Index: src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def
===================================================================
--- src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -26,5 +26,4 @@
 (STLVectorValidator< std::vector<atomId_t> >(AtomIdValidator()))
 
-
 #define statetypes (atomids_t)
 #define statereferences (undoatomids)
Index: src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp
===================================================================
--- src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -53,18 +53,49 @@
 /** =========== define the function ====================== */
 ActionState::ptr SelectionMoleculeByIdAction::performCall() {
-  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex.get()));
-  if (mol != NULL) {
-    if (!World::getInstance().isSelected(mol)) {
-      LOG(1, "Selecting molecule " << mol->name);
-      World::getInstance().selectAllMolecules(MoleculeById(params.molindex.get()));
-      LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
-      return ActionState::ptr(new SelectionMoleculeByIdState(params));
+
+  enum Sucess {
+    NoStatus,
+    AllMoleculesUnselected,
+    MoleculesSelected,
+    MoleculeMissing
+  } status = NoStatus;
+
+  const molids_t molids = params.molids.get();
+  molids_t undomolids;
+  undomolids.reserve(molids.size());
+  for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    if (Walker != NULL) {
+      if (!World::getInstance().isSelected(Walker)) {
+        LOG(1, "Selecting mol " << Walker->getName());
+        World::getInstance().selectMolecule(Walker);
+        undomolids.push_back(*iter);
+        if (status < MoleculeMissing)
+          status = MoleculesSelected;
+      } else {
+        if (status == NoStatus)
+          status = AllMoleculesUnselected;
+      }
     } else {
-      return Action::success;
+      status = MoleculeMissing;
     }
-  } else {
-    STATUS("Cannot find molecule by given index "+toString(params.molindex.get())+".");
-    return Action::failure;
   }
+  LOG(0, World::getInstance().countSelectedMolecules() << " mols selected.");
+
+  switch (status) {
+    case MoleculeMissing:
+      STATUS("Cannot find all mols with given ids.");
+      return Action::failure;
+      break;
+    case AllMoleculesUnselected:
+    case MoleculesSelected:
+      return ActionState::ptr(new SelectionMoleculeByIdState(undomolids, params));
+      break;
+    default:
+      STATUS("No mols have been selected.");
+      return Action::failure;
+      break;
+  }
+  return Action::failure;
 }
 
@@ -72,5 +103,9 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().unselectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);
@@ -80,5 +115,9 @@
   SelectionMoleculeByIdState *state = assert_cast<SelectionMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().selectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);
Index: src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def
===================================================================
--- src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -7,6 +7,10 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <vector>
 #include "types.hpp"
 
+typedef std::vector<moleculeId_t> molids_t;
+
+#include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/MoleculeIdValidator.hpp"
 
@@ -14,14 +18,14 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (moleculeId_t)
+#define paramtypes (molids_t)
 #define paramtokens ("select-molecule-by-id")
-#define paramdescriptions ("molecule index")
+#define paramdescriptions ("molecule indices to select")
 #undef paramdefaults
-#define paramreferences (molindex)
+#define paramreferences (molids)
 #define paramvalids \
-(MoleculeIdValidator())
+(STLVectorValidator< std::vector<moleculeId_t> >(MoleculeIdValidator()))
 
-#undef statetypes
-#undef statereferences
+#define statetypes (molids_t)
+#define statereferences (undomolids)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS
Index: src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp
===================================================================
--- src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -53,18 +53,48 @@
 /** =========== define the function ====================== */
 ActionState::ptr SelectionNotMoleculeByIdAction::performCall() {
-  const molecule *mol = World::getInstance().getMolecule(MoleculeById(params.molindex.get()));
-  if (mol != NULL) {
-    if (World::getInstance().isSelected(mol)) {
-      LOG(1, "Unselecting molecule " << mol->name);
-      World::getInstance().unselectAllMolecules(MoleculeById(params.molindex.get()));
-      LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
-      return ActionState::ptr(new SelectionNotMoleculeByIdState(params));
+  enum Sucess {
+    NoStatus,
+    AllMoleculesSelected,
+    MoleculesUnselected,
+    MoleculeMissing
+  } status = NoStatus;
+
+  const molids_t molids = params.molids.get();
+  molids_t undomolids;
+  undomolids.reserve(molids.size());
+  for (molids_t::const_iterator iter = molids.begin(); iter != molids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    if (Walker != NULL) {
+      if (World::getInstance().isSelected(Walker)) {
