International
Tables for Crystallography Volume B Reciprocal space Edited by U. Shmueli © International Union of Crystallography 2006 
International Tables for Crystallography (2006). Vol. B. ch. 2.5, pp. 322323

Conventional direct phasing techniques, as commonly employed in Xray crystallography (e.g. see Chapter 2.2 ), have also been used for ab initio electroncrystallographic analyses. As in Xray crystallography, probabilistic estimates of a linear combination of phases (Hauptman & Karle, 1953; Hauptman, 1972) are made after normalized structure factors are calculated via electron form factors, i.e. (Here, an overall temperature factor can be found from a Wilson plot. Because of multiple scattering, the value of B may be found occasionally to lie close to 0.0 Å^{2}.) The phase invariant sums can be particularly effective for structure analysis. Of particular importance historically have been the triple invariants where and . The probability of predicting is directly related to the value of where and Z is the value of the scattering factor at . Thus, the values of the phases are related to the measured structure factors, just as they are found to be in Xray crystallography. The normalization described above imposes the pointatom structure (compensating for the falloff of an approximately Gaussian form factor) often assumed in deriving the joint probability distributions. Especially for van der Waals structures, the constraint of positivity also holds in electron crystallography. (It is also quite useful for charged atoms so long as the reflections are not measured at very low angles.) Other useful phase invariant sums are the triples, where , and the quartets, where and . The prediction of a correct phase for an invariant is related in each case to the normalized structurefactor magnitudes.
The procedure for phase determination, therefore, is identical to the one used in Xray crystallography (see Chapter 2.2 ). Using vectorial combinations of Miller indices, one generates triple and quartet invariants from available measured data and ranks them according to parameters such as A, defined above, which, as shown in Chapter 2.2 , are arguments of the Cochran formula. The invariants are thus listed in order of their reliability. This, in fact, generates a set of simultaneous equations in crystallographic phase. In order to begin solving these equations, it is permissible to define arbitrarily the phase values of a limited number of reflections (three for a threedimensional primitive unit cell) for reflections with Millerindex parity and , where g is an even number. This defines the origin of a unit cell. For noncentrosymmetric unit cells, the condition for defining the origin, which depends on the space group, is somewhat more complicated and an enantiomorphdefining reflection must be added.
In the evaluation of phaseinvariant sums above a certain probability threshold, phase values are determined algebraically after origin (and enantiomorph) definition until a large enough set is obtained to permit calculation of an interpretable potential map (i.e. where atomic positions can be seen). There may be a few invariant phase sums above this threshold probability value which are incorrectly predicted, leading either to false phase assignments or at least to phase assignments inconsistent with those found from other invariants. A small number of such errors can generally be tolerated. Another problem arises when an insufficient quantity of new phase values is assigned directly from the phase invariants after the origindefining phases are defined. This difficulty may occur for small data sets, for example. If this is the case, it is possible that a new reflection of proper index parity can be used to define the origin. Alternatively, algebraic unknowns can be used to establish the phase linkage among certain reflections. If the structure is centrosymmetric, and when enough reflections are given at least symbolic phase assignments, maps are calculated and the correct structure is identified by inspection of the potential maps. When all goes well in this socalled `symbolic addition' procedure, the symbols are uniquely determined and there is no need to calculate more than a single map. If algebraic values are retained for certain phases because of limited vectorial connections in the data set, then a few maps may need to be generated so that the correct structure can be identified using the chemical knowledge of the investigator. The atomic positions identified can then be used to calculate phases for all observed data (via the structurefactor calculation) and the structure can be refined by Fourier (or, sometimes, leastsquares) techniques to minimize the crystallographic R factor.
The first actual application of direct phasing techniques to experimental electrondiffraction data, based on symbolic addition procedures, was to two methylene subcell structures (an nparaffin and a phospholipid; Dorset & Hauptman, 1976). Since then, evaluation of phase invariants has led to numerous other structures. For example, early texture electrondiffraction data sets obtained in Moscow (Vainshtein, 1964) were shown to be suitable for direct analysis. The structure of diketopiperazine (Dorset, 1991a) was determined from these electrondiffraction data (Vainshtein, 1955) when directly determined phases allowed computation of potential maps such as the one shown in Fig. 2.5.7.1. Bond distances and angles are in good agreement with the Xray structure, particularly after leastsquares refinement (Dorset & McCourt, 1994a). In addition, the structures of urea (Dorset, 1991b), using data published by Lobachev & Vainshtein (1961), paraelectric thiourea (Dorset, 1991b), using data published by Dvoryankin & Vainshtein (1960), and three mineral structures (Dorset, 1992a), from data published by Zvyagin (1967), have been determined, all using the original texture (or mosaic singlecrystal) diffraction data. The most recent determination based on such texture diffraction data is that of basic copper chloride (Voronova & Vainshtein, 1958; Dorset, 1994c).

