fileName != null) {
+                loadSettings(fileName);
+            }
+        }
+    }
+
+    class SaveSettingsAction extends AbstractAction {
+
+        public SaveSettingsAction() {
+            super("Save Settings...");
+        }
+
+        public void actionPerformed(ActionEvent evt) {
+            String fileName = FileUtils.getInstance().browseForFilenameToSave(settingsFilter, true, "", null);
+            if (fileName != null) {
+                saveSettings(fileName);
+            }
+        }
+    }
+
+    public BaseToolPanel() {
+
+        loadSettingsButton.addActionListener(new LoadSettingsAction());
+        saveSettingsButton.addActionListener(new SaveSettingsAction());
+        applyButton.setEnabled(false);
+        OpenSimDB.getInstance().addObserver(this);
+    }
+
+    public void setSettingsFileDescription(String description) {
+        settingsFilter = FileUtils.getFileFilter(".xml", description);
+    }
+
+    //------------------------------------------------------------------------
+    // Override in derived classes
+    //------------------------------------------------------------------------
+    public void loadSettings(String fileName) {
+
+    }
+
+    abstract void saveSettings(String fileName) ;
+
+    public void pressedCancel() {
+    }
+
+    public void pressedClose() {
+    }
+
+    public void pressedApply() {
+    }
+
+    //------------------------------------------------------------------------
+    // Dialog Operations
+    //------------------------------------------------------------------------
+    public JButton[] getDialogOptions() {
+        return new JButton[]{loadSettingsButton, saveSettingsButton, okButton, helpButton};
+    }
+
+    public void setOwner(Dialog window) {
+        ownerDialog = window;
+    }
+
+    public void updateApplyButton(boolean applyEnabled) {
+        applyButton.setEnabled(applyEnabled);
+    }
+
+    public void actionPerformed(ActionEvent evt) {
+        if (evt.getSource() == okButton) {
+            pressedClose();
+            ownerDialog.dispose();
+        } else if (evt.getSource() == applyButton) {
+            pressedApply();
+        }
+    }
+
+    //------------------------------------------------------------------------
+    // Helper function to create dialog
+    //------------------------------------------------------------------------
+    public static void openToolDialog(final BaseToolPanel panel, String name) {
+        DialogDescriptor dlg = new DialogDescriptor(panel, name, false, panel);
+        dlg.setOptions(panel.getDialogOptions());
+        Dialog dialog = DialogDisplayer.getDefault().createDialog(dlg);
+        panel.setOwner(dialog);
+        dialog.setVisible(true);
+        dialog.requestFocus();
+        //JFrame toolFrame = DialogUtils.createFrameForPanel(panel, name);
+        //DialogUtils.addButtons(toolFrame, (JButton[]) panel.getDialogOptions(), panel);
+        //panel.setOwner(toolFrame);
+        //toolFrame.setVisible(true);      
+        dialog.requestFocus();
+        dialog.addWindowListener(new WindowAdapter() {
+            public void windowClosed(WindowEvent e) {
+                super.windowClosed(e);
+                panel.cleanup();
+                OpenSimDB.getInstance().deleteObserver(panel);
+            }
+
+            public void windowClosing(WindowEvent e) {
+                super.windowClosing(e);
+                panel.cleanup();
+                OpenSimDB.getInstance().deleteObserver(panel);
+            }
+        });
+    }
+    // Relinquish C++ resources by setting references to them to null
+
+    public void cleanup() {
+        // If tool is still running don't do any cleanup until the tool is done otherwise cleanup now
+        // by freeing C++ allocated resources.
+    }
+
+    public void close() {
+        pressedCancel();
+        OpenSimDB.getInstance().deleteObserver(this);
+        ownerDialog.dispose();
+    }
+
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/Bundle.properties b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/Bundle.properties
index 312cad212..a8be4abab 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/Bundle.properties
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/Bundle.properties
@@ -181,12 +181,12 @@ TreatmentOptimizationJPanel.jRCNLTorqueControllerPanel.border.title=RCNL Torque
 TreatmentOptimizationJPanel.jLabel2.text=Surrogate model data directory
 TreatmentOptimizationJPanel.jCoordinatesListPanel3.border.title=Coordinate List
 TreatmentOptimizationJPanel.jSynergyControllerDetailsPanel1.border.title=RCNL Synergy Controller
-TreatmentOptimizationJPanel.jControllersPanel.TabConstraints.tabTitle=RCNL Controllers     
+TreatmentOptimizationJPanel.jControllersPanel.TabConstraints.tabTitle=RCNL Controllers
 TreatmentOptimizationJPanel.jLabel6.text=Tracked Quantities Dir:
 TreatmentOptimizationJPanel.jLabel8.text=Optimal Control Solver Settings File:
 TreatmentOptimizationJPanel.jLabel5.text=Results Dir:
 TreatmentOptimizationJPanel.outputPanel.border.title=Output
-TreatmentOptimizationJPanel.inputOutputPanel.TabConstraints.tabTitle=Settings     
+TreatmentOptimizationJPanel.inputOutputPanel.TabConstraints.tabTitle=Settings
 TreatmentOptimizationJPanel.jLabel4.text=Initial Guess Dir:
 TreatmentOptimizationJPanel.jLabel3.text=Osimx File:
 TreatmentOptimizationJPanel.currentModelFileTextField.toolTipText=Current Model in GUI
@@ -214,3 +214,5 @@ EditCostTermJPanel.jErrorCenterTextField.text=0.
 EditCosnstraintTermJPanel.jComponentTypeTextField.text=\ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ 
 EditCosnstraintTermJPanel.jMaxErrorTextField.text=0
 EditCosnstraintTermJPanel.jMinErrorTextField.text=0
+SelectQuantitiesFromListJPanel.jSelectAllCheckBox.toolTipText=select all shown quantities
+SelectQuantitiesFromListJPanel.jSelectAllCheckBox.text=select all shown
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/ComponentTableModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/ComponentTableModel.java
index a97790d14..941cf12d6 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/ComponentTableModel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/ComponentTableModel.java
@@ -117,5 +117,12 @@ void restrictNamesBy(String pattern){
       fireTableDataChanged();
         
     }
+    
+    void selectShown() {
+        for (int q=0; q<shownQuantities.size(); q++){
+            selected.set(shownQuantities.get(q), true);
+        }
+        fireTableDataChanged();
+    }
 
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/CoordinateTableModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/CoordinateTableModel.java
index 31bbd61ff..00427968d 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/CoordinateTableModel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/CoordinateTableModel.java
@@ -116,5 +116,12 @@ void restrictNamesBy(String pattern){
       fireTableDataChanged();
         
     }
+    
+    void selectShown() {
+        for (int q=0; q<shownQuantities.size(); q++){
+            selected.set(shownQuantities.get(q), true);
+        }
+        fireTableDataChanged();
+    }
 
