To open the Structure Editor window:

• click the Structure Editor  button on the main tool bar.
  
  
• or choose the Tools | Structure Editor menu item.
  
  
• or open a structure by choosing the File | Open | Structure menu item and Structure Editor will start automatically.

When you reduce the size of the Structure Editor window the button array on your desktop changes. The reduced Structure Editor window is more compact, but retains all the buttons on the button bars. A smaller window may prove advantageous if your program desktop is filled with other modules.

In the Structure Editor's default state all buttons are switched off and no atom or bond is selected. The plain arrow cursor indicates that the Structure Editor is in default state. To restore the default state of the editor, choose any of these methods:

To open or save a structure:

• Click on the Open Structure  or Save Structure  button in the Structure Editor window.
  
  
• Choose the File | Open | Structure or the File | Save | Structure menu item.

Structure Editor supports two kinds of structure formats: MDL MOL-files (SDF-files), with the *.mol (*.sdf) extension, and HighChem MCS format (Maximal Compressed Structure), with the *.mcs extension. These formats are also supported in the Database Manager module. Templates are stored in MCS-format, using the extension *.tml.

Mass Frontier is a layout powerhouse. For structures, as well as for other objects, you can change almost anything that it is possible to change. Every layout setting change also affects printing and copying into Clipboard, except background color, which affects only screen display in the Mass Frontier program. The various layout items allow you to tailor the graphics to your individual report or publication needs.

Structure Editor offers the possibility of labeling a structure or displaying a text note on the screen or on the printout.

To enter a text note:

1. Click on the Text button  in the Structure Editor window.
2. Click anywhere in the drawing area to place the text.
3. Type the desired text.
4. Confirm the text by clicking outside the text area or press any button in Structure Editor..

When you click the Templates button  in the Structure Editor window, the Template dialog window appears. Mass Frontier comes with more then 200 predefined templates. To insert a template structure into Structure Editor:

1. Select a group of templates in the directory list box. You can do this using the arrow keys on the keyboard or clicking the appropriate name of the group.
2. Click any atom or bond, depending on whether you want to attach the template to an atom or a bond of a structure in Structure Editor.
3. The Template dialog window will then disappear and you can place or attach the chosen template.
4. Switch off the template button or restore the default state of the Editor.

Any modification that you make to a structure applies only to the selected atoms or bonds In addition, when a (Sub)Structure search is initiated, the program automatically uses the selected (sub)structure in Structure. Before you select one or more atoms you should restore the default state of the editor. To select a group of atoms that are next to each other:

• Hold down the mouse button and drag a rectangle around the atoms you want to select.

To change the charge state or isotope of an atom, or to change the element entirely, use the Atom Properties dialog box.

To open the Atom Properties window, use one of the following methods:

• Select the Atom Properties  button in the Structure Editor window and then click the atom you want to change.
• Or restore defaults, and then double-click on the atom you want to change.

Bond Properties include bond multiplicity, bond style and bond color.

To change the multiplicity of a bond,

Click the , or , or  button in the Structure Editor window and then click the bond you want to change.

Mass spectrometry is often unable to provide information about the exact position of a functional group on a chain or ring portion of a structure. In a number of application areas even incompletely characterized molecules can be sufficient to study a particular phenomenon. A typical example is metabolite characterization in an early drug discovery process, where knowledge of the precise location of biotransformation action is of less importance.

Mass Frontier supports extensive use of the Windows Clipboard for the exchange of structural information between modules. In addition, copy and paste functions may be used inside Structure editor. To draw larger structures efficiently, we recommended taking advantage of the copy and paste functions.

If you have copied a structure or fragment anywhere in the program or in a third party structure drawing tool, you can paste it to Structure Editor. If necessary, the structure can be changed or corrected and then returned to where it originated. This is especially useful for structure elucidation. For example, you can copy a structure from the Database Manager window, paste it to Structure Editor, make appropriate changes, and then move it back to Database Manager. If the spectrum and the structural proposal are not consistent, the process can be repeated.

Mass Frontier allows the processing of structures where the charge site is not specified. This kind of molecule representation is of great importance when dealing with ionic structures, since the favored ionization site or the explicit charge site during fragmentation reactions is often unclear. Several ion types can be chosen in the program.

To move a structure in the Structure Editor:

1. Select the atoms or bonds you wish to move.
2. Point the mouse cursor at any selected atom or bond.
3. Hold down the mouse button and drag the selected structure to the new location.

To resize a structure in the Structure Editor:

1. Select the structure/or part of structure you wish to resize.
   
2. Click the Resize button , or select the Structure | Resize menu item.
   
   
3. Drag one of the small rectangles on the structure edge until the new size is achieved.
   
   
4. Release the mouse button.

The Rotate Structure option allows you to twist a structure in any direction. The center of rotation, indicated by a small circle with a cross in the middle , can be moved to any location.

To rotate a structure in the Structure Editor:

To make a mirror image of your structure in the Structure Editor:

1. Select the structure/or part of structure you want to mirror.
2. Click the Mirror button , or select the Structure | Mirror menu item.
   
   
3. Click one of the small rectangles on the structure edge.

The Clean function allows you to achieve a professional look to your structures. In contrast to other commercial structure drawing programs, with Mass Frontier you can even clean up an individual part of a structure. For example, you can restrict cleaning to certain functional groups, while the main skeleton remains intact. However, the algorithm of cleaning 2D structures is a particularly difficult mathematical problem and has yet to be completely solved. As a result this function may, in some complicated cases, lead to structures you will not be completely satisfied with. If this should occur, simply use the Undo function.

Structure Editor comes complete with a function for checking chemical structures. Structure Checker searches for formal errors and unusual structural features. If a structure is formally incorrect, or Structure Checker considers there is some doubt about its validity, a Structure Check Results window appears with a list of errors and warnings. When this window is closed the program automatically selects the atoms and bonds, which are considered incorrect. As mentioned in the Program Limitation section, structures that are not connected are considered to be mixtures, which are reported as errors.

When you select a part of a structure, Structure Editor automatically displays the molecular formula and monoisotopic molecular mass of the selected atoms (F:) in the status bar of Structure Editor, together with corresponding loss (L:).

You may find this information useful for simple consistency checking of mass spectrum and chemical structure.