diff --git a/LipidCreator/StructureEditor/LipidStructure.cs b/LipidCreator/StructureEditor/LipidStructure.cs
index ab5b447..e5db56f 100644
--- a/LipidCreator/StructureEditor/LipidStructure.cs
+++ b/LipidCreator/StructureEditor/LipidStructure.cs
@@ -82,6 +82,11 @@ public SPointF(Point p)
             return new SPointF(p.X - r.X, p.Y - r.Y);
         }
         
+        public static SPointF operator /(SPointF p, float f)
+        {
+            return new SPointF(p.X / f, p.Y / f);
+        }
+        
         public PointF pF()
         {
             return new PointF(X, Y);
@@ -94,7 +99,8 @@ public Point pI()
     }
     
     
-    public class S {
+    public class S
+    {
         public static string space(int n)
         {
             return new string(' ', 2 * n);
@@ -362,6 +368,7 @@ public Bond(Bond copy)
         
         public Bond(LipidStructure _lipidStructure, XElement element)
         {
+            lipidStructure = _lipidStructure;
             id = Convert.ToInt32(element.Attribute("id").Value);
             startId = Convert.ToInt32(element.Attribute("start").Value);
             endId = Convert.ToInt32(element.Attribute("end").Value);
@@ -386,7 +393,7 @@ public Bond(LipidStructure _lipidStructure, XElement element)
         
         public void toggleState()
         {
-            if (lipidStructure.currentProjection == 0) return;
+            if (lipidStructure.currentProjection == 0 || !bondProjections.ContainsKey(lipidStructure.currentProjection)) return;
             
             bondProjections[lipidStructure.currentProjection] = !bondProjections[lipidStructure.currentProjection];
             lipidStructure.countNodeConnections();
@@ -438,6 +445,13 @@ public LipidStructureFragment(int i, string f, int c = 0)
             charge = c;
         }
         
+        public LipidStructureFragment(XElement element)
+        {
+            id = Convert.ToInt32(element.Attribute("id").Value);
+            fragmentName = element.Attribute("name").Value;
+            charge = Convert.ToInt32(element.Attribute("charge").Value);
+        }
+        
         public void toggleCharge()
         {
             charge = (charge >= maxCharge) ? minCharge : charge + 1;
@@ -483,8 +497,8 @@ public class LipidStructure
         public HashSet<string> specialAtoms = new HashSet<string>(){"N", "O", "P", "S"};
         public Dictionary<string, int> freeElectrons = new Dictionary<string, int>(){{"C", 4}, {"N", 3}, {"O", 2}, {"P", 3}, {"S", 2}};
         public int projectionIds = 1;
-        public int currentNodeId = 0;
-        public int bondIDs = 0;
+        public int nodeIds = 0;
+        public int bondIds = 0;
         
         
         
@@ -525,20 +539,28 @@ public LipidStructure(string file_name, Form form)
             graphics = form.CreateGraphics();
          
             string documentType = doc.Elements().First().Name.LocalName;
-            if (documentType.Equals("CDXML")) loadCDXML(doc);
-            else if (documentType.Equals("LipidStructure")) loadLipidStructure(doc);
-            else throw new Exception("Unknown data format");
-            
-            nodeFont = new Font("Arial", fontSize * factor);
-            decoratorFont = new Font("Arial", (float)(fontSize * factor * 0.5));
-            penEnabled = new Pen(Color.Black, factor);
-            penDisabled = new Pen(Color.FromArgb(180, 180, 180), factor);
-            penHidden = new Pen(Color.FromArgb(220, 220, 220), factor);
+            if (documentType.Equals("CDXML"))
+            {
+                loadCDXML(doc);
+            }
+            else if (documentType.Equals("LipidStructure"))
+            {
+                ((LipidCreatorStructureEditor)form).structureFile = file_name;
+                loadLipidStructure(doc);
+            }
+            else
+            {
+                throw new Exception("Unknown data format");
+            }
             
             currentProjection = 0;
             computeBonds();
             changeFragment();
             countNodeConnections();
+            
+            penEnabled = new Pen(Color.Black, factor);
+            penDisabled = new Pen(Color.FromArgb(180, 180, 180), factor);
+            penHidden = new Pen(Color.FromArgb(220, 220, 220), factor);
         }
         