+        LOG(1, "Unselecting mol " << Walker->getName());
+        World::getInstance().unselectMolecule(Walker);
+        undomolids.push_back(*iter);
+        if (status < MoleculeMissing)
+          status = MoleculesUnselected;
+      } else {
+        if (status == NoStatus)
+          status = AllMoleculesSelected;
+      }
     } else {
-      return Action::success;
+      status = MoleculeMissing;
     }
-  } else {
-    STATUS("Cannot find molecule by given index "+toString(params.molindex.get())+".");
-    return Action::failure;
   }
+  LOG(0, World::getInstance().countSelectedMolecules() << " mols remain selected.");
+
+  switch (status) {
+    case MoleculeMissing:
+      STATUS("Cannot find all mols by given ids.");
+      return Action::failure;
+      break;
+    case AllMoleculesSelected:
+    case MoleculesUnselected:
+      return ActionState::ptr(new SelectionNotMoleculeByIdState(undomolids, params));
+      break;
+    default:
+      STATUS("No mols have been selected.");
+      return Action::failure;
+      break;
+  }
+  return Action::failure;
 }
 
@@ -72,5 +102,9 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().selectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().selectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);
@@ -80,5 +114,9 @@
   SelectionNotMoleculeByIdState *state = assert_cast<SelectionNotMoleculeByIdState*>(_state.get());
 
-  World::getInstance().unselectAllMolecules(MoleculeById(state->params.molindex.get()));
+  for (molids_t::const_iterator iter = state->undomolids.begin();
+      iter != state->undomolids.end(); ++iter) {
+    const molecule *Walker = World::getInstance().getMolecule(MoleculeById(*iter));
+    World::getInstance().unselectMolecule(Walker);
+  }
 
   return ActionState::ptr(_state);
Index: src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def
===================================================================
--- src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -7,6 +7,10 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <vector>
 #include "types.hpp"
 
+typedef std::vector<moleculeId_t> molids_t;
+
+#include "Parameters/Validators/STLVectorValidator.hpp"
 #include "Parameters/Validators/Specific/MoleculeIdValidator.hpp"
 
@@ -14,14 +18,14 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (moleculeId_t)
+#define paramtypes (molids_t)
 #define paramtokens ("unselect-molecule-by-id")
-#define paramdescriptions ("molecule index")
+#define paramdescriptions ("molecule indices to unselect")
 #undef paramdefaults
-#define paramreferences (molindex)
+#define paramreferences (molids)
 #define paramvalids \
-(MoleculeIdValidator())
+(STLVectorValidator< std::vector<moleculeId_t> >(MoleculeIdValidator()))
 
-#undef statetypes
-#undef statereferences
+#define statetypes (molids_t)
+#define statereferences (undomolids)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS
Index: src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp
===================================================================
--- src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -150,8 +150,9 @@
      const molecule *mol = Walker->getMolecule();
      ASSERT(mol, "Atom without molecule has been clicked.");
+     molids_t ids(1, mol->getId());
      if (!World::getInstance().isSelected(mol))
-       SelectionMoleculeById(mol->getId());
+       SelectionMoleculeById(ids);
      else
-       SelectionNotMoleculeById(mol->getId());
+       SelectionNotMoleculeById(ids);
    }
    emit clicked(no);
@@ -163,8 +164,9 @@
    const molecule *mol= World::getInstance().getMolecule(MoleculeById(no));
    ASSERT(mol, "Atom without molecule has been clicked.");
+   molids_t ids(1, mol->getId());
    if (!World::getInstance().isSelected(mol))
-     SelectionMoleculeById(mol->getId());
+     SelectionMoleculeById(ids);
    else
-     SelectionNotMoleculeById(mol->getId());
+     SelectionNotMoleculeById(ids);
    emit clicked(no);
 }
Index: src/UIElements/Views/Qt4/QtMoleculeList.cpp
===================================================================
--- src/UIElements/Views/Qt4/QtMoleculeList.cpp	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ src/UIElements/Views/Qt4/QtMoleculeList.cpp	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -268,24 +268,34 @@
   // Select all molecules which belong to newly selected rows.
   QModelIndex index;
-  QModelIndexList items = selected.indexes();
-  foreach (index, items)
-    if (index.column() == 0){
-      int mol_id = model()->data(index, Qt::UserRole).toInt();
-      if (mol_id < 0)
-        continue;
-      //std::cout << "select molecule" << std::endl;
-      MoleCuilder::SelectionMoleculeById(mol_id);
-    }
+  {
+    QModelIndexList items = selected.indexes();
+    molids_t ids;
+    ids.reserve(items.size());
+    foreach (index, items)
+      if (index.column() == 0){
+        int mol_id = model()->data(index, Qt::UserRole).toInt();
+        if (mol_id < 0)
+          continue;
+        ids.push_back(mol_id);
+        //std::cout << "select molecule" << std::endl;
+      }
+    MoleCuilder::SelectionMoleculeById(ids);
+  }
 
   // Unselect all molecules which belong to newly unselected rows.
