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The Hand Calibration plugin should be rather straightforward: put the joint in the correct position using the calibration gigs (you can read the calibrated value in the right column), then double click on the corresponding row. The row should turn green and the raw value should be updated.

To save, just press the Save button, and select the file you want to save the calibration (you should save it to sr_robot_lib/config/calibration.yaml by default). This will update the calibration file, modifying only the newly calibrated joints.