Tables for
Volume B
Reciprocal space
Edited by U. Shmueli

International Tables for Crystallography (2010). Vol. B, ch. 2.5, pp. 297-402   | 1 | 2 |

Chapter 2.5. Electron diffraction and electron microscopy in structure determination

J. M. Cowley,a J. C. H. Spence,b M. Tanaka,f B. K. Vainshtein,c B. B. Zvyagin,d P. A. Penczekg and D. L. Dorsete

aArizona State University, Box 871504, Department of Physics and Astronomy, Tempe, AZ 85287–1504, USA, bDepartment of Physics, Arizona State University, Tempe, AZ 95287–1504, USA, cInstitute of Crystallography, Academy of Sciences of Russia, Leninsky prospekt 59, Moscow B-117333, Russia, dInstitute of Ore Mineralogy (IGEM), Academy of Sciences of Russia, Staromonetny 35, 109017 Moscow, Russia, eExxonMobil Research and Engineering Co., 1545 Route 22 East, Clinton Township, Annandale, New Jersey 08801, USA,fInstitute of Multidisciplinary Research for Advanced Materials, Tohoku University, Japan, and gThe University of Texas – Houston Medical School, Department of Biochemistry and Molecular Biology, 6431 Fannin, MSB 6.218, Houston, TX 77030, USA


Adiga, P. S., Malladi, R., Baxter, W. & Glaeser, R. M. (2004). A binary segmentation approach for boxing ribosome particles in cryo EM micrographs. J. Struct. Biol. 145, 142–151.
Agrawal, R. K., Penczek, P., Grassucci, R. A., Li, Y., Leith, A., Nierhaus, K. H. & Frank, J. (1996). Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science, 271, 1000–1002.
Avilov, A. S. (1979). Electrical measurement of reflection intensities on electron diffraction from mosaic single crystals. Sov. Phys. Crystallogr. 24, 103–104.
Avilov, A. S., Kuligin, A. K., Pietsch, U., Spence, J. C. H., Tsirelson, V. G. & Zuo, J. M. (1999). Scanning system for high-energy electron diffractometry. J. Appl. Cryst. 32, 1033–1038.
Avilov, A. S., Parmon, V. S., Semiletov, S. A. & Sirota, M. I. (1984). Calculation of reflected intensities in multiple-beam diffraction of fast electrons by polycrystalline specimens. Sov. Phys. Crystallogr. 29, 5–7.
Baldwin, P. R. & Penczek, P. A. (2007). The transform class in SPARX and EMAN2. J. Struct. Biol. 157, 250–261.
Basokur, A. T. (1998). Digital filter design using the hyperbolic tangent functions. J. Balkan Geophys. Soc. 1, 14–18.
Bendersky, L. A. (1985). Quasicrystal with one-dimensional translational symmetry and a tenfold rotation axis. Phys. Rev. Lett. 55, 1461–1467.
Bendersky, L. A. (1986). Decagonal phase. J. Phys. Colloq. 47, C3, 457–464.
Bendersky, L. A. & Kaufman, M. J. (1986). Determination of the point group of the icosahedral phase in an Al–Mn–Si alloy using convergent-beam electron diffraction. Philos. Mag. B53, L75–L80.
Bethe, H. A. (1928). Theorie der Beugung von Elektronen an Kristallen. Ann. Phys. (Leipzig), 87, 55–129.
Biemond, J., Lagendijk, R. L. & Mersereau, R. M. (1990). Iterative methods for image deblurring. Proc. IEEE, 78, 856–883.
Blackman, M. (1939). On the intensities of electron diffraction rings. Proc. R. Soc. London Ser. A, 173, 68–82.
Boisset, N., Penczek, P., Pochon, F., Frank, J. & Lamy, J. (1993). Three-dimensional architecture of human alpha 2-macroglobulin transformed with methylamine. J. Mol. Biol. 232, 522–529.
Boisset, N., Penczek, P., Taveau, J. C., Lamy, J. & Frank, J. (1995). Three-dimensional reconstruction of Androctonus australis hemocyanin labeled with a monoclonal Fab fragment. J. Struct. Biol. 115, 16–29.
Böttcher, B., Wynne, S. A. & Crowther, R. A. (1997). Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy. Nature (London), 386, 88–91.