-  items = deselected.indexes();
-  foreach (index, items)
-    if (index.column() == 0){
-      int mol_id = model()->data(index, Qt::UserRole).toInt();
-      if (mol_id < 0)
-        continue;
-      //std::cout << "unselect molecule" << std::endl;
-      MoleCuilder::SelectionNotMoleculeById(mol_id);
-    }
+  {
+    QModelIndexList items = deselected.indexes();
+    molids_t ids;
+    ids.reserve(items.size());
+    foreach (index, items)
+      if (index.column() == 0){
+        int mol_id = model()->data(index, Qt::UserRole).toInt();
+        if (mol_id < 0)
+          continue;
+        //std::cout << "unselect molecule" << std::endl;
+        ids.push_back(mol_id);
+      }
+    MoleCuilder::SelectionNotMoleculeById(ids);
+  }
 
   selecting = false;
Index: tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz
===================================================================
--- tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
+++ tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -0,0 +1,1025 @@
+1023
+	Created by molecuilder for select-molecule-by-id test
+O	0	0	0.504284
+H	0.758602	0	1.00857
+H	0.758602	0	0
+O	0	0	3.36143
+H	0.758602	0	3.86571
+H	0.758602	0	2.85714
+O	0	0	9.07571
+H	0.758602	0	9.58
+H	0.758602	0	8.57143
+O	0	0	14.79
+H	0.758602	0	15.2943
+H	0.758602	0	14.2857
+O	0	0	17.6471
+H	0.758602	0	18.1514
+H	0.758602	0	17.1429
+O	0	2.85714	0.504284
+H	0.758602	2.85714	1.00857
+H	0.758602	2.85714	0
+O	0	2.85714	3.36143
+H	0.758602	2.85714	3.86571
+H	0.758602	2.85714	2.85714
+O	0	2.85714	6.21857
+H	0.758602	2.85714	6.72285
+H	0.758602	2.85714	5.71429
+O	0	2.85714	9.07571
+H	0.758602	2.85714	9.58
+H	0.758602	2.85714	8.57143
+O	0	2.85714	11.9329
+H	0.758602	2.85714	12.4371
+H	0.758602	2.85714	11.4286
+O	0	2.85714	14.79
+H	0.758602	2.85714	15.2943
+H	0.758602	2.85714	14.2857
+O	0	2.85714	17.6471
+H	0.758602	2.85714	18.1514
+H	0.758602	2.85714	17.1429
+O	0	5.71429	0.504284
+H	0.758602	5.71429	1.00857
+H	0.758602	5.71429	0
+O	0	5.71429	3.36143
+H	0.758602	5.71429	3.86571
+H	0.758602	5.71429	2.85714
+O	0	5.71429	6.21857
+H	0.758602	5.71429	6.72285
+H	0.758602	5.71429	5.71429
+O	0	5.71429	9.07571
+H	0.758602	5.71429	9.58
+H	0.758602	5.71429	8.57143
+O	0	5.71429	11.9329
+H	0.758602	5.71429	12.4371
+H	0.758602	5.71429	11.4286
+O	0	5.71429	14.79
+H	0.758602	5.71429	15.2943
+H	0.758602	5.71429	14.2857
+O	0	5.71429	17.6471
+H	0.758602	5.71429	18.1514
+H	0.758602	5.71429	17.1429
+O	0	8.57143	0.504284
+H	0.758602	8.57143	1.00857
+H	0.758602	8.57143	0
+O	0	8.57143	3.36143
+H	0.758602	8.57143	3.86571
+H	0.758602	8.57143	2.85714
+O	0	8.57143	6.21857
+H	0.758602	8.57143	6.72285
+H	0.758602	8.57143	5.71429
+O	0	8.57143	9.07571
+H	0.758602	8.57143	9.58
+H	0.758602	8.57143	8.57143
+O	0	8.57143	11.9329
+H	0.758602	8.57143	12.4371
+H	0.758602	8.57143	11.4286
+O	0	8.57143	14.79
+H	0.758602	8.57143	15.2943
+H	0.758602	8.57143	14.2857
+O	0	8.57143	17.6471
+H	0.758602	8.57143	18.1514
+H	0.758602	8.57143	17.1429
+O	0	11.4286	0.504284
+H	0.758602	11.4286	1.00857
+H	0.758602	11.4286	0
+O	0	11.4286	3.36143
+H	0.758602	11.4286	3.86571
+H	0.758602	11.4286	2.85714
+O	0	11.4286	6.21857
+H	0.758602	11.4286	6.72285
+H	0.758602	11.4286	5.71429
+O	0	11.4286	9.07571
+H	0.758602	11.4286	9.58
+H	0.758602	11.4286	8.57143
+O	0	11.4286	11.9329
+H	0.758602	11.4286	12.4371
+H	0.758602	11.4286	11.4286
+O	0	11.4286	14.79
+H	0.758602	11.4286	15.2943
+H	0.758602	11.4286	14.2857
+O	0	11.4286	17.6471
+H	0.758602	11.4286	18.1514
+H	0.758602	11.4286	17.1429
+O	0	14.2857	0.504284
+H	0.758602	14.2857	1.00857
+H	0.758602	14.2857	0
+O	0	14.2857	3.36143
+H	0.758602	14.2857	3.86571
+H	0.758602	14.2857	2.85714
+O	0	14.2857	6.21857
+H	0.758602	14.2857	6.72285
+H	0.758602	14.2857	5.71429
+O	0	14.2857	9.07571
+H	0.758602	14.2857	9.58
+H	0.758602	14.2857	8.57143
+O	0	14.2857	11.9329
