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*   Using the Fragments & Mechanisms Window
When the application finishes a reaction-generating process, a Fragments & Mechanisms window opens. You cannot directly open this window from any menu or toolbar. A Fragments & Mechanisms window displays either the complete mechanisms of ion-decomposition reactions or only the resulting fragments.
To customize the m/z tab display
Choose Options > Settings from the Mass Frontier main menu.
The Options dialog box opens.
Click Reaction in the Layouts section.
The m/z page of the Options: Reaction Layout dialog box opens.
The Sample area shows how each display style will look.
The next time you generate fragments and mechanisms, the application uses the specified display changes. Current Fragments & Mechanisms windows are not affected.
To display a mechanism or fragment for an m/z value
Do one of the following:
Click the appropriate m/z tab.
–or –
Choose the m/z value from the m/z list.
The display style depends on the settings you specified in the Options dialog box.
To copy fragments or mechanisms
Click the Copy button on the Mass Frontier main menu and choose one of the following:
This command copies mechanisms in both graphic format (Enhanced Windows Metafile) and data format.
This command is available only when you have a selected fragment in the Fragments & Mechanisms window.
This command copies all fragments listed in the Fragments & Mechanisms window.
To display the isobaric fragments for a particular m/z value
You can generate several possible isobaric fragments for a particular m/z value. When more than one fragment is generated for an m/z value, the application displays each numbered fragment separately.
To display the isobaric fragments with their corresponding mechanisms, click the numbered button next to the hand pointer.
The fragments are sorted according to the simplicity of their production mechanism, so fragment No.1 is produced by the simplest (shortest) mechanism. The isobaric fragments are usually isomers of the same fragments with a different charge, radical, or p-bond location.

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