Oblique section reconstruction can produce a 3-D image from electron micrographs of a sectioned crystal when the orientation of the section plane is not aligned with the principal planes of the unit cell. We describe here the reconstruction protocol and the specialized computer software for a Fourier space method that can extract 3-D information from 2-D projection images of oblique sections. The protocol encompasses correction for image defects and image distortions, determination and refinement of reciprocal lattices, calculation of the crystal orientation in 3-D space, extraction of periodic information, alignment in Fourier space, determination and deconvolution of section thickness, and calculation of structure factors of the original crystal. A 3-D map of the unit cell can then be computed by standard crystallographic procedures. Oblique section reconstruction provides an alternative to tomography for 3-D imaging of crystalline objects with large unit cells. The method provides an excellent means of obtaining a 3-D transform using electron microscopy for comparison with X-ray diffraction data from native specimens. (C) 1996 Academic Press, Inc.