+H	0.758602	14.2857	12.4371
+H	0.758602	14.2857	11.4286
+O	0	14.2857	14.79
+H	0.758602	14.2857	15.2943
+H	0.758602	14.2857	14.2857
+O	0	14.2857	17.6471
+H	0.758602	14.2857	18.1514
+H	0.758602	14.2857	17.1429
+O	0	17.1429	0.504284
+H	0.758602	17.1429	1.00857
+H	0.758602	17.1429	0
+O	0	17.1429	3.36143
+H	0.758602	17.1429	3.86571
+H	0.758602	17.1429	2.85714
+O	0	17.1429	6.21857
+H	0.758602	17.1429	6.72285
+H	0.758602	17.1429	5.71429
+O	0	17.1429	9.07571
+H	0.758602	17.1429	9.58
+H	0.758602	17.1429	8.57143
+O	0	17.1429	11.9329
+H	0.758602	17.1429	12.4371
+H	0.758602	17.1429	11.4286
+O	0	17.1429	14.79
+H	0.758602	17.1429	15.2943
+H	0.758602	17.1429	14.2857
+O	0	17.1429	17.6471
+H	0.758602	17.1429	18.1514
+H	0.758602	17.1429	17.1429
+O	2.85714	0	0.504284
+H	3.61574	0	1.00857
+H	3.61574	0	0
+O	2.85714	0	3.36143
+H	3.61574	0	3.86571
+H	3.61574	0	2.85714
+O	2.85714	0	6.21857
+H	3.61574	0	6.72285
+H	3.61574	0	5.71429
+O	2.85714	0	9.07571
+H	3.61574	0	9.58
+H	3.61574	0	8.57143
+O	2.85714	0	11.9329
+H	3.61574	0	12.4371
+H	3.61574	0	11.4286
+O	2.85714	0	14.79
+H	3.61574	0	15.2943
+H	3.61574	0	14.2857
+O	2.85714	0	17.6471
+H	3.61574	0	18.1514
+H	3.61574	0	17.1429
+O	2.85714	2.85714	0.504284
+H	3.61574	2.85714	1.00857
+H	3.61574	2.85714	0
+O	2.85714	2.85714	3.36143
+H	3.61574	2.85714	3.86571
+H	3.61574	2.85714	2.85714
+O	2.85714	2.85714	6.21857
+H	3.61574	2.85714	6.72285
+H	3.61574	2.85714	5.71429
+O	2.85714	2.85714	9.07571
+H	3.61574	2.85714	9.58
+H	3.61574	2.85714	8.57143
+O	2.85714	2.85714	11.9329
+H	3.61574	2.85714	12.4371
+H	3.61574	2.85714	11.4286
+O	2.85714	2.85714	14.79
+H	3.61574	2.85714	15.2943
+H	3.61574	2.85714	14.2857
+O	2.85714	2.85714	17.6471
+H	3.61574	2.85714	18.1514
+H	3.61574	2.85714	17.1429
+O	2.85714	5.71429	0.504284
+H	3.61574	5.71429	1.00857
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+H	17.9015	17.1429	5.71429
+O	17.1429	17.1429	9.07571
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+H	17.9015	17.1429	8.57143
+O	17.1429	17.1429	11.9329
+H	17.9015	17.1429	12.4371
+H	17.9015	17.1429	11.4286
+O	17.1429	17.1429	14.79
+H	17.9015	17.1429	15.2943
+H	17.9015	17.1429	14.2857
+O	17.1429	17.1429	17.6471
+H	17.9015	17.1429	18.1514
+H	17.9015	17.1429	17.1429
Index: sts/regression/Selection/Molecules/MoleculeById/post/id4_missing.xyz
===================================================================
--- tests/regression/Selection/Molecules/MoleculeById/post/id4_missing.xyz	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ 	(revision )
@@ -1,1028 +1,0 @@
-1026
-	Created by molecuilder for select-molecule-by-id test
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-H	9.33003	5.71429	8.57143
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-H	9.33003	5.71429	12.4371
-H	9.33003	5.71429	11.4286
-O	8.57143	5.71429	14.79
-H	9.33003	5.71429	15.2943
-H	9.33003	5.71429	14.2857
-O	8.57143	5.71429	17.6471
-H	9.33003	5.71429	18.1514
-H	9.33003	5.71429	17.1429
-O	8.57143	8.57143	0.504284
-H	9.33003	8.57143	1.00857
-H	9.33003	8.57143	0
-O	8.57143	8.57143	3.36143
-H	9.33003	8.57143	3.86571
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-O	8.57143	8.57143	6.21857
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-H	9.33003	8.57143	5.71429
-O	8.57143	8.57143	9.07571
-H	9.33003	8.57143	9.58
-H	9.33003	8.57143	8.57143
-O	8.57143	8.57143	11.9329
-H	9.33003	8.57143	12.4371
-H	9.33003	8.57143	11.4286
-O	8.57143	8.57143	14.79
-H	9.33003	8.57143	15.2943
-H	9.33003	8.57143	14.2857
-O	8.57143	8.57143	17.6471
-H	9.33003	8.57143	18.1514
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-O	8.57143	11.4286	0.504284
-H	9.33003	11.4286	1.00857
-H	9.33003	11.4286	0
-O	8.57143	11.4286	3.36143
-H	9.33003	11.4286	3.86571
-H	9.33003	11.4286	2.85714
-O	8.57143	11.4286	6.21857
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-H	9.33003	11.4286	5.71429
-O	8.57143	11.4286	9.07571