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.form b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.form
index ffdffc54f..a19125c67 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.form
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.form
@@ -19,28 +19,23 @@
           <Group type="102" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Group type="103" groupAlignment="0" attributes="0">
-                  <Group type="102" attributes="0">
-                      <Group type="103" groupAlignment="1" attributes="0">
-                          <Component id="jComponentListPanel" alignment="0" pref="0" max="32767" attributes="0"/>
-                          <Group type="103" groupAlignment="0" attributes="0">
-                              <Component id="jEnabledCheckBox" min="-2" max="-2" attributes="0"/>
-                              <Group type="102" alignment="0" attributes="0">
-                                  <Component id="jLabel11" min="-2" max="-2" attributes="0"/>
-                                  <EmptySpace max="-2" attributes="0"/>
-                                  <Component id="jComponentTypeTextField" min="-2" pref="220" max="-2" attributes="0"/>
-                              </Group>
-                              <Group type="102" alignment="0" attributes="0">
-                                  <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
-                                  <EmptySpace max="-2" attributes="0"/>
-                                  <Component id="jMaxErrorTextField" min="-2" pref="150" max="-2" attributes="0"/>
-                                  <EmptySpace min="-2" pref="131" max="-2" attributes="0"/>
-                                  <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
-                                  <EmptySpace max="-2" attributes="0"/>
-                                  <Component id="jErrorCenterTextField" min="-2" pref="215" max="-2" attributes="0"/>
-                              </Group>
-                          </Group>
+                  <Component id="jComponentListPanel" alignment="0" pref="0" max="32767" attributes="0"/>
+                  <Group type="103" alignment="1" groupAlignment="0" attributes="0">
+                      <Component id="jEnabledCheckBox" min="-2" max="-2" attributes="0"/>
+                      <Group type="102" alignment="0" attributes="0">
+                          <Component id="jLabel11" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jComponentTypeTextField" min="-2" pref="220" max="-2" attributes="0"/>
+                      </Group>
+                      <Group type="102" alignment="0" attributes="0">
+                          <Component id="jLabel2" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jMaxErrorTextField" min="-2" pref="150" max="-2" attributes="0"/>
+                          <EmptySpace min="-2" pref="131" max="-2" attributes="0"/>
+                          <Component id="jLabel3" min="-2" max="-2" attributes="0"/>
+                          <EmptySpace max="-2" attributes="0"/>
+                          <Component id="jErrorCenterTextField" min="-2" pref="215" max="-2" attributes="0"/>
                       </Group>
-                      <EmptySpace max="-2" attributes="0"/>
                   </Group>
                   <Group type="102" attributes="0">
                       <Group type="103" groupAlignment="0" attributes="0">
@@ -55,9 +50,10 @@
                               <Component id="jCostTermNameTextField" min="-2" pref="460" max="-2" attributes="0"/>
                           </Group>
                       </Group>
-                      <EmptySpace max="32767" attributes="0"/>
+                      <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
                   </Group>
               </Group>
+              <EmptySpace max="-2" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -130,9 +126,9 @@
         <DimensionLayout dim="0">
           <Group type="103" groupAlignment="0" attributes="0">
               <Group type="102" alignment="0" attributes="0">
-                  <Component id="jScrollPane2" min="-2" pref="780" max="-2" attributes="0"/>
+                  <Component id="jScrollPane2" min="-2" pref="559" max="-2" attributes="0"/>
                   <EmptySpace max="-2" attributes="0"/>
-                  <Component id="editComonentListButton" min="-2" max="-2" attributes="0"/>
+                  <Component id="editComonentListButton" min="-2" pref="89" max="-2" attributes="0"/>
                   <EmptySpace max="32767" attributes="0"/>
               </Group>
           </Group>
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.java
index 2aaf915af..1dd90989e 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/EditCostTermJPanel.java
@@ -136,9 +136,9 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         jComponentListPanelLayout.setHorizontalGroup(
             jComponentListPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(jComponentListPanelLayout.createSequentialGroup()
-                .addComponent(jScrollPane2, javax.swing.GroupLayout.PREFERRED_SIZE, 780, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addComponent(jScrollPane2, javax.swing.GroupLayout.PREFERRED_SIZE, 559, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addComponent(editComonentListButton)
+                .addComponent(editComonentListButton, javax.swing.GroupLayout.PREFERRED_SIZE, 89, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         jComponentListPanelLayout.setVerticalGroup(
@@ -216,24 +216,21 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addGroup(layout.createSequentialGroup()
-                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
-                            .addComponent(jComponentListPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
-                            .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                                .addComponent(jEnabledCheckBox)
-                                .addGroup(layout.createSequentialGroup()
-                                    .addComponent(jLabel11)
-                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                    .addComponent(jComponentTypeTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 220, javax.swing.GroupLayout.PREFERRED_SIZE))
-                                .addGroup(layout.createSequentialGroup()
-                                    .addComponent(jLabel2)
-                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                    .addComponent(jMaxErrorTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                    .addGap(131, 131, 131)
-                                    .addComponent(jLabel3)
-                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                    .addComponent(jErrorCenterTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 215, javax.swing.GroupLayout.PREFERRED_SIZE))))
-                        .addContainerGap())
+                    .addComponent(jComponentListPanel, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
+                    .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                        .addComponent(jEnabledCheckBox)
+                        .addGroup(layout.createSequentialGroup()
+                            .addComponent(jLabel11)
+                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                            .addComponent(jComponentTypeTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 220, javax.swing.GroupLayout.PREFERRED_SIZE))
+                        .addGroup(layout.createSequentialGroup()
+                            .addComponent(jLabel2)
+                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                            .addComponent(jMaxErrorTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 150, javax.swing.GroupLayout.PREFERRED_SIZE)
+                            .addGap(131, 131, 131)
+                            .addComponent(jLabel3)
+                            .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
+                            .addComponent(jErrorCenterTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 215, javax.swing.GroupLayout.PREFERRED_SIZE)))
                     .addGroup(layout.createSequentialGroup()
                         .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                             .addGroup(layout.createSequentialGroup()
@@ -244,7 +241,8 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
                                 .addComponent(jLabel4)
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                                 .addComponent(jCostTermNameTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 460, javax.swing.GroupLayout.PREFERRED_SIZE)))
-                        .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))))
+                        .addGap(0, 0, Short.MAX_VALUE)))
+                .addContainerGap())
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/GCPPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/GCPPersonalizationJPanel.java
index d8193e138..daa538eaf 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/GCPPersonalizationJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/GCPPersonalizationJPanel.java
@@ -417,14 +417,9 @@ public void pressedCancel() {
         super.pressedCancel(); //To change body of generated methods, choose Tools | Templates.
     }
 
-    @Override
-    String getToolXML() {
-        return gcpPersonalizationToolModel.getToolAsObject().dump();
-    }
-
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        gcpPersonalizationToolModel = new GCPPersonalizationToolModel(model, fileName);
@@ -453,9 +448,8 @@ public void setSettingsFileDescription(String description) {
     }
 
