A surgical system having a patient side cart having at least one telesurgically operated instrument, the at least one telesurgically operated instrument comprising a surgical end effector having a plurality of effector components. A transmission is coupled to a motor. The drive train includes at least a first effector drive train and a second effector drivetrain. A controller comprises at least one processor for controlling the transmission. The controller is performs a method by locking an output gear of the second effector drivetrain rotating a camshaft to shift coupling of the motor from the first effector drivetrain to the second effector drivetrain determining that the output gear is aligned by driving the locked output gear using a first torque determining that the output gear is properly braked by driving the locked output gear using a second torque disengaging the lock from the output gear and driving the second effector drivetrain using the motor.