-H	9.33003	11.4286	9.58
-H	9.33003	11.4286	8.57143
-O	8.57143	11.4286	11.9329
-H	9.33003	11.4286	12.4371
-H	9.33003	11.4286	11.4286
-O	8.57143	11.4286	14.79
-H	9.33003	11.4286	15.2943
-H	9.33003	11.4286	14.2857
-O	8.57143	11.4286	17.6471
-H	9.33003	11.4286	18.1514
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-O	8.57143	14.2857	0.504284
-H	9.33003	14.2857	1.00857
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-O	8.57143	14.2857	3.36143
-H	9.33003	14.2857	3.86571
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-O	8.57143	14.2857	9.07571
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-H	9.33003	14.2857	8.57143
-O	8.57143	14.2857	11.9329
-H	9.33003	14.2857	12.4371
-H	9.33003	14.2857	11.4286
-O	8.57143	14.2857	14.79
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-H	9.33003	14.2857	14.2857
-O	8.57143	14.2857	17.6471
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-O	8.57143	17.1429	0.504284
-H	9.33003	17.1429	1.00857
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-O	8.57143	17.1429	3.36143
-H	9.33003	17.1429	3.86571
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-O	8.57143	17.1429	9.07571
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-H	9.33003	17.1429	8.57143
-O	8.57143	17.1429	11.9329
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-H	9.33003	17.1429	11.4286
-O	8.57143	17.1429	14.79
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-O	8.57143	17.1429	17.6471
-H	9.33003	17.1429	18.1514
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-O	11.4286	0	0.504284
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-O	11.4286	0	9.07571
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-O	11.4286	0	17.6471
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-O	11.4286	2.85714	3.36143
-H	12.1872	2.85714	3.86571
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-H	12.1872	2.85714	5.71429
-O	11.4286	2.85714	9.07571
-H	12.1872	2.85714	9.58
-H	12.1872	2.85714	8.57143
-O	11.4286	2.85714	11.9329
-H	12.1872	2.85714	12.4371
-H	12.1872	2.85714	11.4286
-O	11.4286	2.85714	14.79
-H	12.1872	2.85714	15.2943
-H	12.1872	2.85714	14.2857
-O	11.4286	2.85714	17.6471
-H	12.1872	2.85714	18.1514
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-O	11.4286	5.71429	0.504284
-H	12.1872	5.71429	1.00857
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-O	11.4286	5.71429	3.36143
-H	12.1872	5.71429	3.86571
-H	12.1872	5.71429	2.85714
-O	11.4286	5.71429	6.21857
-H	12.1872	5.71429	6.72285
-H	12.1872	5.71429	5.71429
-O	11.4286	5.71429	9.07571
-H	12.1872	5.71429	9.58
-H	12.1872	5.71429	8.57143
-O	11.4286	5.71429	11.9329
-H	12.1872	5.71429	12.4371
-H	12.1872	5.71429	11.4286
-O	11.4286	5.71429	14.79
-H	12.1872	5.71429	15.2943
-H	12.1872	5.71429	14.2857
-O	11.4286	5.71429	17.6471
-H	12.1872	5.71429	18.1514
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-O	11.4286	8.57143	0.504284
-H	12.1872	8.57143	1.00857
-H	12.1872	8.57143	0
-O	11.4286	8.57143	3.36143
-H	12.1872	8.57143	3.86571
-H	12.1872	8.57143	2.85714
-O	11.4286	8.57143	6.21857
-H	12.1872	8.57143	6.72285
-H	12.1872	8.57143	5.71429
-O	11.4286	8.57143	9.07571
-H	12.1872	8.57143	9.58
-H	12.1872	8.57143	8.57143
-O	11.4286	8.57143	11.9329
-H	12.1872	8.57143	12.4371
-H	12.1872	8.57143	11.4286
-O	11.4286	8.57143	14.79
-H	12.1872	8.57143	15.2943
-H	12.1872	8.57143	14.2857
-O	11.4286	8.57143	17.6471
-H	12.1872	8.57143	18.1514
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-O	11.4286	11.4286	0.504284
-H	12.1872	11.4286	1.00857
-H	12.1872	11.4286	0
-O	11.4286	11.4286	3.36143
-H	12.1872	11.4286	3.86571
-H	12.1872	11.4286	2.85714
-O	11.4286	11.4286	6.21857
-H	12.1872	11.4286	6.72285
-H	12.1872	11.4286	5.71429
-O	11.4286	11.4286	9.07571
-H	12.1872	11.4286	9.58
-H	12.1872	11.4286	8.57143
-O	11.4286	11.4286	11.9329
-H	12.1872	11.4286	12.4371
-H	12.1872	11.4286	11.4286