Bracewell, R. N. (1956). Strip integration in radio astronomy. Austr. J. Phys. 9, 198–217.
Bracewell, R. N. & Riddle, A. C. (1967) Inversion of fan-beam scans in radio astronomy. Astrophys. J. 150, 427–434.
Bricogne, G. & Gilmore, C. J. (1990). A multisolution method of phase determination by combined maximization of entropy and likelihood. I. Theory, algorithms and strategy. Acta Cryst. A46, 284–297.
Brisse, F. (1989). Electron diffraction of synthetic polymers: the model compound approach to polymer structure. J. Electron Microsc. Tech. 11, 272–279.
Buxton, B., Eades, J. A., Steeds, J. W. & Rackham, G. M. (1976). The symmetry of electron diffraction zone axis patterns. Philos. Trans. R. Soc. London Ser. A, 181, 171–193.
Carazo, J. M. (1992). The fidelity of 3D reconstruction from incomplete data and the use of restoration methods. In Electron Tomography, edited by J. Frank, pp. 117–166. New York: Plenum.
Carazo, J. M. & Carrascosa, J. L. (1986). Information recovery in missing angular data cases: an approach by the convex projections method in three dimensions. J. Microsc. 145, 23–43.
Carazo, J. M. & Carrascosa, J. L. (1987). Restoration of direct Fourier three-dimensional reconstructions of crystalline specimens by the method of convex projections. J. Microsc. 145, 159–177.
Cherns, D., Kiely, C. J. & Preston, A. R. (1988). Electron diffraction studies of strain in epitaxial bicrystals and multilayers. Ultramicroscopy, 24, 355–370.
Cherns, D. & Preston, A. R. (1986). Convergent beam diffraction studies of crystal defects. Proc. XI Int. Congr. Electron Microsc., Kyoto, Japan, p. 721.
Clark, J. J., Palmer, M. R. & Lawrence, P. D. (1985). A transformation method for the reconstruction of functions from nonuniformly spaced samples. IEEE Trans. Acoust. Speech Signal Process. 33, 1151–1165.
Cochran, W., Crick, F. H. C. & Vand, V. (1952). The structure of synthetic polypeptides. 1. The transform of atoms on a helix. Acta Cryst. 5, 581–586.
Conway, J. F., Cheng, N., Zlotnick, A., Wingfield, P. T., Stahl, S. J. & Steven, A. C. (1997). Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature (London), 386, 91–94.
Cowley, J. M. (1953). Structure analysis of single crystals by electron diffraction. II. Disordered boric acid structure. Acta Cryst. 6, 522–529.
Cowley, J. M. (1956). A modified Patterson function. Acta Cryst. 9, 397–398.
Cowley, J. M. (1961). Diffraction intensities from bent crystals. Acta Cryst. 14, 920–927.
Cowley, J. M. (1981). Diffraction Physics, 2nd ed. Amsterdam: North-Holland.
Cowley, J. M. (1995). Diffraction Physics, 3rd ed. Amsterdam: North-Holland.
Cowley, J. M. & Au, A. Y. (1978). Image signals and detector configurations for STEM. In Scanning Electron Microscopy, Vol. 1, pp. 53–60. AFM O'Hare: SEM Inc.
Cowley, J. M. & Moodie, A. F. (1957). The scattering of electrons by atoms and crystals. I. A new theoretical approach. Acta Cryst. 10, 609–619.
Cowley, J. M. & Moodie, A. F. (1959). The scattering of electrons by atoms and crystals. III. Single-crystal diffraction patterns. Acta Cryst. 12, 360–367.
Cowley, J. M. & Moodie, A. F. (1960). Fourier images. IV. The phase grating. Proc. Phys. Soc. London, 76, 378–384.
Cowley, J. M., Moodie, A. F., Miyake, S., Takagi, S. & Fujimoto, F. (1961). The extinction rules for reflections in symmetrical electron diffraction spot patterns. Acta Cryst. 14, 87–88.
Cowley, J. M., Rees, A. L. G. & Spink, J. A. (1951). Secondary elastic scattering in electron diffraction. Proc. Phys. Soc. London Sect. A, 64, 609–619.
Cramér, H. (1954). Mathematical Methods of Statistics. Princeton University Press.
