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Synchrotron X-ray Laue microdiffraction is used to investigate the microstructure of deformed quartz, which has trigonal symmetry. The unambiguous indexing of a Laue diffraction pattern can only be achieved by taking the intensities of the diffraction peaks into account. The intensities are compared with theoretical structure factors after correction for the incident X-ray beam flux, X-ray beam polarization, air absorption, detector response and Lorentz factor. This allows mapping of not only the grain orientation but also the stress tensor. The method is applicable for correct orientation determination of all crystals with trigonal symmetry and is indispensable for structure refinements of such materials from Laue diffraction data.