-O	11.4286	11.4286	14.79
-H	12.1872	11.4286	15.2943
-H	12.1872	11.4286	14.2857
-O	11.4286	11.4286	17.6471
-H	12.1872	11.4286	18.1514
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-O	11.4286	14.2857	0.504284
-H	12.1872	14.2857	1.00857
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-O	11.4286	14.2857	3.36143
-H	12.1872	14.2857	3.86571
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-O	11.4286	14.2857	6.21857
-H	12.1872	14.2857	6.72285
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-O	11.4286	14.2857	9.07571
-H	12.1872	14.2857	9.58
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-O	11.4286	14.2857	11.9329
-H	12.1872	14.2857	12.4371
-H	12.1872	14.2857	11.4286
-O	11.4286	14.2857	14.79
-H	12.1872	14.2857	15.2943
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-O	11.4286	14.2857	17.6471
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-O	11.4286	17.1429	0.504284
-H	12.1872	17.1429	1.00857
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-O	11.4286	17.1429	3.36143
-H	12.1872	17.1429	3.86571
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-O	11.4286	17.1429	6.21857
-H	12.1872	17.1429	6.72285
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-O	11.4286	17.1429	9.07571
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-O	11.4286	17.1429	11.9329
-H	12.1872	17.1429	12.4371
-H	12.1872	17.1429	11.4286
-O	11.4286	17.1429	14.79
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-O	11.4286	17.1429	17.6471
-H	12.1872	17.1429	18.1514
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-O	14.2857	0	0.504284
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-O	14.2857	0	9.07571
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-O	14.2857	0	11.9329
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-O	14.2857	0	14.79
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-O	14.2857	0	17.6471
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-O	14.2857	2.85714	0.504284
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-O	14.2857	2.85714	3.36143
-H	15.0443	2.85714	3.86571
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-O	14.2857	2.85714	6.21857
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-H	15.0443	2.85714	5.71429
-O	14.2857	2.85714	9.07571
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-O	14.2857	2.85714	11.9329
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-H	15.0443	2.85714	11.4286
-O	14.2857	2.85714	14.79
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-O	14.2857	5.71429	3.36143
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-O	14.2857	5.71429	9.07571
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-O	14.2857	5.71429	11.9329
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-O	14.2857	5.71429	14.79
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-O	14.2857	5.71429	17.6471
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-O	14.2857	8.57143	0.504284
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-O	14.2857	8.57143	3.36143
-H	15.0443	8.57143	3.86571
-H	15.0443	8.57143	2.85714
-O	14.2857	8.57143	6.21857
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-O	14.2857	8.57143	9.07571
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-O	14.2857	8.57143	11.9329
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-O	14.2857	8.57143	14.79
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-O	14.2857	8.57143	17.6471
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-O	14.2857	11.4286	0.504284
-H	15.0443	11.4286	1.00857
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-O	14.2857	11.4286	3.36143
-H	15.0443	11.4286	3.86571
-H	15.0443	11.4286	2.85714
-O	14.2857	11.4286	6.21857
-H	15.0443	11.4286	6.72285
-H	15.0443	11.4286	5.71429
-O	14.2857	11.4286	9.07571
-H	15.0443	11.4286	9.58
-H	15.0443	11.4286	8.57143
-O	14.2857	11.4286	11.9329
-H	15.0443	11.4286	12.4371