Crowther, R. A. & Amos, L. A. (1971). Harmonic analysis of electron microscope images with rotational symmetry. J. Mol. Biol. 60, 123–130.
Crowther, R. A. & Amos, L. A. (1972). Three-dimensional image reconstructions of some small spherical viruses. Cold Spring Harbor Symp. Quant. Biol. 36, 489–494.
Crowther, R. A., Amos, L. A., Finch, J. T., DeRosier, D. J. & Klug, A. (1970). Three dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Nature (London), 226, 421–425.
Crowther, R. A., DeRosier, D. J. & Klug, A. (1970). The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc. R. Soc. London Ser. A, 317, 319–340.
Dawson, B., Goodman, P., Johnson, A. W. S., Lynch, D. F. & Moodie, A. F. (1974). Some definitions and units in electron diffraction. Acta Cryst. A30, 297–298.
De Titta, G. T., Edmonds, J. W., Langs, D. A. & Hauptman, H. (1975). Use of negative quartet cosine invariants as a phasing figure of merit: NQEST. Acta Cryst. A31, 472–479.
DeRosier, D. J. & Klug, A. (1968). Reconstruction of three dimensional structures from electron micrographs. Nature (London), 217, 130–134.
Dong, W., Baird, T., Fryer, J. R., Gilmore, C. J., MacNicol, D. D., Bricogne, G., Smith, D. J., O'Keefe, M. A. & Hovmöller, S. (1992). Electron microscopy at 1 Å resolution by entropy maximization and likelihood ranking. Nature (London), 355, 605–609.
Dorset, D. L. (1976). The interpretation of quasi-kinematical single-crystal electron diffraction intensity data from paraffins. Acta Cryst. A32, 207–215.
Dorset, D. L. (1987). Electron diffraction structure analysis of phospholipids. J. Electron Microsc. Tech. 7, 35–46.
Dorset, D. L. (1990a). Direct structure analysis of a paraffin solid solution. Proc. Natl Acad. Sci. USA, 87, 8541–8544.
Dorset, D. L. (1990b). Direct determination of crystallographic phases for diffraction data from phospholipid multilamellar arrays. Biophys. J. 58, 1077–1087.
Dorset, D. L. (1991a). Electron diffraction structure analysis of diketopiperazine – a direct phase determination. Acta Cryst. A47, 510–515.
Dorset, D. L. (1991b). Is electron crystallography possible? The direct determination of organic crystal structures. Ultramicroscopy, 38, 23–40.
Dorset, D. L. (1991c). Electron diffraction structure analysis of polyethylene. A direct phase determination. Macromolecules, 24, 1175–1178.
Dorset, D. L. (1991d). Electron crystallography of linear polymers: direct structure analysis of poly([epsilon]-caprolactone). Proc. Natl Acad. Sci. USA, 88, 5499–5502.
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.
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.
Dorset, D. L. (1992a). Direct phasing in electron crystallography: determination of layer silicate structures. Ultramicroscopy, 45, 5–14.
Dorset, D. L. (1992b). Direct methods in electron crystallography – structure analysis of boric acid. Acta Cryst. A48, 568–574.
Dorset, D. L. (1992c). Electron crystallography of linear polymers: direct phase determination for zonal data sets. Macromolecules, 25, 4425–4430.
Dorset, D. L. (1992d). Automated phase determination in electron crystallography: thermotropic phases of thiourea. Ultramicroscopy, 45, 357–364.
Dorset, D. L. (1994a). Electron crystallography of organic molecules. Adv. Electron. Electron Phys. 88, 111–197.
Dorset, D. L. (1994b). Electron crystallography of linear polymers. In Characterization of Solid Polymers. New Techniques and Developments, edited by S. J. Spells, pp. 1–16. London: Chapman and Hall.
Dorset, D. L. (1994c). Electron crystallography of inorganic compounds. Direct determination of the basic copper chloride structure CuCl2·3Cu(OH)2. J. Chem. Crystallogr. 24, 219–224.
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.
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.
Dorset, D. L. & Hauptman, H. A. (1976). Direct phase determination for quasi-kinematical electron diffraction intensity data from organic microcrystals. Ultramicroscopy, 1, 195–201.