     @Override
-    public void saveSettings(String fileName, String contents) {
+    public void saveSettings(String fileName) {
         
-        String adjustedContents = contents;
         // Before saving the settings, we need to make motion file and grf file relative to input_directory
         String inputDir = gcpPersonalizationToolModel.getDataDir();
         String saveInputMotion = gcpPersonalizationToolModel.getInputMotionFile();
@@ -469,10 +463,11 @@ public void saveSettings(String fileName, String contents) {
             String relativeGRFFile = FileUtils.makePathRelative(saveGRFfile, inputDir);
             if (relativeGRFFile != null)
                 gcpPersonalizationToolModel.setInputGRFFile(relativeGRFFile);
-            adjustedContents = getToolXML();
         }
         // Set proprties from relative path
-        super.saveSettings(fileName, adjustedContents); //To change body of generated methods, choose Tools | Templates.
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        gcpPersonalizationToolModel.getToolAsObject().print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
         // Restore from model
         gcpPersonalizationToolModel.setInputMotionFile(saveInputMotion);
         gcpPersonalizationToolModel.setInputGRFFile(saveGRFfile);
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationJPanel.java
index 65db1de2c..e0eaf57b3 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationJPanel.java
@@ -304,13 +304,17 @@ public void pressedCancel() {
     }
 
     @Override
-    public String getToolXML() {
-        return jointPersonalizationToolModel.getToolAsObject().dump();
+    public void saveSettings(String fileName) {
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = jointPersonalizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
     }
 
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        jointPersonalizationToolModel = new JointPersonalizationToolModel(model, fileName);
@@ -331,6 +335,24 @@ public void setSettingsFileDescription(String description) {
         super.setSettingsFileDescription(description); //To change body of generated methods, choose Tools | Templates.
     }
 
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        // For each JMPTask in tasklist, force write of parent_frame_transformation, child_frame_transformation
+        // dObject is an instance of JointModelPersonalizationTool
+        AbstractProperty ap = dObject.getPropertyByName("JMPTaskList");
+        PropertyObjectList olist = PropertyObjectList.getAs(ap);
+        for (int i=0; i< olist.size(); i++){
+            OpenSimObject ithTask = olist.getValue(i);
+            AbstractProperty apJnts = ithTask.getPropertyByName("JMPJointSet");
+            PropertyObjectList poJointList = PropertyObjectList.updAs(apJnts);
+             for (int j=0; j<poJointList.size(); j++){
+                poJointList.getValue(j).updPropertyByName("parent_frame_transformation").setValueIsDefault(false);
+                poJointList.getValue(j).updPropertyByName("child_frame_transformation").setValueIsDefault(false);
+             }
+        }
+    }
+
 
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JButton addJointTaskButton;
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationToolModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationToolModel.java
index 4e3d95d5b..c5d582e4f 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationToolModel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/JointPersonalizationToolModel.java
@@ -112,9 +112,7 @@ public void setToolAsObject(OpenSimObject toolAsObject) {
     public PropertyObjectList getJointTaskListAsObjectList() {
         AbstractProperty ap = toolAsObject.getPropertyByName("JMPTaskList");
         PropertyObjectList olist = PropertyObjectList.getAs(ap);
-        for (int i=0; i< olist.size(); i++){
-            OpenSimObject ithTask = olist.getValue(i);
-        }
+
         return olist;
     }
     
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MTPPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MTPPersonalizationJPanel.java
index f5073ed51..cf5d9d74f 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MTPPersonalizationJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MTPPersonalizationJPanel.java
@@ -633,7 +633,7 @@ public void pressedCancel() {
 
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        mtpPersonalizationToolModel = new MTPPersonalizationToolModel(model, fileName);
@@ -701,8 +701,20 @@ public void setSettingsFileDescription(String description) {
     // End of variables declaration//GEN-END:variables
 
     @Override
-    String getToolXML() {
-        return mtpPersonalizationToolModel.getToolAsObject().dump();
+    public void saveSettings(String fileName) {
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = mtpPersonalizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
     }
 
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        dObject.updPropertyByName("MuscleTendonLengthInitialization").setValueIsDefault(false);
+        dObject.updPropertyByName("MTPSynergyExtrapolation").setValueIsDefault(false);
+    }
+    
+    
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MuscleGroupTableModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MuscleGroupTableModel.java
index decad07f1..fd914f5c2 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MuscleGroupTableModel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/MuscleGroupTableModel.java
@@ -115,4 +115,12 @@ void restrictNamesBy(String pattern){
       fireTableDataChanged();
         
     }
+    void selectShown() {
+        for (int q=0; q<shownQuantities.size(); q++){
+           selected.set(shownQuantities.get(q), true);
+        }
+        fireTableDataChanged();
+    }
+    
+    
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/NCPPersonalizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/NCPPersonalizationJPanel.java
index f4132ad6b..4cd157a14 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/NCPPersonalizationJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/NCPPersonalizationJPanel.java
@@ -571,7 +571,7 @@ public void pressedCancel() {
 
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
        ncpPersonalizationToolModel = new NCPPersonalizationToolModel(model, fileName);
@@ -633,8 +633,18 @@ public void setSettingsFileDescription(String description) {
     // End of variables declaration//GEN-END:variables
 
     @Override
-    String getToolXML() {
-        return ncpPersonalizationToolModel.getToolAsObject().dump();
+    public void saveSettings(String fileName) {
+        String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = ncpPersonalizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
+    }
+
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        dObject.updPropertyByName("MuscleTendonLengthInitialization").setValueIsDefault(false);
     }
 
