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*   Generating Fragments and Mechanisms
You can generate fragmentation and rearrangement pathways from any structure you supply, including ions and isotopically-labeled compounds. The structure can originate from the Structure Editor, the Database Manager, or a Fragments & Mechanisms window. Before the Mass Frontier application generates the program, it checks the input structure for errors. If it finds any errors, a message box displays the errors and cancels the generation.
When you start a generation from the Structure Editor, the application assumes that the complete structure is intended as input for the generation.
When you start a generation from the Database Manager window, the application automatically links the generated fragments in the Fragments & Mechanisms window with the corresponding spectrum in the Database Manager window. The application highlights peaks that have the same m/z value as the generated fragments. Selecting a highlighted peak reveals all the pathways leading to it. By default, peaks are highlighted in red.
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To start a generation of possible fragmentation and rearrangement pathways
1.
Click the Fragments and Mechanism button, , in the Mass Frontier toolbar.
–or–
Choose Tools > Fragments and Mechanisms from the Mass Frontier main menu.
The Reaction Restrictions dialog box opens. For detailed information about the Reaction Restrictions dialog box, see Specifying Reaction Restrictions.
Reaction Restrictions dialog box
2.
The Generation of Fragments & Mechanisms dialog box displays the progress as the application checks for structure errors. See Generation of Fragments & Mechanisms dialog box.
When the checks are complete, the Fragments & Mechanisms window opens. See Using the Fragments & Mechanisms Window.
Generation of Fragments & Mechanisms dialog box
List of m/z values of the ions that have already been generated and the total number of ions that have already been generated.
Indicates approximately how many temporary internal reactions have been generated from a particular structure. Large and structurally complicated molecules can produce an enormous number of reactions but consume a large amount of memory. This memory consumption limits the number of temporarily generated reactions. If the reactions limit is reached, the generation stops and the application displays an error message, but the fragments and mechanisms generated up to that point are displayed. The most important fragments are generated first, so even if a generation stops, the most important fragments have likely been generated. However, if you are missing an important fragment because you assume the generation was interrupted, you can increase the reactions limit. For additional information, see Sizes Page.
With this multithreading strategy, you can simultaneously perform multiple tasks. For example, while the application is generating reactions, you can search libraries or analyze your spectra. You can also run two or more generations of fragments and mechanisms at the same time.
Temporarily interrupts generation to redirect processing power to other processes that might be simultaneously running in the application or to other Windows applications.
Stops the current generation. The application displays fragments and any production mechanisms that are generated up to that point.
Cancels the current generation. The application does not display any generated fragments. It can take several seconds before the window closes.


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Related Topics:
  Features
  Using the Fragments & Mechanisms Window
  Previewing Unimolecular Reactions
  Generating Fragments for Multiple Structures
  Specifying Reaction Restrictions
  Working with Generated Fragments
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