Dorset, D. L., Jap, B. K., Ho, M.-H. & Glaeser, R. M. (1979). Direct phasing of electron diffraction data from organic crystals: the effect of n-beam dynamical scattering. Acta Cryst. A35, 1001–1009.
Dorset, D. L., Kopp, S., Fryer, J. R. & Tivol, W. F. (1995). The Sayre equation in electron crystallography. Ultramicroscopy, 57, 59–89.
Dorset, D. L. & McCourt, M. P. (1992). Effect of dynamical scattering on successful direct phase determination in electron crystallography – a model study. Trans. Am. Crystallogr. Assoc. 28, 105–113.
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.
Dorset, D. L. & McCourt, M. P. (1994a). Automated structure analysis in electron crystallography: phase determination with the tangent formula and least-squares refinement. Acta Cryst. A50, 287–292.
Dorset, D. L. & McCourt, M. P. (1994b). Disorder and molecular packing of C60 buckminsterfullerene: a direct electron-crystallographic analysis. Acta Cryst. A50, 344–351.
Dorset, D. L., McCourt, M. P., Fryer, J. R., Tivol, W. F. & Turner, J. N. (1994). The tangent formula in electron crystallography: phase determination of copper perchlorophthalocyanine. Microsc. Soc. Am. Bull. 24, 398–404.
Dorset, D. L., McCourt, M. P., Kopp, S., Wittmann, J.-C. & Lotz, B. (1994). Direct determination of polymer crystal structures by electron crystallography – isotactic poly(1-butene), form III. Acta Cryst. B50, 201–208.
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.
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.
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.
Dorset, D. L. & Zemlin, F. (1990). Direct phase determination in electron crystallography: the crystal structure of an n-paraffin. Ultramicroscopy, 33, 227–236.
Dorset, D. L. & Zhang, W. P. (1991). Electron crystallography at atomic resolution: the structure of the odd-chain paraffin n-tritriacontane. J. Electron Microsc. Tech. 18, 142–147.
Dowell, W. C. T. & Goodman, P. (1973). Image formation and contrast from convergent electron beam. Philos. Mag. 28, 471–473.
Dube, P., Tavares, P., Lurz, R. & van Heel, M. (1993). The portal protein of bacteriophage SPP1: a DNA pump with 13-fold symmetry. EMBO J. 12, 1303–1309.
Dvoryankin, V. F. & Vainshtein, B. K. (1960). An electron diffraction study of thiourea. Sov. Phys. Crystallogr. 5, 564–574.
Dvoryankin, V. F. & Vainshtein, B. K. (1962). An electron diffraction study of the low-temperature ferroelectric form of thiourea. Sov. Phys. Crystallogr. 6, 765–772.
Eades, J. A. (1988). Microbeam Analysis, edited by D. Newbuly, p. 75. San Francisco Press.
Eades, J. A. & Spence, J. C. H. (1987). Private communication.
Egelman, E. (1986). An algorithm for straightening images of curved filamentous structures. Ultramicroscopy, 19, 367–374.
Egelman, E. H. (2000). A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy, 85, 225–234.
Egelman, E. H., Francis, N. & DeRosier, D. J. (1982). F-actin is a helix with a random variable twist. Nature (London), 298, 131–135.
Egelman, E. H. & Stasiak, A. (1988). Structure of helical RecA–DNA complexes. II. Local conformational changes visualized in bundles of RecA–ATP gamma S filaments. J. Mol. Biol. 200, 329–349.
Erickson, H. P. & Klug, A. (1971). Measurements and compensation of defocusing and aberrations by Fourier processing of electron micrographs. Philos. Trans. R. Soc. London Ser. B, 261, 105–118.
Fan, H. F., Xiang, S. B., Li, F. H., Pan, Q., Uyeda, N. & Fujiyoshi, Y. (1991). Image resolution enhancement by combining information from electron diffraction pattern and micrograph. Ultramicroscopy, 36, 361–365.
Fan, H.-F., Zhong, Z.-Y., Zheng, C.-D. & Li, F.-H. (1985). Image processing in high-resolution electron microscopy using the direct method. I. Phase extension. Acta Cryst. A41, 163–165.
Farrow, N. A. & Ottensmeyer, F. P. (1992). A posteriori determination of relative projection directions of arbitrarily oriented macromolecules. J. Opt. Soc. Am. A, 9, 1749–1760.
