These menus allows the user to manipulate a molecule, that is, to move around atoms or groups of atoms. The coordinates in the database are updated as the atom(s) move and can therefore be tagged with distances and neighbour calculations. However, the updated coordinates are not written to disk until one of the following commands Save_DB, Stop, BackUp_db, or Sam_atom_out is issued. In general, the Manip commands are terminated by selecting Yes or No to accept or reject the new coordinates.
Each minor menu has a so called dial set associated with it. All dial sets have the same four dials associated with the view rotations around x, y and z, and the zoom. The remaining dials may have different functions in the different dial sets, depending on the requirements of the particular menu activating the dial set. These will be called the auxiliary dials. For example, the Move_atom menu has a dial set in which the three auxiliary dials control the translations along x, y & z, respectively. Some commands, for example Move_zone need to activate two dial sets, one for the rotations and one for the translations. To switch between different dial sets, the two commands Dial_previous and Dial_next are used. In fact, we recommend that these two commands are on the screen at all times. Dial set 1 is the default viewing dial set, activated when O is invoked.