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Amaya provides the same method to create and edit matrices as to edit HTML tables. Similar to tables, a specific command (Delete matrix column) deletes a column in a matrix, even if it's not empty. This command is located at the end of the Math submenu on the XML menu.
You may want to change the structure of an existing expression, such as appending a superscript or putting parentheses around an expression. To do that, select the expression and enter the new construct with the palette, the Math menu or the keyboard. You can also use Transform on the Edit menu. Select the expression you want to transform and Transform will display a menu with all possible changes.