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.