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The optional 'controls.tmd' file adds 3D click spots to the virtual cockpit in the shape of a cylinder, box or sphere. Each of the clickspots can have different messages assigned to it that allow the user to interact with the cockpit using the left and right mouse buttons as well as the mouse wheel. A message that is sent from the 'controls.tmd' has a value and qualifier assigned to it that allows either direct assignment of a value, increment/decrement or toggling of. The messages are received by the 'control_input' objects in dynamics section of the main .tmd file as described in the examples above.
The definition of a click spot is rather simple. After deciding on the best shape that fits best the position is adjusted in the R0 attribute, the orientation is set by the B0 matrix and then the size is adjusted. If another aircraft already uses a similar function, then its best to copy the message name from its 'controls.tmd' file. But it is also ok to use own custom names for the messages if desired.
Experience shows that it is good practice to sort the click spots within the 'controls.tmd' file similar to how a pilot would scan the cockpit. For example, most airliner overhead panels have columns which are gone through one by one from top to bottom starting with the left column. Sorting the click spots in a similar way will make it easier to find a click spot again later.
Please note that a click spot cannot work if there is an analog axis assigned in the controls setting of the Aerofly FS 2 Flight Simulator that uses the exact same message name. An example would be the Throttle command, which pretty much always has an axis assigned to it. A click spot with the same message would be obsolete because the user can't actually overwrite the analog input.