The method of alignment of a glass capillaries depends on how it mounted. Brass sample holders with holes drilled to the outside diameter of the capillary plus a few microns tolerance may be used.

A more common method is to mount the sample on a single-crystal style goniometer head (but without the vertical adjustment) and then adjust the arcs and translations (as seen in the picture on the left and in the figure on the right) so that the capillary appears vertical when viewed through a telescope mounted on the diffractometer. Adjustments are made on a stationary sample: first adjust φx,Tx and check that the telescope is centred by rotating the goniometer head 180° about θ; then rotate it 90° about θ and adjust φy,Ty. Finally, spin the capillary and check that it appears stationary while viewed through the telescope. Occasionally, a small amount of precession may be observed if the capillary is not perfectly straight.

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