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.form b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.form
index c8a04edf0..85fbcf367 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.form
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.form
@@ -21,12 +21,10 @@
               <Component id="jPanel" max="32767" attributes="0"/>
               <EmptySpace max="-2" attributes="0"/>
           </Group>
-          <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
-              <Group type="102" alignment="0" attributes="0">
-                  <EmptySpace max="-2" attributes="0"/>
-                  <Component id="jScrollPane1" pref="335" max="32767" attributes="2"/>
-                  <EmptySpace max="-2" attributes="0"/>
-              </Group>
+          <Group type="102" alignment="0" attributes="0">
+              <EmptySpace min="-2" pref="9" max="-2" attributes="0"/>
+              <Component id="jSelectAllCheckBox" min="-2" max="-2" attributes="0"/>
+              <EmptySpace max="32767" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -35,14 +33,9 @@
           <Group type="102" alignment="0" attributes="0">
               <EmptySpace max="-2" attributes="0"/>
               <Component id="jPanel" min="-2" max="-2" attributes="0"/>
-              <EmptySpace pref="268" max="32767" attributes="0"/>
-          </Group>
-          <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
-              <Group type="102" alignment="0" attributes="0">
-                  <EmptySpace min="-2" pref="73" max="-2" attributes="0"/>
-                  <Component id="jScrollPane1" min="-2" pref="227" max="-2" attributes="0"/>
-                  <EmptySpace max="32767" attributes="0"/>
-              </Group>
+              <EmptySpace max="32767" attributes="0"/>
+              <Component id="jSelectAllCheckBox" min="-2" max="-2" attributes="0"/>
+              <EmptySpace min="-2" pref="12" max="-2" attributes="0"/>
           </Group>
       </Group>
     </DimensionLayout>
@@ -56,7 +49,10 @@
               <Group type="102" alignment="0" attributes="0">
                   <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
                   <EmptySpace max="-2" attributes="0"/>
-                  <Component id="FilterTextField" pref="243" max="32767" attributes="0"/>
+                  <Component id="FilterTextField" pref="388" max="32767" attributes="0"/>
+              </Group>
+              <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
+                  <Component id="jScrollPane1" alignment="1" pref="504" max="32767" attributes="0"/>
               </Group>
           </Group>
         </DimensionLayout>
@@ -67,7 +63,13 @@
                       <Component id="jLabel1" min="-2" max="-2" attributes="0"/>
                       <Component id="FilterTextField" min="-2" max="-2" attributes="0"/>
                   </Group>
-                  <EmptySpace min="0" pref="0" max="32767" attributes="0"/>
+                  <EmptySpace min="-2" pref="433" max="-2" attributes="0"/>
+              </Group>
+              <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
+                  <Group type="102" alignment="1" attributes="0">
+                      <EmptySpace min="0" pref="52" max="32767" attributes="0"/>
+                      <Component id="jScrollPane1" min="-2" pref="420" max="-2" attributes="0"/>
+                  </Group>
               </Group>
           </Group>
         </DimensionLayout>
@@ -87,24 +89,45 @@
             </Property>
           </Properties>
         </Component>
-      </SubComponents>
-    </Container>
-    <Container class="javax.swing.JScrollPane" name="jScrollPane1">
+        <Container class="javax.swing.JScrollPane" name="jScrollPane1">
 
-      <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
-      <SubComponents>
-        <Component class="javax.swing.JTable" name="jTable1">
-          <Properties>
-            <Property name="model" type="javax.swing.table.TableModel" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
-              <Connection code="tableModel" type="code"/>
-            </Property>
-            <Property name="autoResizeMode" type="int" value="3"/>
-          </Properties>
-          <AuxValues>
-            <AuxValue name="JavaCodeGenerator_CreateCodePost" type="java.lang.String" value="&#xa;"/>
-          </AuxValues>
-        </Component>
+          <Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
+          <SubComponents>
+            <Component class="javax.swing.JTable" name="jTable1">
+              <Properties>
+                <Property name="model" type="javax.swing.table.TableModel" editor="org.netbeans.modules.form.RADConnectionPropertyEditor">
+                  <Connection code="tableModel" type="code"/>
+                </Property>
+                <Property name="autoResizeMode" type="int" value="3"/>
+              </Properties>
+              <AuxValues>
+                <AuxValue name="JavaCodeGenerator_CreateCodePost" type="java.lang.String" value="&#xa;"/>
+              </AuxValues>
+            </Component>
+          </SubComponents>
+        </Container>
       </SubComponents>
     </Container>
+    <Component class="javax.swing.JCheckBox" name="jSelectAllCheckBox">
+      <Properties>
+        <Property name="text" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="org/opensim/rcnl/Bundle.properties" key="SelectQuantitiesFromListJPanel.jSelectAllCheckBox.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+        <Property name="toolTipText" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
+          <ResourceString bundle="org/opensim/rcnl/Bundle.properties" key="SelectQuantitiesFromListJPanel.jSelectAllCheckBox.toolTipText" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
+        </Property>
+        <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+          <Border info="org.netbeans.modules.form.compat2.border.EmptyBorderInfo">
+            <EmptyBorder bottom="0" left="0" right="0" top="0"/>
+          </Border>
+        </Property>
+        <Property name="margin" type="java.awt.Insets" editor="org.netbeans.beaninfo.editors.InsetsEditor">
+          <Insets value="[0, 0, 0, 0]"/>
+        </Property>
+      </Properties>
+      <Events>
+        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jSelectAllCheckBoxActionPerformed"/>
+      </Events>
+    </Component>
   </SubComponents>
 </Form>
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.java
index 0955b1b60..7c31a73e9 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/SelectQuantitiesFromListJPanel.java
@@ -6,6 +6,7 @@
 package org.opensim.rcnl;
 
 import java.util.ArrayList;
+import javax.swing.JCheckBox;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 import javax.swing.event.TableModelListener;
@@ -55,10 +56,16 @@ private void initComponents() {
         jScrollPane1 = new javax.swing.JScrollPane();
         jTable1 = new javax.swing.JTable();
 
+        jSelectAllCheckBox = new javax.swing.JCheckBox();
+
         org.openide.awt.Mnemonics.setLocalizedText(jLabel1, org.openide.util.NbBundle.getMessage(SelectQuantitiesFromListJPanel.class, "SelectQuantitiesFromListJPanel.jLabel1.text")); // NOI18N
 
         FilterTextField.setToolTipText(org.openide.util.NbBundle.getMessage(SelectQuantitiesFromListJPanel.class, "SelectQuantitiesFromListJPanel.FilterTextField.toolTipText")); // NOI18N
 
+        jTable1.setModel(tableModel);
+        jTable1.setAutoResizeMode(javax.swing.JTable.AUTO_RESIZE_LAST_COLUMN);
+        jScrollPane1.setViewportView(jTable1);
+
         javax.swing.GroupLayout jPanelLayout = new javax.swing.GroupLayout(jPanel);
         jPanel.setLayout(jPanelLayout);
         jPanelLayout.setHorizontalGroup(
@@ -66,7 +73,9 @@ private void initComponents() {
             .addGroup(jPanelLayout.createSequentialGroup()
                 .addComponent(jLabel1)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                .addComponent(FilterTextField, javax.swing.GroupLayout.DEFAULT_SIZE, 243, Short.MAX_VALUE))
+                .addComponent(FilterTextField, javax.swing.GroupLayout.DEFAULT_SIZE, 388, Short.MAX_VALUE))
+            .addGroup(jPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                .addComponent(jScrollPane1, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 504, Short.MAX_VALUE))
         );
         jPanelLayout.setVerticalGroup(
             jPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
@@ -74,12 +83,22 @@ private void initComponents() {
                 .addGroup(jPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addComponent(jLabel1)
                     .addComponent(FilterTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
-                .addGap(0, 0, Short.MAX_VALUE))
+                .addGap(433, 433, 433))
+            .addGroup(jPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+                .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanelLayout.createSequentialGroup()
+                    .addGap(0, 52, Short.MAX_VALUE)
+                    .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 420, javax.swing.GroupLayout.PREFERRED_SIZE)))
         );
 