Potential map for diketopiperazine ([001] projection) after a direct phase determination with texture electrondiffraction intensity data obtained originally by Vainshtein (1955). 
Symbolic addition has also been used to assign phases to selectedarea diffraction data. The crystal structure of boric acid (Cowley, 1953) has been redetermined, adding an independent lowtemperature analysis (Dorset, 1992b). Additionally, a direct structure analysis has been reported for graphite, based on highvoltage intensity data (Ogawa et al., 1994). Twodimensional data from several polymer structures have also been analysed successfully (Dorset, 1992c) as have threedimensional intensity data (Dorset, 1991c,d; Dorset & McCourt, 1993).
Phase information from electron micrographs has also been used to aid phase determination by symbolic addition. Examples include the epitaxically oriented paraffins nhexatriacontane (Dorset & Zemlin, 1990), ntritriacontane (Dorset & Zhang, 1991) and a 1:1 solid solution of nC_{32}H_{66}/nC_{36}H_{74} (Dorset, 1990a). Similarly, lamellar electrondiffraction data to ca 3 Å resolution from epitaxically oriented phospholipids have been phased by analysis of and triplet invariants (Dorset, 1990b, 1991e,f), in one case combined with values from a 6 Å resolution electron microscope image (Dorset et al., 1990, 1993). Most recently, such data have been used to determine the layer packing of a phospholipid binary solid solution (Dorset, 1994d).
An ab initio direct phase analysis was carried out with zonal electrondiffraction data from copper perchlorophthalocyanine. Using intensities from a ca 100 Å thick sample collected at 1.2 MeV, the best map from a phase set with symbolic unknowns retrieves the positions of all the heavy atoms, equivalent to the results of the best images (Uyeda et al., 1978–1979). Using these positions to calculate an initial phase set, the positions of the remaining light C, N atoms were found by Fourier refinement so that the final bond distances and angles were in good agreement with those from Xray structures of similar compounds (Dorset et al., 1991). A similar analysis has been carried out for the perbromo analogue (Dorset et al., 1992). Although dynamical scattering and secondary scattering significantly perturb the observed intensity data, the total molecular structure can be visualized after a Fourier refinement. Most recently, a threedimensional structure determination was reported for C_{60} buckminsterfullerene based on symbolic addition with results most in accord with a rotationally disordered molecular packing (Dorset & McCourt, 1994b).
References
Cowley, J. M. (1953). Structure analysis of single crystals by electron diffraction. II. Disordered boric acid structure. Acta Cryst. 6, 522–529.Google ScholarDorset, D. L. (1990a). Direct structure analysis of a paraffin solid solution. Proc. Natl Acad. Sci. USA, 87, 8541–8544.Google Scholar
Dorset, D. L. (1990b). Direct determination of crystallographic phases for diffraction data from phospholipid multilamellar arrays. Biophys. J. 58, 1077–1087.Google Scholar
Dorset, D. L. (1991a). Electron diffraction structure analysis of diketopiperazine – a direct phase determination. Acta Cryst. A47, 510–515.Google Scholar
Dorset, D. L. (1991b). Is electron crystallography possible? The direct determination of organic crystal structures. Ultramicroscopy, 38, 23–40.Google Scholar
Dorset, D. L. (1991c). Electron diffraction structure analysis of polyethylene. A direct phase determination. Macromolecules, 24, 1175–1178.Google Scholar
Dorset, D. L. (1991d). Electron crystallography of linear polymers: direct structure analysis of poly(caprolactone). Proc. Natl Acad. Sci. USA, 88, 5499–5502.Google Scholar
Dorset, D. L. (1991e). Direct determination of crystallographic phases for diffraction data from lipid bilayers. I. Reliability and phase refinement. Biophys. J. 60, 1356–1365.Google Scholar
Dorset, D. L. (1991f). Direct determination of crystallographic phases for diffraction data from lipid bilayers. II. Refinement of phospholipid structures. Biophys. J. 60, 1366–1373.Google Scholar
Dorset, D. L. (1992a). Direct phasing in electron crystallography: determination of layer silicate structures. Ultramicroscopy, 45, 5–14.Google Scholar
