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The IDXREF step of [[XDS]]
# reads a list of spot positions from SPOT.XDS and converts them to vectors in reciprocal space(which requires suitable values for ORGX, ORGY, DETECTOR_DISTANCE, OSCILLATION_RANGE, X-RAY_WAVELENGTH, QX, QY, DIRECTION_OF_DETECTOR_X-AXIS, DIRECTION_OF_DETECTOR_Y-AXIS, INCIDENT_BEAM_DIRECTION, ROTATION_AXIS)
# calculates primitive unit cell parameters from the (clustered) difference vectors
# as a control, prints out indices (which should be close to integer numbers) corresponding to difference vectors