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*   Working with the Structure Editor
You can open multiple Structure Editor modules in the Mass Frontier application. Use the list in the Mass Frontier main window to switch between them.
The Structure Editor supports two kinds of structure formats:
These formats are also supported in the Database Manager module. Templates are stored in MCS format, using the .tml extension. For additional information, see Using Templates.
The Mass Frontier application restricts searches using a set of structural constraints or the “Good-Bad” list. For example, you can instruct the system to conduct a library search comparing an unknown spectrum with only the spectra of ketones. This feature provides many possibilities for targeting your search results. For additional information, see Search Constraints.
The “Good-Bad” structures are stored in the …\Constraints directory, and the structures are saved in MCS format (.mcs). The Mass Frontier application automatically retrieves all MCS structures from the Constraints directory and puts them in a “Good-Bad” list in the Constraints dialog box.
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To open the Structure Editor window
Do one of the following:
Click the Structure Editor button, , in the Mass Frontier toolbar.
–or–
Choose Tools > Structure Editor from the Mass Frontier main menu.
The Structure Editor window opens.
Structure Editor window
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To begin drawing a chemical structure
1.
The cursor changes shape to represent the current drawing mode.
2.
Click the drawing area to place an element.
–or–
Drag the cursor to create elements such as single/double/triple bonds or a chain.
All elements are recursive—that is, the application draws a new element each time you click.
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To change the size of the Structure Editor window
Drag the borders of the Structure Editor to change the width or height.
With a smaller window, you can have several open modules on your application window; a larger window gives you more drawing area.
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To restore the default state of the Structure Editor
Do one of the following:
Click the Default Mode button, , in the upper left corner of the window.
–or–
Right-click the drawing area and choose Default Mode from the shortcut menu.
By default, no drawing element is selected. The plain arrow cursor indicates that the Structure Editor is in the default state.
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To open a structure
Click the Open Structure button, , select a structure, and click Open.
When you open a file that contains more than one structure (.sdf file), only the first structure in the file is loaded into the Structure Editor.
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To save a structure
1.
Click the Save Structure button, .
–or–
Choose File > Save > Structure from the Mass Frontier main menu.
2.
Because Mass Frontier is a 32-bit application, you can save structures under their actual names, regardless of length (for example, 1-Amino-2-hydroxyindane.mol).


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Related Topics:
  Customizing the Structure Layout
  Using Templates
  Modifying Atoms and Bonds
  Using Toolbar Functions
  Displaying the Monoisotopic Molecular Mass
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