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In principle, structural analysis answers the following questions:
         i) Unit cell and space group symmetry,
         ii) Atomic positions,
         iii) Anisotropic atomic displacements.
However, for complex structures, those questions normally can not be addressed by a single technique.

The general procedure for determining a crystal structure is:
         i) Obtain a suitable specimen,
         ii) Collect raw data,
         iii) Determine a trial structure using ab initio methods,
         iv) Refine the data.

Two ways are normally used to collect raw data for unknown crystal structures:
         i) Use electron diffraction intensities, similar to X-ray diffraction. In EM (electron microscopy) crystallography, kinematic and quasi-kinematic approximations to the scattering of fast electrons allow for successfully solving and refining of unknown crystal structures, known as “structural electron crystallography”.
         ii) Combine electron diffraction and HRTEM.

For electron diffraction analysis, crystalline specimens have to be tilted in a goniometer in TEM in order to:
         i) Observe lattice fringes and crystal structures.
         ii) Determine the crystal orientation.
         iii) Observe diffraction contrast of lattice defects with certain Bragg reflections or known orientation.
         iv) Determine the Burgers vector of lattice defects.

However, for complex structures, e.g. zeolites, subtle changes of structures can affect both the observed intensities and symmetry. These effects in the observed intensities and symmetry can cause serious problems in the structure analysis [1]:
         i) Severe overlap of reflections, and thus addtional techniques, e.g. software, are needed to decompose the peaks into individual reflections.
         ii) Incorrect determination of the space group, especially when the true symmetry is masked by pseudo-symmetry.
         iii) The effect of framework flexibility on the structure analysis, e.g. for zeolites [1].
         iv) Disorder of the structure and faulting, and their effects on the structure solution.
         v) Problems caused by isomorphous replacement of framework atoms, e.g. in zeolites. [1]
         vi) The effects due to small crystal size and the limits on the crystal size that can be used.

[1] Structures and Structure Determination, Molecular Sieves Science and Technology, Editors: H. G. Karge • J. Weitkamp, Volume 2, 1999.