         
@@ -555,6 +577,7 @@ public void loadLipidStructure(XDocument doc)
                 StructureNode sn = new StructureNode(this, element);
                 idToNode.Add(sn.id, sn);
                 nodes.Add(sn);
+                nodeIds = Math.Max(nodeIds, sn.id + 1);
             }
             
             foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("AdditionalNodes")).Elements().Where(el => el.Name.LocalName.Equals("NodeID")))
@@ -577,6 +600,26 @@ public void loadLipidStructure(XDocument doc)
                 int id = Convert.ToInt32(element.Attribute("id").Value);
                 additionalBonds.Add(bond_dict[id]);
             }
+            
+            
+            
+            foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("PositiveFragments")).Elements().Where(el => el.Name.LocalName.Equals("LipidStructureFragment")))
+            {
+                LipidStructureFragment fragment = new LipidStructureFragment(element);
+                positiveFragments.Add(fragment.fragmentName, fragment);
+            }
+            
+            foreach (var element in doc.Element("LipidStructure").Elements().Where(el => el.Name.LocalName.Equals("NegativeFragments")).Elements().Where(el => el.Name.LocalName.Equals("LipidStructureFragment")))
+            {
+                LipidStructureFragment fragment = new LipidStructureFragment(element);
+                negativeFragments.Add(fragment.fragmentName, fragment);
+            }
+            
+            nodeFont = new Font("Arial", fontSize * factor);
+            decoratorFont = new Font("Arial", (float)(fontSize * factor * 0.5));
+            
+            bondIds = bonds.Count + 1;
+            projectionIds = negativeFragments.Count + positiveFragments.Count + 1;
         }
         
         
@@ -645,7 +688,7 @@ public void loadCDXML(XDocument doc)
                         idToNode.Add(nodeId, sn);
                     }
                     
-                    currentNodeId = Math.Max(currentNodeId, nodeId);
+                    nodeIds = Math.Max(nodeIds, nodeId + 1);
                 }
                 catch(Exception ex){
                     Console.WriteLine(ex);
@@ -697,7 +740,7 @@ public void loadCDXML(XDocument doc)
                     // get the edge color
                     bool isDoubleBond = ((string)edge.Attribute("Order") != null) && edge.Attribute("Order").Value.ToString().Equals("2");
                     
-                    bond = new Bond(this, bondIDs++, idB, idE, isDoubleBond);
+                    bond = new Bond(this, bondIds++, idB, idE, isDoubleBond);
                     bonds.Add(bond);
                 }
                 catch(Exception){}
@@ -728,6 +771,9 @@ public void loadCDXML(XDocument doc)
             float offsetY = /* (float)form.Size.Height / 2.0f */ - midY * factor;
             
             
+            nodeFont = new Font("Arial", fontSize * factor);
+            decoratorFont = new Font("Arial", (float)(fontSize * factor * 0.5));
+            
             foreach (var node in nodes)
             {
                 float x = node.position.X * factor + offsetX;
@@ -976,7 +1022,7 @@ public void addNode(SPointF pos)
             float w = size.Width * 0.9f;
             float h = size.Height * 0.9f;
             RectangleF drawRect = new RectangleF(pos.X - w * 0.5f, pos.Y - h * 0.5f, w, h);
-            StructureNode sn = new StructureNode(this, ++currentNodeId, pos, drawRect, "C");
+            StructureNode sn = new StructureNode(this, nodeIds, pos, drawRect, "C");
             
         
             int fragId = currentFragment.id;
@@ -984,7 +1030,7 @@ public void addNode(SPointF pos)
             
             nodes.Add(sn);
             additionalNodes.Add(sn);
-            idToNode.Add(currentNodeId, sn);
+            idToNode.Add(nodeIds++, sn);
             
             computeBonds();
         }
@@ -1012,7 +1058,7 @@ public StructureNode removeNode(StructureNode node)
         public void addBond(StructureNode start, StructureNode end)
         {
             if (currentProjection == 0) return;
-            Bond bond = new Bond(this, bondIDs++, start.id, end.id, false);
+            Bond bond = new Bond(this, bondIds++, start.id, end.id, false);
             bond.bondProjections.Add(currentProjection, false);
             bonds.Add(bond);
             additionalBonds.Add(bond);
diff --git a/LipidCreator/StructureEditor/StructureEditor.Designer.cs b/LipidCreator/StructureEditor/StructureEditor.Designer.cs
index 09e40cb..b27f515 100644
--- a/LipidCreator/StructureEditor/StructureEditor.Designer.cs
+++ b/LipidCreator/StructureEditor/StructureEditor.Designer.cs
@@ -82,6 +82,7 @@ partial class LipidCreatorStructureEditor
         public Button actionRemoveBond = new Button();
         public Button actionFinalView = new Button();
         public Button actionMoveAtom = new Button();
+        public Button actionSaveStructure = new Button();
         
         public List<Button> actionButtons = new List<Button>();
         
@@ -330,6 +331,14 @@ private void InitializeComponent()
             bb4Hydro.TextChanged += computeFragmentMass;
             