-        jTable1.setModel(tableModel);
-        jTable1.setAutoResizeMode(javax.swing.JTable.AUTO_RESIZE_LAST_COLUMN);
-        jScrollPane1.setViewportView(jTable1);
+        org.openide.awt.Mnemonics.setLocalizedText(jSelectAllCheckBox, org.openide.util.NbBundle.getMessage(SelectQuantitiesFromListJPanel.class, "SelectQuantitiesFromListJPanel.jSelectAllCheckBox.text")); // NOI18N
+        jSelectAllCheckBox.setToolTipText(org.openide.util.NbBundle.getMessage(SelectQuantitiesFromListJPanel.class, "SelectQuantitiesFromListJPanel.jSelectAllCheckBox.toolTipText")); // NOI18N
+        jSelectAllCheckBox.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
+        jSelectAllCheckBox.setMargin(new java.awt.Insets(0, 0, 0, 0));
+        jSelectAllCheckBox.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                jSelectAllCheckBoxActionPerformed(evt);
+            }
+        });
 
         javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
         this.setLayout(layout);
@@ -89,32 +108,43 @@ private void initComponents() {
                 .addContainerGap()
                 .addComponent(jPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                 .addContainerGap())
-            .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                .addGroup(layout.createSequentialGroup()
-                    .addContainerGap()
-                    .addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 335, Short.MAX_VALUE)
-                    .addContainerGap()))
+            .addGroup(layout.createSequentialGroup()
+                .addGap(9, 9, 9)
+                .addComponent(jSelectAllCheckBox)
+                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(layout.createSequentialGroup()
                 .addContainerGap()
                 .addComponent(jPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                .addContainerGap(268, Short.MAX_VALUE))
-            .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                .addGroup(layout.createSequentialGroup()
-                    .addGap(73, 73, 73)
-                    .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 227, javax.swing.GroupLayout.PREFERRED_SIZE)
-                    .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
+                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                .addComponent(jSelectAllCheckBox)
+                .addGap(12, 12, 12))
         );
     }// </editor-fold>//GEN-END:initComponents
 
+    private void jSelectAllCheckBoxActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jSelectAllCheckBoxActionPerformed
+//        tableModel.selectShown(true);
+//        updateSelected();
+        ((JCheckBox)evt.getSource()).setSelected(false);
+        if (tableModel instanceof MuscleGroupTableModel)
+           ((MuscleGroupTableModel) tableModel).selectShown();
+        else if (tableModel instanceof CoordinateTableModel)
+           ((CoordinateTableModel) tableModel).selectShown();
+        else if (tableModel instanceof ComponentTableModel)
+           ((ComponentTableModel) tableModel).selectShown();
+
+        // TODO add your handling code here:
+    }//GEN-LAST:event_jSelectAllCheckBoxActionPerformed
+
 
     // Variables declaration - do not modify//GEN-BEGIN:variables
     private javax.swing.JFormattedTextField FilterTextField;
     private javax.swing.JLabel jLabel1;
     private javax.swing.JPanel jPanel;
     private javax.swing.JScrollPane jScrollPane1;
+    private javax.swing.JCheckBox jSelectAllCheckBox;
     private javax.swing.JTable jTable1;
     // End of variables declaration//GEN-END:variables
 
