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mol

Load, modify, or delete a molecule in VMD. In the following, molecule_number is a string describing which molecules are to be affected by the command. It is one of the following: all, top, active, inactive, displayed, on, off, fixed, free, or one of the unique integer ID codes assigned to the molecules when they are loaded (starting with 0). The codes (molIDs) are not reused after a molecule is deleted, so if you, for example, have three molecules loaded (numbered 0, 1, 2), delete molecule with molID equal to 0, and then load another molecule, the new molecule will have molID 3. Thus, the list of available molecule IDs becomes (1 2 3). The index of the molecule on this list is, among many other things, accessible through the molinfo command. In the above case, for example, molecule that was loaded the last has molID equal to 3, however, it is the third on the list of molecules, so it has the index equal to 2 (since we start countin from 0).

The molecule representations (views) are assigned integer number (starting with 0 for each molecule), which appear in the list on the Graphics form. The representations can be added, deleted or changed with the mol command. See also sections on molinfo command for more ways of retrieving information about the representations. See Chapter §  for information on how to use mol command to load user-defined graphics.


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