Dorset, D. L. (1992b). Direct methods in electron crystallography – structure analysis of boric acid. Acta Cryst. A48, 568–574.Google Scholar
Dorset, D. L. (1992c). Electron crystallography of linear polymers: direct phase determination for zonal data sets. Macromolecules, 25, 4425–4430.Google Scholar
Dorset, D. L. (1994c). Electron crystallography of inorganic compounds. Direct determination of the basic copper chloride structure CuCl_{2}·3Cu(OH)_{2}. J. Chem. Crystallogr. 24, 219–224.Google Scholar
Dorset, D. L. (1994d). Direct determination of layer packing for a phospholipid solid solution at 0.32 nm resolution. Proc. Natl Acad. Sci. USA, 91, 4920–4924.Google Scholar
Dorset, D. L., Beckmann, E. & Zemlin, F. (1990). Direct determination of a phospholipid lamellar structure at 0.34 nm resolution. Proc. Natl Acad. Sci. USA, 87, 7570–7573.Google Scholar
Dorset, D. L. & Hauptman, H. A. (1976). Direct phase determination for quasikinematical electron diffraction intensity data from organic microcrystals. Ultramicroscopy, 1, 195–201.Google Scholar
Dorset, D. L. & McCourt, M. P. (1993). Electron crystallographic analysis of a polysaccharide structure – direct phase determination and model refinement for mannan I. J. Struct. Biol. 111, 118–124.Google Scholar
Dorset, D. L. & McCourt, M. P. (1994a). Automated structure analysis in electron crystallography: phase determination with the tangent formula and leastsquares refinement. Acta Cryst. A50, 287–292.Google Scholar
Dorset, D. L. & McCourt, M. P. (1994b). Disorder and molecular packing of C_{60} buckminsterfullerene: a direct electroncrystallographic analysis. Acta Cryst. A50, 344–351.Google Scholar
Dorset, D. L., McCourt, M. P., Tivol, W. F. & Turner, J. N. (1993). Electron diffraction from phospholipids – an approximate correction for dynamical scattering and tests for a correct phase determination. J. Appl. Cryst. 26, 778–786.Google Scholar
Dorset, D. L., Tivol, W. F. & Turner, J. N. (1991). Electron crystallography at atomic resolution: ab initio structure analysis of copper perchlorophthalocyanine. Ultramicroscopy, 38, 41–45.Google Scholar
Dorset, D. L., Tivol, W. F. & Turner, J. N. (1992). Dynamical scattering and electron crystallography – ab initio structure analysis of copper perbromophthalocyanine. Acta Cryst. A48, 562–568.Google Scholar
Dorset, D. L. & Zemlin, F. (1990). Direct phase determination in electron crystallography: the crystal structure of an nparaffin. Ultramicroscopy, 33, 227–236.Google Scholar
Dorset, D. L. & Zhang, W. P. (1991). Electron crystallography at atomic resolution: the structure of the oddchain paraffin ntritriacontane. J. Electron Microsc. Tech. 18, 142–147.Google Scholar
Dvoryankin, V. F. & Vainshtein, B. K. (1960). An electron diffraction study of thiourea. Sov. Phys. Crystallogr. 5, 564–574.Google Scholar
Hauptman, H. (1972). Crystal structure determination. The role of the cosine seminvariants. NY: Plenum Press.Google Scholar
Hauptman, H. & Karle, J. (1953). Solution of the phase problem. I. The centrosymmetric crystal. American Crystallographic Association Monograph No. 3. Ann Arbor, MI: Edwards Brothers.Google Scholar
Lobachev, A. N. & Vainshtein, B. K. (1961). An electron diffraction study of urea. Sov. Phys. Crystallogr. 6, 313–317.Google Scholar
Ogawa, T., Moriguchi, S., Isoda, S. & Kobayashi, T. (1994). Application of an imaging plate to electron crystallography at atomic resolution. Polymer, 35, 1132–1136.Google Scholar
Uyeda, N., Kobayashi, T., Ishizuka, K. & Fujiyoshi, Y. (1978–1979). High voltage electron microscopy for image discrimination of constituent atoms in crystals and molecules. Chem. Scr. 14, 47–61.Google Scholar
Vainshtein, B. K. (1955). Elektronograficheskoe issledovanie diketopiperazina. Zh. Fiz. Khim. 29, 327–344.Google Scholar
Vainshtein, B. K. (1964). Structure analysis by electron diffraction. Oxford: Pergamon Press.Google Scholar
Voronova, A. A. & Vainshtein, B. K. (1958). An electron diffraction study of CuCl_{2}·3Cu(OH)_{2}. Sov. Phys. Crystallogr. 3, 445–451.Google Scholar
Zvyagin, B. B. (1967). Electrondiffraction analysis of clay mineral structures. New York: Plenum.Google Scholar