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.form b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.form
index 30f4fa0c5..3819a82c4 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.form
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.form
@@ -91,7 +91,7 @@
   <Layout>
     <DimensionLayout dim="0">
       <Group type="103" groupAlignment="0" attributes="0">
-          <Component id="jTabbedPane1" min="-2" pref="1061" max="-2" attributes="0"/>
+          <Component id="jTabbedPane1" alignment="0" max="32767" attributes="0"/>
       </Group>
     </DimensionLayout>
     <DimensionLayout dim="1">
@@ -111,7 +111,7 @@
         <Container class="javax.swing.JPanel" name="inputOutputPanel">
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
-              <JTabbedPaneConstraints tabName="Settings     ">
+              <JTabbedPaneConstraints tabName="Settings">
                 <Property name="tabTitle" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
                   <ResourceString bundle="org/opensim/rcnl/Bundle.properties" key="TreatmentOptimizationJPanel.inputOutputPanel.TabConstraints.tabTitle" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
                 </Property>
@@ -174,7 +174,7 @@
                               <Component id="jLabel5" min="-2" max="-2" attributes="0"/>
                               <EmptySpace max="-2" attributes="0"/>
                               <Component id="outputDirPath" max="32767" attributes="3"/>
-                              <EmptySpace min="-2" pref="13" max="-2" attributes="0"/>
+                              <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
                           </Group>
                       </Group>
                   </Group>
@@ -243,7 +243,7 @@
                                   </Group>
                               </Group>
                           </Group>
-                          <EmptySpace max="-2" attributes="0"/>
+                          <EmptySpace min="0" pref="0" max="-2" attributes="0"/>
                       </Group>
                   </Group>
                 </DimensionLayout>
@@ -297,6 +297,9 @@
                       <ResourceString bundle="org/opensim/rcnl/Bundle.properties" key="TreatmentOptimizationJPanel.jRadioButton2.text" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
                     </Property>
                   </Properties>
+                  <Events>
+                    <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jRadioButton2ActionPerformed"/>
+                  </Events>
                 </Component>
               </SubComponents>
             </Container>
@@ -327,17 +330,9 @@
                           </Group>
                           <EmptySpace max="-2" attributes="0"/>
                           <Group type="103" groupAlignment="0" attributes="0">
-                              <Group type="102" attributes="0">
-                                  <Group type="103" groupAlignment="0" attributes="0">
-                                      <Group type="102" attributes="0">
-                                          <Component id="osimxFilePath" pref="708" max="32767" attributes="3"/>
-                                          <EmptySpace min="-2" pref="3" max="-2" attributes="0"/>
-                                      </Group>
-                                      <Component id="trackedQuantitiesDirPath" max="32767" attributes="3"/>
-                                      <Component id="InitialGuessDirPath" alignment="0" max="32767" attributes="3"/>
-                                  </Group>
-                                  <EmptySpace max="-2" attributes="0"/>
-                              </Group>
+                              <Component id="osimxFilePath" linkSize="1" min="-2" pref="708" max="-2" attributes="3"/>
+                              <Component id="trackedQuantitiesDirPath" linkSize="1" min="-2" pref="711" max="-2" attributes="3"/>
+                              <Component id="InitialGuessDirPath" linkSize="1" alignment="0" min="-2" pref="711" max="-2" attributes="3"/>
                               <Component id="currentModelFileTextField" max="32767" attributes="1"/>
                           </Group>
                       </Group>
@@ -442,7 +437,7 @@
                 <DimensionLayout dim="0">
                   <Group type="103" groupAlignment="0" attributes="0">
                       <Group type="102" alignment="0" attributes="0">
-                          <Component id="jScrollPane2" pref="871" max="32767" attributes="0"/>
+                          <Component id="jScrollPane2" max="32767" attributes="0"/>
                           <EmptySpace max="-2" attributes="0"/>
                           <Component id="jButtonEditSettingsCoordinateList" min="-2" pref="158" max="-2" attributes="0"/>
                           <EmptySpace max="-2" attributes="0"/>
@@ -451,7 +446,7 @@
                 </DimensionLayout>
                 <DimensionLayout dim="1">
                   <Group type="103" groupAlignment="0" attributes="0">
-                      <Component id="jScrollPane2" alignment="0" pref="284" max="32767" attributes="0"/>
+                      <Component id="jScrollPane2" alignment="0" pref="424" max="32767" attributes="0"/>
                       <Group type="102" alignment="0" attributes="0">
                           <EmptySpace min="-2" pref="98" max="-2" attributes="0"/>
                           <Component id="jButtonEditSettingsCoordinateList" min="-2" max="-2" attributes="0"/>
@@ -499,7 +494,7 @@
         <Container class="javax.swing.JPanel" name="jControllersPanel">
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout" value="org.netbeans.modules.form.compat2.layouts.support.JTabbedPaneSupportLayout$JTabbedPaneConstraintsDescription">
-              <JTabbedPaneConstraints tabName="RCNL Controllers     ">
+              <JTabbedPaneConstraints tabName="RCNL Controllers">
                 <Property name="tabTitle" type="java.lang.String" editor="org.netbeans.modules.i18n.form.FormI18nStringEditor">
                   <ResourceString bundle="org/opensim/rcnl/Bundle.properties" key="TreatmentOptimizationJPanel.jControllersPanel.TabConstraints.tabTitle" replaceFormat="org.openide.util.NbBundle.getMessage({sourceFileName}.class, &quot;{key}&quot;)"/>
                 </Property>
@@ -524,7 +519,7 @@
               <Group type="103" groupAlignment="0" attributes="0">
                   <Group type="102" alignment="0" attributes="0">
                       <EmptySpace max="-2" attributes="0"/>
-                      <Component id="jSynergyControllerDetailsPanel1" min="-2" pref="533" max="-2" attributes="0"/>
+                      <Component id="jSynergyControllerDetailsPanel1" min="-2" max="-2" attributes="0"/>
                       <EmptySpace max="32767" attributes="0"/>
                       <Component id="jRCNLTorqueControllerPanel" min="-2" max="-2" attributes="0"/>
                       <EmptySpace max="-2" attributes="0"/>
@@ -578,7 +573,7 @@
                               <Component id="jLabel2" alignment="0" min="-2" max="-2" attributes="0"/>
                               <Component id="surrogateModelDirPath" alignment="0" min="-2" max="-2" attributes="0"/>
                           </Group>
-                          <EmptySpace max="32767" attributes="0"/>
+                          <EmptySpace pref="93" max="32767" attributes="0"/>
                       </Group>
                   </Group>
                 </DimensionLayout>
@@ -609,7 +604,7 @@
                     <DimensionLayout dim="0">
                       <Group type="103" groupAlignment="0" attributes="0">
                           <Group type="102" alignment="0" attributes="0">
-                              <Component id="jScrollPane7" pref="783" max="32767" attributes="0"/>
+                              <Component id="jScrollPane7" pref="777" max="32767" attributes="0"/>
                               <EmptySpace max="-2" attributes="0"/>
                               <Component id="jButtonEditSynergyCoordinateList" min="-2" pref="232" max="-2" attributes="0"/>
                           </Group>
@@ -691,7 +686,7 @@
               <Layout>
                 <DimensionLayout dim="0">
                   <Group type="103" groupAlignment="0" attributes="0">
-                      <EmptySpace min="0" pref="1035" max="32767" attributes="0"/>
+                      <EmptySpace min="0" pref="1029" max="32767" attributes="0"/>
                       <Group type="103" rootIndex="1" groupAlignment="0" attributes="0">
                           <Component id="JTorqueControllerDetailsPanel1" alignment="1" max="32767" attributes="0"/>
                       </Group>
@@ -827,7 +822,7 @@
                 <DimensionLayout dim="0">
                   <Group type="103" groupAlignment="0" attributes="0">
                       <Group type="102" alignment="0" attributes="0">
-                          <Component id="jScrollPane6" pref="861" max="32767" attributes="0"/>
+                          <Component id="jScrollPane6" pref="855" max="32767" attributes="0"/>
                           <EmptySpace min="-2" max="-2" attributes="0"/>
                           <Group type="103" groupAlignment="0" max="-2" attributes="0">
                               <Component id="deleteCostTermButton" alignment="0" max="32767" attributes="0"/>
@@ -847,7 +842,7 @@
                           <Component id="editCostTermButton" min="-2" max="-2" attributes="0"/>
                           <EmptySpace min="-2" pref="14" max="-2" attributes="0"/>
                           <Component id="deleteCostTermButton" min="-2" max="-2" attributes="0"/>
-                          <EmptySpace pref="180" max="32767" attributes="0"/>
+                          <EmptySpace pref="346" max="32767" attributes="0"/>
                       </Group>
                   </Group>
                 </DimensionLayout>
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.java
index b23aa4023..29bd80e13 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationJPanel.java
@@ -6,6 +6,8 @@
 package org.opensim.rcnl;
 
 import java.awt.Dialog;
+import java.io.BufferedWriter;
+import java.io.FileWriter;
 import java.io.IOException;
 import java.util.Observable;
 import java.util.Observer;
@@ -13,12 +15,15 @@
 import javax.swing.ListSelectionModel;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
+import javax.swing.filechooser.FileFilter;
 import org.openide.DialogDescriptor;
 import org.openide.DialogDisplayer;
+import org.openide.util.Exceptions;
 import org.opensim.modeling.AbstractProperty;
 import org.opensim.modeling.Model;
 import org.opensim.modeling.OpenSimObject;
 import org.opensim.modeling.PropertyObjectList;
+import org.opensim.utils.FileUtils;
 import org.opensim.view.pub.OpenSimDB;
 