             
+            
+            this.Controls.Add(actionSaveStructure);
+            actionSaveStructure.Size = new Size(120, 25);
+            actionSaveStructure.Text = "Save structure";
+            actionSaveStructure.Location = new Point(10, 750);
+            actionSaveStructure.Click += saveStructure;
+            
+            
             this.Controls.Add(adductComboBox);
             adductComboBox.Location = new Point(800, 10);
             adductComboBox.Size = new Size(120, 25);
diff --git a/LipidCreator/StructureEditor/StructureEditor.cs b/LipidCreator/StructureEditor/StructureEditor.cs
index 6aa62a5..be5202d 100644
--- a/LipidCreator/StructureEditor/StructureEditor.cs
+++ b/LipidCreator/StructureEditor/StructureEditor.cs
@@ -31,6 +31,7 @@ public partial class LipidCreatorStructureEditor : Form
         public static double ELECTRON_REST_MASS = 0.00054857990946;
         public const string FRAGMENT_LABEL = "fragment";
         public bool semaphore = false;
+        public string structureFile = "";
         
         
         public LipidCreatorStructureEditor()
@@ -39,11 +40,11 @@ public LipidCreatorStructureEditor()
             InitializeComponent();
             this.DoubleBuffered = true;
             
-            /*
+            
             using (OpenFileDialog openFileDialog = new OpenFileDialog())
             {
                 openFileDialog.InitialDirectory = "c:\\";
-                openFileDialog.Filter = "txt files (*.cdxml)|*.cdxml|(*.stXL)|*.stXL";
+                openFileDialog.Filter = "chemdraw file (*.cdxml)|*.cdxml|structure file (*.stXL)|*.stXL";
                 openFileDialog.FilterIndex = 2;
                 openFileDialog.RestoreDirectory = true;
 
@@ -52,35 +53,46 @@ public LipidCreatorStructureEditor()
                     //Get the path of specified file
                     string filePath = openFileDialog.FileName;
 
-                    
+                    try
+                    {
+                        lipidStructure = new LipidStructure(filePath, this);
+                    }
+                    catch
+                    {
+                        MessageBox.Show("An error happened, please speak with Dominik and explain how you caused the error.", "Error happened");
+                        Environment.Exit(-1);
+                    }
                     Console.WriteLine(filePath);
                 }
+                else
+                {
+                    Environment.Exit(0);
+                }
             }
-            */
             
-            
-            if (true)
+            foreach (var kvp in lipidStructure.positiveFragments)
             {
-                string file = "foo.stXL";
-                lipidStructure = new LipidStructure(file, this);
+                positiveFragmentsListBox.Items.Add(kvp.Value.fragmentName);
             }
-            else
-            {
-                string file = "/home/dominik/workspace/src/LipidCreator/LipidCreator/data/structures/PC genNeg.cdxml";
-                lipidStructure = new LipidStructure(file, this);
-                positiveFragmentsListBox.Items.Add("HG 164");
-                lipidStructure.addFragment("HG 164", true);
-                
-                positiveFragmentsListBox.Items.Add("HG 181");
-                lipidStructure.addFragment("HG 181", true);
-                
-                negativeFragmentsListBox.Items.Add("HG -OH");
-                lipidStructure.addFragment("HG -OH", false);
-                
             
-                lipidStructure.serialize("foo.stXL");
+            foreach (var kvp in lipidStructure.negativeFragments)
+            {
+                negativeFragmentsListBox.Items.Add(kvp.Value.fragmentName);
             }
             
+            /*
+            string file = "/home/dominik/workspace/src/LipidCreator/LipidCreator/data/structures/PC genNeg.cdxml";
+            lipidStructure = new LipidStructure(file, this);
+            positiveFragmentsListBox.Items.Add("HG 164");
+            lipidStructure.addFragment("HG 164", true);
+            
+            positiveFragmentsListBox.Items.Add("HG 181");
+            lipidStructure.addFragment("HG 181", true);
+            
+            negativeFragmentsListBox.Items.Add("HG -OH");
+            lipidStructure.addFragment("HG -OH", false);
+            */
+            
             computeFragmentMass(null, null);
         }
         
@@ -116,9 +128,8 @@ private void DrawScene(Graphics g)
                 if (currentBond != null)
                 {
                     Pen pen = new Pen(Color.DeepSkyBlue, 2);
-                    int xb = (int)((currentBond.edgeSingle.start.X + currentBond.edgeSingle.end.X) * 0.5);
-                    int yb = (int)((currentBond.edgeSingle.start.Y + currentBond.edgeSingle.end.Y) * 0.5);
-                    g.DrawEllipse(pen, xb - cursorCircleRadius, yb - cursorCircleRadius, cursorCircleRadius * 2, cursorCircleRadius * 2);
+                    SPointF p = (currentBond.edgeSingle.start + currentBond.edgeSingle.end) / 2.0f + lipidStructure.middlePoint;
+                    g.DrawEllipse(pen, p.X - cursorCircleRadius, p.Y - cursorCircleRadius, cursorCircleRadius * 2, cursorCircleRadius * 2);
                 }
             }
             
