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Linear Fragmentation
After a structure has been drawn, you can switch to Fragment mode to examine the fragmentation patterns. Select the 'Analyze' mode option from the palette, or click the F3 Shortcut key, or right-click the mouse and select Analyze from the Popup menu. The normal default fragmentation mode is linear. To carry out a linear fragmentation, confirm that the Linear option is selected in the Speedbutton bar at the top of the screen (see Toolbar). Then move the mouse pointer to the desired starting point of the fragment line, depress the (left) mouse button and hold it while adjusting the line as desired. On release of the button, the molecule will be 'fragmented' and the two fragment masses will be displayed in either nominal or accurate mass depending on the currently selected mass accuracy state. Each non-hydrogen atom in the fragment will be drawn with a colored dot -- either red or blue (or the colors specified in Preferences) -- with the color of the fragment mass corresponding to that part of the molecule.
MSC will automatically clear the previous fragmentation line when a new one is drawn unless the Multifragment option is turned on. If the desired fragmentation cannot be carried out effectively in linear mode, you can choose either Box or Region fragmentations. Note that the linear fragmentation line is treated as if it has infinite length when classifying fragment atoms.