-H	15.0443	11.4286	11.4286
-O	14.2857	11.4286	14.79
-H	15.0443	11.4286	15.2943
-H	15.0443	11.4286	14.2857
-O	14.2857	11.4286	17.6471
-H	15.0443	11.4286	18.1514
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-O	14.2857	14.2857	0.504284
-H	15.0443	14.2857	1.00857
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-O	14.2857	14.2857	3.36143
-H	15.0443	14.2857	3.86571
-H	15.0443	14.2857	2.85714
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-O	14.2857	14.2857	9.07571
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-O	14.2857	14.2857	11.9329
-H	15.0443	14.2857	12.4371
-H	15.0443	14.2857	11.4286
-O	14.2857	14.2857	14.79
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-O	14.2857	17.1429	0.504284
-H	15.0443	17.1429	1.00857
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-O	14.2857	17.1429	3.36143
-H	15.0443	17.1429	3.86571
-H	15.0443	17.1429	2.85714
-O	14.2857	17.1429	6.21857
-H	15.0443	17.1429	6.72285
-H	15.0443	17.1429	5.71429
-O	14.2857	17.1429	9.07571
-H	15.0443	17.1429	9.58
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-O	14.2857	17.1429	11.9329
-H	15.0443	17.1429	12.4371
-H	15.0443	17.1429	11.4286
-O	14.2857	17.1429	14.79
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-O	14.2857	17.1429	17.6471
-H	15.0443	17.1429	18.1514
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-O	17.1429	0	0.504284
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-H	17.9015	0	5.71429
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-O	17.1429	0	14.79
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-H	17.9015	2.85714	3.86571
-H	17.9015	2.85714	2.85714
-O	17.1429	2.85714	6.21857
-H	17.9015	2.85714	6.72285
-H	17.9015	2.85714	5.71429
-O	17.1429	2.85714	9.07571
-H	17.9015	2.85714	9.58
-H	17.9015	2.85714	8.57143
-O	17.1429	2.85714	11.9329
-H	17.9015	2.85714	12.4371
-H	17.9015	2.85714	11.4286
-O	17.1429	2.85714	14.79
-H	17.9015	2.85714	15.2943
-H	17.9015	2.85714	14.2857
-O	17.1429	2.85714	17.6471
-H	17.9015	2.85714	18.1514
-H	17.9015	2.85714	17.1429
-O	17.1429	5.71429	0.504284
-H	17.9015	5.71429	1.00857
-H	17.9015	5.71429	0
-O	17.1429	5.71429	3.36143
-H	17.9015	5.71429	3.86571
-H	17.9015	5.71429	2.85714
-O	17.1429	5.71429	6.21857
-H	17.9015	5.71429	6.72285
-H	17.9015	5.71429	5.71429
-O	17.1429	5.71429	9.07571
-H	17.9015	5.71429	9.58
-H	17.9015	5.71429	8.57143
-O	17.1429	5.71429	11.9329
-H	17.9015	5.71429	12.4371
-H	17.9015	5.71429	11.4286
-O	17.1429	5.71429	14.79
-H	17.9015	5.71429	15.2943
-H	17.9015	5.71429	14.2857
-O	17.1429	5.71429	17.6471
-H	17.9015	5.71429	18.1514
-H	17.9015	5.71429	17.1429
-O	17.1429	8.57143	0.504284
-H	17.9015	8.57143	1.00857
-H	17.9015	8.57143	0
-O	17.1429	8.57143	3.36143
-H	17.9015	8.57143	3.86571
-H	17.9015	8.57143	2.85714
-O	17.1429	8.57143	6.21857
-H	17.9015	8.57143	6.72285
-H	17.9015	8.57143	5.71429
-O	17.1429	8.57143	9.07571
-H	17.9015	8.57143	9.58
-H	17.9015	8.57143	8.57143
-O	17.1429	8.57143	11.9329
-H	17.9015	8.57143	12.4371
-H	17.9015	8.57143	11.4286
-O	17.1429	8.57143	14.79
-H	17.9015	8.57143	15.2943
-H	17.9015	8.57143	14.2857
-O	17.1429	8.57143	17.6471
-H	17.9015	8.57143	18.1514
-H	17.9015	8.57143	17.1429
-O	17.1429	11.4286	0.504284
-H	17.9015	11.4286	1.00857
-H	17.9015	11.4286	0
-O	17.1429	11.4286	3.36143
-H	17.9015	11.4286	3.86571
-H	17.9015	11.4286	2.85714
-O	17.1429	11.4286	6.21857
-H	17.9015	11.4286	6.72285
-H	17.9015	11.4286	5.71429
-O	17.1429	11.4286	9.07571
-H	17.9015	11.4286	9.58
-H	17.9015	11.4286	8.57143
-O	17.1429	11.4286	11.9329
-H	17.9015	11.4286	12.4371
-H	17.9015	11.4286	11.4286
-O	17.1429	11.4286	14.79
-H	17.9015	11.4286	15.2943
-H	17.9015	11.4286	14.2857
-O	17.1429	11.4286	17.6471
-H	17.9015	11.4286	18.1514
-H	17.9015	11.4286	17.1429
-O	17.1429	14.2857	0.504284
-H	17.9015	14.2857	1.00857
-H	17.9015	14.2857	0
-O	17.1429	14.2857	3.36143
-H	17.9015	14.2857	3.86571
-H	17.9015	14.2857	2.85714
