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Box Fragmentation
Box fragmentation is an alternative fragmentation mode. The normal default fragmentation mode is a line through the structure as described in Linear fragmentation. In some cases, however, the latter mode will not permit the exact fragmentation needed. Box fragmentation is one of the two additional options available for use in those cases (along with Region fragmentation).
Box fragmentation is selected by clicking the appropriate Speedbutton on the Toolbar when in Fragment mode. In this mode you locate the mouse pointer at an appropriate starting point, and then click and hold the (left) mouse button. As the mouse is moved, a rectangular region will be outlined on the molecule. On release of the button, the structure will be 'fragmented' into the structure portion within the box, and the remainder of the molecule outside of the box. The masses of the two fragments are displayed above the box, and also in a popup window at the lower right hand corner of the screen if the Show Boxfrag Popup option is selected on the Options menu.