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I do not completely understand why one uses the second angle measured from the vertical y-axis for the second generalized coordinate. The second angle is not independent of the first, that is if the first angle moves, so does the second. Why not use the angle measured relative from the first mass to measure the second mass, that is use the angle that is calculated from being in the first masses reference frame for the second mass. This way, the second angle is independent of the first angle. Thanks for any help, I really appreciate it!