Fernandez, J.-J., Sanjurjo, J. R. & Carazo, J. M. (1997). A spectral estimation approach to contrast transfer function detection in electron microscopy. Ultramicroscopy, 68, 267–295.
Fishman, G. (1995). Monte Carlo: Concepts, Algorithms, and Applications. New York: Springer.
Frangakis, A. S., Bohm, J., Forster, F., Nickell, S., Nicastro, D., Typke, D., Hegerl, R. & Baumeister, W. (2002). Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl Acad. Sci. USA, 99, 14153–14158.
Frank, J. (1975). Averaging of low exposure electron micrographs of non-periodic objects. Ultramicroscopy, 1, 159–162.
Frank, J. (1980). The role of correlation techniques in computer image processing. In Computer Processing of Electron Microscopy Images, edited by P. W. Hawkes, pp. 187–222. Berlin: Springer-Verlag.
Frank, J. (1990). Classification of macromolecular assemblies studied as `single particles'. Quart. Rev. Biophys. 23, 281–329.
Frank, J. (2006). Three-Dimensional Electron Microscopy of Macromolecular Assemblies. New York: Oxford University Press.
Frank, J. & Mcewen, B. (1992). Alignment by crosscorrelation. In Electron Tomography, edited by J. Frank, pp. 205–214. New York: Plenum.
Frank, J., Penczek, P., Agrawal, R. K., Grassucci, R. A. & Heagle, A. B. (2000). Three-dimensional cryoelectron microscopy of ribosomes. Methods Enzymol. 317, 276–291.
Frank, J., Penczek, P. & Liu, W. (1992). Alignment, classification, and three-dimensional reconstruction of single particles embedded in ice. Scan. Microsc. Suppl. 6, 11–20.
Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M. & Leith, A. (1996). SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199.
Frank, J., Radermacher, M., Wagenknecht, T. & Verschoor, A. (1988). Studying ribosome structure by electron microscopy and computer-image processing. Methods Enzymol. 164, 3–35.
Frank, J., Verschoor, A. & Boublik, M. (1981). Computer averaging of electron micrographs of 40S ribosomal subunits. Science, 214, 1353–1355.
Frank, J., Verschoor, A. & Boublik, M. (1982). Multivariate statistical analysis of ribosome electron micrographs. L and R lateral views of the 40 S subunit from HeLa cells. J. Mol. Biol. 161, 107–133.
Frank, J. & Wagenknecht, T. (1984). Automatic selection of molecular images from electron micrographs. Ultramicroscopy, 12, 169–176.
Fryer, J. R. (1993). Electron crystallography of small organic molecules. Microsc. Soc. Am. Bull. 23, 44–56.
Fujimoto, F. (1959). Dynamical theory of electron diffraction in Laue-case. I. General theory. J. Phys. Soc. Jpn, 14, 1158–1168.
Fujiwara, K. (1961). Relativistic dynamical theory of electron diffraction. J. Phys. Soc. Jpn, 16, 2226–2238.
Fukuhara, A. (1966). Many-ray approximations in the dynamical theory of electron diffraction. J. Phys. Soc. Jpn, 21, 2645–2662.
Fuller, S. D., Butcher, S. J., Cheng, R. H. & Baker, T. S. (1996). Three-dimensional reconstruction of icosahedral particles – the uncommon line. J. Struct. Biol. 116, 48–55.
Fung, K. K., Steeds, J. W. & Eades, J. A. (1980). Application of convergent beam electron diffraction to study the stacking of layers in transition-metal dichalcogenides. Physica (Utrecht), B99, 47–50.
Gabashvili, I. S., Agrawal, R. K., Spahn, C. M., Grassucci, R. A., Svergun, D. I., Frank, J. & Penczek, P. (2000). Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell, 100, 537–549.
Gabor, D. (1949). Microscopy by reconstructed wavefronts. Proc. R. Soc. London Ser. A, 197, 454–487.
Gassmann, J. (1976). Improvement and extension of approximate phase sets in structure determination. In Crystallographic Computing Techniques, edited by F. R. Ahmed, pp. 144–154. Copenhagen: Munksgaard.
Gassmann, J. & Zechmeister, K. (1972). Limits of phase expansion in direct methods. Acta Cryst. A28, 270–280.