-O	17.1429	14.2857	6.21857
-H	17.9015	14.2857	6.72285
-H	17.9015	14.2857	5.71429
-O	17.1429	14.2857	9.07571
-H	17.9015	14.2857	9.58
-H	17.9015	14.2857	8.57143
-O	17.1429	14.2857	11.9329
-H	17.9015	14.2857	12.4371
-H	17.9015	14.2857	11.4286
-O	17.1429	14.2857	14.79
-H	17.9015	14.2857	15.2943
-H	17.9015	14.2857	14.2857
-O	17.1429	14.2857	17.6471
-H	17.9015	14.2857	18.1514
-H	17.9015	14.2857	17.1429
-O	17.1429	17.1429	0.504284
-H	17.9015	17.1429	1.00857
-H	17.9015	17.1429	0
-O	17.1429	17.1429	3.36143
-H	17.9015	17.1429	3.86571
-H	17.9015	17.1429	2.85714
-O	17.1429	17.1429	6.21857
-H	17.9015	17.1429	6.72285
-H	17.9015	17.1429	5.71429
-O	17.1429	17.1429	9.07571
-H	17.9015	17.1429	9.58
-H	17.9015	17.1429	8.57143
-O	17.1429	17.1429	11.9329
-H	17.9015	17.1429	12.4371
-H	17.9015	17.1429	11.4286
-O	17.1429	17.1429	14.79
-H	17.9015	17.1429	15.2943
-H	17.9015	17.1429	14.2857
-O	17.1429	17.1429	17.6471
-H	17.9015	17.1429	18.1514
-H	17.9015	17.1429	17.1429
Index: tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz
===================================================================
--- tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
+++ tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -0,0 +1,8 @@
+6
+	Created by molecuilder for select-molecule-by-id test
+O	0	0	6.21857
+H	0.758602	0	6.72285
+H	0.758602	0	5.71429
+O	0	0	11.9329
+H	0.758602	0	12.4371
+H	0.758602	0	11.4286
Index: sts/regression/Selection/Molecules/MoleculeById/post/water_id4.xyz
===================================================================
--- tests/regression/Selection/Molecules/MoleculeById/post/water_id4.xyz	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ 	(revision )
@@ -1,5 +1,0 @@
-3
-	Created by molecuilder for select-molecule-by-id test
-O	0	0	11.9329
-H	0.758602	0	12.4371
-H	0.758602	0	11.4286
Index: tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at
===================================================================
--- tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -25,7 +25,7 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=water_id4.xyz
+targetfile=water_id2_4.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -41,5 +41,5 @@
 targetfile=empty.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 --undo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 --undo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -53,7 +53,7 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=water_id4.xyz
+targetfile=water_id2_4.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-molecule-by-id 2 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
Index: tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at
===================================================================
--- tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at	(revision b6d92e374e7b56b8a8b8399faf64a7363294d1b4)
+++ tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at	(revision d7cad13fbfec0974d4bd77f1cbca6c59fac0ad61)
@@ -25,7 +25,7 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=id4_missing.xyz
+targetfile=id2_4_missing.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -41,5 +41,5 @@
 targetfile=box.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 --undo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 --undo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
@@ -53,7 +53,7 @@
 srcfile=box.xyz
 testfile=test.xyz
-targetfile=id4_missing.xyz
+targetfile=id2_4_missing.xyz
 AT_CHECK([cp -n ${regressionpath}/pre/$srcfile $testfile], 0)
-AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
+AT_CHECK([../../molecuilder -i $testfile -I --select-all-molecules --unselect-molecule-by-id 2 4 --undo --redo -s $targetfile], 0, [stdout], [stderr])
 AT_CHECK([diff -I '.*Created by molecuilder.*' $targetfile ${regressionpath}/post/$targetfile], 0, [ignore], [ignore])
 