 /**
@@ -222,11 +227,11 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
                     .addComponent(jLabel5)
                     .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                     .addComponent(outputDirPath, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
-                    .addGap(13, 13, 13)))
+                    .addGap(0, 0, 0)))
         );
         outputPanelLayout.setVerticalGroup(
             outputPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addGap(0, 69, Short.MAX_VALUE)
+            .addGap(0, 95, Short.MAX_VALUE)
             .addGroup(outputPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                 .addGroup(outputPanelLayout.createSequentialGroup()
                     .addContainerGap()
@@ -252,6 +257,11 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
 
         buttonGroup1.add(jRadioButton2);
         org.openide.awt.Mnemonics.setLocalizedText(jRadioButton2, org.openide.util.NbBundle.getMessage(TreatmentOptimizationJPanel.class, "TreatmentOptimizationJPanel.jRadioButton2.text")); // NOI18N
+        jRadioButton2.addActionListener(new java.awt.event.ActionListener() {
+            public void actionPerformed(java.awt.event.ActionEvent evt) {
+                jRadioButton2ActionPerformed(evt);
+            }
+        });
 
         javax.swing.GroupLayout jSolverSettingsPanelLayout = new javax.swing.GroupLayout(jSolverSettingsPanel);
         jSolverSettingsPanel.setLayout(jSolverSettingsPanelLayout);
@@ -272,7 +282,7 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
                                 .addComponent(jRadioButton1)
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                 .addComponent(solverSettingsFilePath, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))))
-                .addContainerGap())
+                .addGap(0, 0, 0))
         );
         jSolverSettingsPanelLayout.setVerticalGroup(
             jSolverSettingsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
@@ -333,16 +343,14 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
                     .addComponent(jLabel6))
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addGroup(inputModelPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                    .addGroup(inputModelPanelLayout.createSequentialGroup()
-                        .addGroup(inputModelPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                            .addGroup(inputModelPanelLayout.createSequentialGroup()
-                                .addComponent(osimxFilePath, javax.swing.GroupLayout.DEFAULT_SIZE, 708, Short.MAX_VALUE)
-                                .addGap(3, 3, 3))
-                            .addComponent(trackedQuantitiesDirPath, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
-                            .addComponent(InitialGuessDirPath, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
-                        .addContainerGap())
+                    .addComponent(osimxFilePath, javax.swing.GroupLayout.PREFERRED_SIZE, 708, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(trackedQuantitiesDirPath, javax.swing.GroupLayout.PREFERRED_SIZE, 711, javax.swing.GroupLayout.PREFERRED_SIZE)
+                    .addComponent(InitialGuessDirPath, javax.swing.GroupLayout.PREFERRED_SIZE, 711, javax.swing.GroupLayout.PREFERRED_SIZE)
                     .addComponent(currentModelFileTextField, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)))
         );
+
+        inputModelPanelLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {InitialGuessDirPath, osimxFilePath, trackedQuantitiesDirPath});
+
         inputModelPanelLayout.setVerticalGroup(
             inputModelPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(inputModelPanelLayout.createSequentialGroup()
@@ -386,14 +394,14 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         jCoordinatesListPanel2Layout.setHorizontalGroup(
             jCoordinatesListPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(jCoordinatesListPanel2Layout.createSequentialGroup()
-                .addComponent(jScrollPane2, javax.swing.GroupLayout.DEFAULT_SIZE, 871, Short.MAX_VALUE)
+                .addComponent(jScrollPane2)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addComponent(jButtonEditSettingsCoordinateList, javax.swing.GroupLayout.PREFERRED_SIZE, 158, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addContainerGap())
         );
         jCoordinatesListPanel2Layout.setVerticalGroup(
             jCoordinatesListPanel2Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addComponent(jScrollPane2, javax.swing.GroupLayout.DEFAULT_SIZE, 284, Short.MAX_VALUE)
+            .addComponent(jScrollPane2, javax.swing.GroupLayout.DEFAULT_SIZE, 424, Short.MAX_VALUE)
             .addGroup(jCoordinatesListPanel2Layout.createSequentialGroup()
                 .addGap(98, 98, 98)
                 .addComponent(jButtonEditSettingsCoordinateList)
@@ -459,7 +467,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         jCoordinatesListPanel3Layout.setHorizontalGroup(
             jCoordinatesListPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(jCoordinatesListPanel3Layout.createSequentialGroup()
-                .addComponent(jScrollPane7, javax.swing.GroupLayout.DEFAULT_SIZE, 783, Short.MAX_VALUE)
+                .addComponent(jScrollPane7, javax.swing.GroupLayout.DEFAULT_SIZE, 777, Short.MAX_VALUE)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addComponent(jButtonEditSynergyCoordinateList, javax.swing.GroupLayout.PREFERRED_SIZE, 232, javax.swing.GroupLayout.PREFERRED_SIZE))
         );
@@ -511,7 +519,7 @@ public void stateChanged(javax.swing.event.ChangeEvent evt) {
                 .addGroup(jSynergyControllerDetailsPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                     .addComponent(jLabel2)
                     .addComponent(surrogateModelDirPath, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
-                .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                .addContainerGap(93, Short.MAX_VALUE))
         );
 
         jRCNLTorqueControllerPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(org.openide.util.NbBundle.getMessage(TreatmentOptimizationJPanel.class, "TreatmentOptimizationJPanel.jRCNLTorqueControllerPanel.border.title"))); // NOI18N
@@ -555,13 +563,13 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         jRCNLTorqueControllerPanel.setLayout(jRCNLTorqueControllerPanelLayout);
         jRCNLTorqueControllerPanelLayout.setHorizontalGroup(
             jRCNLTorqueControllerPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addGap(0, 1035, Short.MAX_VALUE)
+            .addGap(0, 1029, Short.MAX_VALUE)
             .addGroup(jRCNLTorqueControllerPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                 .addComponent(JTorqueControllerDetailsPanel1, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         jRCNLTorqueControllerPanelLayout.setVerticalGroup(
             jRCNLTorqueControllerPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addGap(0, 347, Short.MAX_VALUE)
+            .addGap(0, 383, Short.MAX_VALUE)
             .addGroup(jRCNLTorqueControllerPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                 .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jRCNLTorqueControllerPanelLayout.createSequentialGroup()
                     .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
@@ -584,7 +592,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
             jControllersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(jControllersPanelLayout.createSequentialGroup()
                 .addContainerGap()
-                .addComponent(jSynergyControllerDetailsPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, 533, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addComponent(jSynergyControllerDetailsPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                 .addComponent(jRCNLTorqueControllerPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                 .addContainerGap())
@@ -625,7 +633,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         jCostTermsPanelLayout.setHorizontalGroup(
             jCostTermsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
             .addGroup(jCostTermsPanelLayout.createSequentialGroup()
-                .addComponent(jScrollPane6, javax.swing.GroupLayout.DEFAULT_SIZE, 861, Short.MAX_VALUE)
+                .addComponent(jScrollPane6, javax.swing.GroupLayout.DEFAULT_SIZE, 855, Short.MAX_VALUE)
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addGroup(jCostTermsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
                     .addComponent(deleteCostTermButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
@@ -642,7 +650,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
                 .addComponent(editCostTermButton)
                 .addGap(14, 14, 14)
                 .addComponent(deleteCostTermButton)
-                .addContainerGap(180, Short.MAX_VALUE))
+                .addContainerGap(346, Short.MAX_VALUE))
         );
 
         jConstTermsPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(org.openide.util.NbBundle.getMessage(TreatmentOptimizationJPanel.class, "TreatmentOptimizationJPanel.jConstTermsPanel.border.title"))); // NOI18N
@@ -721,7 +729,7 @@ public void actionPerformed(java.awt.event.ActionEvent evt) {
         this.setLayout(layout);
         layout.setHorizontalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-            .addComponent(jTabbedPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 1061, javax.swing.GroupLayout.PREFERRED_SIZE)
+            .addComponent(jTabbedPane1)
         );
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
@@ -753,6 +761,22 @@ private void trackedQuantitiesDirPathStateChanged(javax.swing.event.ChangeEvent
 
     private void deleteConstraintTermButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_deleteConstraintTermButtonActionPerformed
         // TODO add your handling code here:
+        int[] sels = jConstraintTermList.getSelectedIndices();
+        PropertyObjectList poList = treatmentOptimizationToolModel.getConstraintTermListAsObjectList();
+        Vector<Integer> tasksToDelete = new Vector<Integer>();
+        for (int i=0; i<sels.length; i++){
+            //OpenSimObject selectedJointTask = (OpenSimObject)jJointPersonalizationList.get(sels[i]);
+            tasksToDelete.add(sels[i]);
+        }
+        //jJointPersonalizationList
+        // Delete items from jmpJointListModel in reverse order
+        for (int r=tasksToDelete.size(); r >0; r-- ){
+            constraintTermListModel.remove(tasksToDelete.get(r-1));
+            poList.removeValueAtIndex(tasksToDelete.get(r-1));
+        }
+        // Recreate list model to cleanup
+        constraintTermListModel = new ConstraintTermListModel(poList);
+        jConstraintTermList.setModel(constraintTermListModel);
     }//GEN-LAST:event_deleteConstraintTermButtonActionPerformed
 
     private void editConstraintTermButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_editConstraintTermButtonActionPerformed
@@ -925,6 +949,20 @@ private void jOptimizeSynVecCheckBoxActionPerformed(java.awt.event.ActionEvent e
         treatmentOptimizationToolModel.setOptimizeSynergyVector(jOptimizeSynVecCheckBox.isSelected());
     }//GEN-LAST:event_jOptimizeSynVecCheckBoxActionPerformed
 
+    private void jRadioButton2ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jRadioButton2ActionPerformed
+        // TODO add your handling code here:
+        OpenSimObject settingsAsObject = OpenSimObject.newInstanceOfType("OptimalControlSolverSettings");
+        OpenSimObject.setSerializeAllDefaults(true);
+        FileFilter settingsFilter = FileUtils.getFileFilter(".xml", "Optimal Control Solver Settings");
+        String fileName = FileUtils.getInstance().browseForFilenameToSave(settingsFilter, true, "", null);
+        if(fileName!=null) {
+            String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+            settingsAsObject.print(fullFilename);
+            treatmentOptimizationToolModel.setOCSettingsFile(fullFilename);
+        }
+        OpenSimObject.setSerializeAllDefaults(false);
+    }//GEN-LAST:event_jRadioButton2ActionPerformed
+
     @Override
     public void update(Observable o, Object o1) {
         throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
@@ -935,14 +973,9 @@ public void pressedCancel() {
         super.pressedCancel(); //To change body of generated methods, choose Tools | Templates.
     }
 
-    @Override
-    public String getToolXML() {
-        return treatmentOptimizationToolModel.getToolAsObject().dump();
-    }
-
     @Override
     public void loadSettings(String nmsmFilename) {
-        String fileName = super.stripOuterTags(nmsmFilename);
+        String fileName = BaseToolPanel.stripOuterTags(nmsmFilename);
         Model model = OpenSimDB.getInstance().getCurrentModel();
         
        //if(model==null) throw new IOException("JointPersonalizationJPanel got null model");
@@ -963,6 +996,9 @@ public void loadSettings(String nmsmFilename) {
        
        // Cost+Constraints
        costTermListModel = new CostTermListModel(treatmentOptimizationToolModel.getCostTermListAsObjectList());
+       jCostTermList.setModel(costTermListModel);
+       constraintTermListModel = new ConstraintTermListModel(treatmentOptimizationToolModel.getConstraintTermListAsObjectList());
+       jConstraintTermList.setModel(constraintTermListModel);
     }  
 
     @Override
@@ -1058,5 +1094,25 @@ public void valueChanged(ListSelectionEvent lse) {
             deleteConstraintTermButton.setEnabled(sels.length>=1);
         }
     }
+    @Override
+    public void saveSettings(String fileName) {
+         String fullFilename = FileUtils.addExtensionIfNeeded(fileName, ".xml");
+        OpenSimObject obj = treatmentOptimizationToolModel.getToolAsObject();
+        forceWritableProperties(obj);
+        obj.print(fullFilename);
+        replaceOpenSimDocumentTags(fullFilename);
+   }
+
+    @Override
+    void forceWritableProperties(OpenSimObject dObject) {
+        super.forceWritableProperties(dObject); //To change body of generated methods, choose Tools | Templates.
+        AbstractProperty ap = dObject.getPropertyByName("RCNLCostTermSet");
+        PropertyObjectList olist = PropertyObjectList.getAs(ap);
+        for (int i=0; i< olist.size(); i++){
+            OpenSimObject costterm = olist.getValue(i);
+            costterm.updPropertyByName("max_allowable_error").setValueIsDefault(false);
+        }
+    }
 
+    
 }
diff --git a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationToolModel.java b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationToolModel.java
index 2aa38d65c..b71cf05aa 100644
--- a/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationToolModel.java
+++ b/Gui/opensim/rice_cnl/src/org/opensim/rcnl/TreatmentOptimizationToolModel.java
@@ -113,7 +113,9 @@ private void connectPropertiesToClassMembers() {
         propOCSettingsFileString = PropertyStringList.getAs(propOCSettingsFile);
         AbstractProperty propStatesCoordinateList = toolAsObject.updPropertyByName("states_coordinate_list");        
         propStatesCoordinateListString = PropertyStringList.getAs(propStatesCoordinateList);
-        propRCNLSynergyControllerObject = toolAsObject.updPropertyByName("RCNLSynergyController").getValueAsObject(); 
+        boolean defaultProp = toolAsObject.getPropertyByName("RCNLSynergyController").getValueIsDefault();
+        propRCNLSynergyControllerObject = toolAsObject.updPropertyByName("RCNLSynergyController").getValueAsObject();
+        defaultProp = toolAsObject.getPropertyByName("RCNLSynergyController").getValueIsDefault();
         // Convert to ObjectProperty so we can dig deeper
         propOptimizeForSynvergyVectorBool = PropertyBoolList.getAs(propRCNLSynergyControllerObject.updPropertyByName("optimize_synergy_vectors"));
         propSurrogateModelDirString = PropertyStringList.getAs(propRCNLSynergyControllerObject.updPropertyByName("surrogate_model_data_directory"));