--- trunk/src/selection/NameFinder.cpp	2013/12/05 18:19:26	1953
+++ trunk/src/selection/NameFinder.cpp	2015/01/09 19:06:35	2052
@@ -60,6 +60,8 @@ namespace OpenMD {
     nObjects_.push_back(info_->getNGlobalBends());
     nObjects_.push_back(info_->getNGlobalTorsions());
     nObjects_.push_back(info_->getNGlobalInversions());
+    nObjects_.push_back(info_->getNGlobalMolecules());
+    
     loadNames();
   }
 
@@ -93,6 +95,7 @@ namespace OpenMD {
            
       std::string molName = mol->getMoleculeName();
       TreeNode* molNode = createNode(root_, molName);
+      molNode->bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
         
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
 	std::string atomName = atom->getType();
@@ -110,13 +113,18 @@ namespace OpenMD {
 	molNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
 	rbNode->bs.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
 
-	//create nodes for atoms belong to this rigidbody
-	for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
-	  std::string rbAtomName = atom->getType();
-	  TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
+        // COMMENTED OUT because rigid bodies are IntegrableObjects
+        // (e.g. they are independently mobile, so selecting their
+        // member atoms will give some odd results if we are computing
+        // degrees of freedom elsewhere.
 
-	  rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
-	}
+	// //create nodes for atoms belong to this rigidbody
+	// for(atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
+	//   std::string rbAtomName = atom->getType();
+	//   TreeNode* rbAtomNode = createNode(rbNode, rbAtomName);
+
+	//   rbAtomNode->bs.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
+	// }
       }
 
       for (bond = mol->beginBond(bondIter); bond != NULL;