Germain, G., Main, P. & Woolfson, M. M. (1971). The application of phase relationships to complex structures. III. The optimum use of phase relationships. Acta Cryst. A27, 368–376.
Gilbert, P. F. C. (1972). Iterative methods for the three-dimensional reconstruction of an object from projections. J. Theor. Biol. 36, 105–117.
Gilmore, C. J., Bricogne, G. & Bannister, C. (1990). A multisolution method of phase determination by combined maximization of entropy and likelihood. II. Application to small molecules. Acta Cryst. A46, 297–308.
Gilmore, C. J., Shankland, K. & Bricogne, G. (1993). Applications of the maximum entropy method to powder diffraction and electron crystallography. Proc. R. Soc. London Ser. A, 442, 97–111.
Gilmore, C. J., Shankland, K. & Fryer, J. R. (1992). The application of the maximum entropy method to electron microscopy data for purple membrane. Trans. Am. Crystallogr. Assoc. 28, 129–139.
Gilmore, C. J., Shankland, K. & Fryer, J. R. (1993). Phase extension in electron crystallography using the maximum entropy method and its application to two-dimensional purple membrane data from Halobacterium halobium. Ultramicroscopy, 49, 132–146.
Gjønnes, J. & Gjønnes, K. (1985). Bloch wave symmetries and inclined surfaces. Ultramicroscopy, 18, 77–82.
Gjønnes, J. & Høier, R. (1971). The application of non-systematic many-beam dynamic effects to structure-factor determination. Acta Cryst. A27, 313–316.
Gjønnes, J. & Moodie, A. F. (1965). Extinction conditions in dynamic theory of electron diffraction patterns. Acta Cryst. 19, 65–67.
Glauber, R. & Schomaker, V. (1953). The theory of electron diffraction. Phys. Rev. 89, 667–670.
Golub, G. H. & Van Loan, C. F. (1996). Matrix Computations. Baltimore: Johns Hopkins University Press.
Goncharov, A. B., Vainshtein, B. K., Ryskin, A. I. & Vagin, A. A. (1987). Three-dimensional reconstruction of arbitrarily oriented identical particles from their electron photomicrographs. Sov. Phys. Crystallogr. 32, 504–509.
Gonzalez, R. F. & Woods, R. E. (2002). Digital Image Processing. Upper Saddle River: Prentice Hall.
Goodman, P. (1975). A practical method of three-dimensional space-group analysis using convergent-beam electron diffraction. Acta Cryst. A31, 804–810.
Goodman, P. & Johnson, A. W. S. (1977). Identification of enantiomorphically related space groups by electron diffraction – a second method. Acta Cryst. A33, 997–1001.
Goodman, P. & Lehmpfuhl, G. (1964). Verbotene elektronenbeugungs­reflexe von CdS. Z. Naturforsch. Teil A, 19, 818–820.
Goodman, P. & Lehmpfuhl, G. (1965). Elektronenbeugungsunter­suchungen im konvergenten bundel mit dem Siemens Elmiskop I. Z. Naturforsch. Teil A, 20, 110–114.
Goodman, P. & Lehmpfuhl, G. (1967). Electron diffraction study of MgO h00-systematic interactions. Acta Cryst. 22, 14–24.
Goodman, P. & Secomb, T. W. (1977). Identification of enantiomorphously related space groups by electron diffraction. Acta Cryst. A33, 126–133.
Gordon, R., Bender, R. & Herman, G. T. (1970). Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and X-ray photography. J. Theor. Biol. 29, 471–481.
Grigorieff, N. (1998). Three-dimensional structure of bovine NADH: ubiquinone oxidoreductase (complex I) at 22 Å in ice. J. Mol. Biol. 277, 1033–1046.
Grigorieff, N. (2007). FREALIGN: High-resolution refinement of single particle structures. J. Struct. Biol. 157, 117.
Gurskaya, G. V., Lobanova, G. M. & Vainshtein, B. K. (1971). X-ray diffraction and electron-microscope study of hexagonal catalase crystal. Sov. Phys. Crystallogr. 16, 662–669.
Hall, R. J. & Patwardhan, A. (2004). A two step approach for semi-automated particle selection from low contrast cryo-electron micrographs. J. Struct. Biol. 145, 19–28.