@@ -198,6 +209,7 @@ private void mouseUp(Object sender, MouseEventArgs e)
                     }
                     else if (action == Action.ChangeBond && currentBond != null)
                     {
+                        Console.WriteLine(currentBond);
                         currentBond.toggleState(); 
                         lipidStructure.computeBonds();
                         updateStructure();
@@ -239,7 +251,7 @@ private void mouseUp(Object sender, MouseEventArgs e)
                     }
                     else if (action == Action.ChangeBond && currentBond != null)
                     {
-                        currentBond.toggleState(); 
+                        currentBond.toggleState();
                         lipidStructure.computeBonds();
                         updateStructure();
                     }
@@ -413,9 +425,9 @@ private void mouseMove(Object sender, MouseEventArgs e)
                 double minDistC = 1e10;
                 foreach (var bond in lipidStructure.bonds)
                 {
-                    double xb = (bond.edgeSingle.start.X + bond.edgeSingle.end.X) * 0.5;
-                    double yb = (bond.edgeSingle.start.Y + bond.edgeSingle.end.Y) * 0.5;
-                    double dist  = Math.Pow(xb - mouse.X, 2) + Math.Pow(yb - mouse.Y, 2);
+                    SPointF b = (bond.edgeSingle.start + bond.edgeSingle.end) / 2.0f + lipidStructure.middlePoint - mouse;
+                    
+                    double dist  = Math.Pow(b.X, 2) + Math.Pow(b.Y, 2);
                     if (dist <= Math.Pow(10 + cursorCircleRadius, 2) && dist < minDistC)
                     {
                         minDistC = dist;
@@ -596,7 +608,9 @@ private void positiveFragmentDoubleClicked(Object sender, EventArgs e)
             string newFragmentName = InputBox.Show("Please write a new fragment name:", "New fragment name", currentFragmentName);
             if (newFragmentName.Length == 0 || newFragmentName.Equals(currentFragmentName) || lipidStructure.positiveFragments.ContainsKey(newFragmentName)) return;
             
-            lipidStructure.positiveFragments.Add(newFragmentName, lipidStructure.positiveFragments[currentFragmentName]);
+            LipidStructureFragment fragment = lipidStructure.positiveFragments[currentFragmentName];
+            fragment.fragmentName = newFragmentName;
+            lipidStructure.positiveFragments.Add(newFragmentName, fragment);
             lipidStructure.positiveFragments.Remove(currentFragmentName);
             positiveFragmentsListBox.Items[selectedIndex] = newFragmentName;
         }
@@ -614,7 +628,9 @@ private void negativeFragmentDoubleClicked(Object sender, EventArgs e)
             string newFragmentName = InputBox.Show("Please write a new fragment name:", "New fragment name", currentFragmentName);
             if (newFragmentName.Length == 0 || newFragmentName.Equals(currentFragmentName) || lipidStructure.negativeFragments.ContainsKey(newFragmentName)) return;
             
-            lipidStructure.negativeFragments.Add(newFragmentName, lipidStructure.negativeFragments[currentFragmentName]);
+            LipidStructureFragment fragment = lipidStructure.negativeFragments[currentFragmentName];
+            fragment.fragmentName = newFragmentName;
+            lipidStructure.negativeFragments.Add(newFragmentName, fragment);
             lipidStructure.negativeFragments.Remove(currentFragmentName);
             negativeFragmentsListBox.Items[selectedIndex] = newFragmentName;
         }
@@ -668,6 +684,31 @@ public void updateStructure()
         
         
         
+        public void saveStructure(Object sender, EventArgs e)
+        {
+            if (structureFile.Length == 0)
+            {
+                using (SaveFileDialog saveFileDialog = new SaveFileDialog())
+                {
+                    saveFileDialog.InitialDirectory = "c:\\";
+                    saveFileDialog.Filter = "structure file (*.stXL)|*.stXL";
+                    saveFileDialog.FilterIndex = 0;
+                    saveFileDialog.RestoreDirectory = true;
+                    saveFileDialog.ShowDialog();
+                    
+                    structureFile = saveFileDialog.FileName;   
+                }
+            }
+            
+            if (structureFile.Length > 0)
+            {
+                lipidStructure.serialize(structureFile);
+                MessageBox.Show("The structure was saved.", "Structure saved");
+            }
+        }
+        
+        
+        
         private void addPositiveFragment(Object sender, EventArgs e)
         {
             if (!lipidStructure.positiveFragments.ContainsKey(FRAGMENT_LABEL))