Hamaker, C. & Solmon, D. C. (1978). Angles between null spaces of X-rays. J. Math. Anal. Appl. 62, 1–23.
Harauz, G. & van Heel, M. (1986). Exact filters for general geometry three-dimensional reconstruction. Optik, 73, 146–156.
Hashimoto, H., Endoh, H., Tanji, T., Ono, A. & Watanabe, E. (1977). Direct observation of fine structure within images of atoms in crystals by transmission electron microscopy. J. Phys. Soc. Jpn, 42, 1073–1074.
Hashimoto, H., Mannami, M. & Naiki, T. (1961). Dynamical theory of electron diffraction for the electron microscope image of crystal lattices. I. Image of single crystals. II. Image of superposed crystals (moiré pattern). Philos. Trans. R. Soc. London, 253, 459–516.
Hauptman, H. (1972). Crystal Structure Determination. The Role of the Cosine Seminvariants. New York: Plenum Press.
Hauptman, H. (1993). A minimal principle in X-ray crystallography: starting in a small way. Proc. R. Soc. London Ser. A, 442, 3–12.
Hauptman, H. & Karle, J. (1953). Solution of the Phase Problem. I. The Centrosymmetric Crystal. American Crystallographic Association Monograph No. 3. Ann Arbor: Edwards Brothers.
Havelka, W., Henderson, R., Heymann, J. A. W. & Oesterhelt, D. (1993). Projection structure of halorhodopsin from Halobacterium halobium at 6 Å resolution obtained by electron cryomicroscopy. J. Mol. Biol. 234, 837–846.
He, L. X., Wu, Y. K. & Kuo, K. H. (1988). Decagonal quasicrystals with different periodicities along the tenfold axis in rapidly solidified Al65Cu20Mn15, Al65Cu20Fe15, Al65Cu20Co15 or Al65Cu20Ni15. J. Mater. Sci. Lett. 7, 1284–1286.
Heel, M. van (1982). Detection of objects in quantum-noise limited images. Ultramicroscopy, 8, 331–342.
Heel, M. van (1987a). Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy, 21, 111–124.
Heel, M. van (1987b). Similarity measures between images. Ultramicroscopy, 21, 95–100.
Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. (2000). Single-particle electron cryo-microscopy: towards atomic resolution. Quart. Rev. Biophys. 33, 307–369.
Heel, M. van, Harauz, G. & Orlova, E. V. (1996). A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24.
Heel, M. van & Hollenberg, J. (1980). The stretching of distorted images of two-dimensional crystals. In Electron Microscopy at Molecular Dimensions, edited by W. Baumeister, pp. 256–260. Berlin: Springer.
Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E. & Downing, K. H. (1990). Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy. J. Mol. Biol. 213, 899–929.
Henderson, R., Baldwin, J. M., Downing, K. H., Lepault, J. & Zemlin, F. (1986). Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5 Å resolution. Ultramicroscopy, 19, 147–178.
Henderson, R. & Unwin, P. N. T. (1975). Three-dimensional model of purple membrane obtained by electron microscopy. Nature (London), 257, 28–32.
Herman, G. T. & Meyer, L. B. (1993). Algebraic reconstruction techniques can be made computationally efficient. IEEE Trans. Med. Imaging, 12, 600–609.
Herrmann, K. H., Krahl, D. & Rust, H.-P. (1980). Low-dose image recording by TV techniques. In Electron Microscopy at Molecular Dimensions, edited by W. Baumeister & W. Vogell, pp. 186–193. Berlin: Springer-Verlag.
Hirsch, P. B., Howie, A., Nicholson, R. B., Pashley, D. W. & Whelan, M. J. (1965). Electron Microscopy of Thin Crystals. London: Butterworths.
Hohn, M., Tang, G., Goodyear, G., Baldwin, P. R., Huang, Z., Penczek, P. A., Yang, C., Glaeser, R. M., Adams, P. D. & Ludtke, S. J. (2007). SPARX, a new environment for cryo-EM image processing. J. Struct. Biol. 157, 47–55.
Holmes, K. C., Angert, I., Kull, F. J., Jahn, W. & Schroder, R. R. (2003). Electron cryo-microscopy shows how strong binding of myosin to actin releases nucleotide. Nature (London), 425, 423–427.
Hoppe, W. (1971). Use of zone correction plate and other techniques for structure determination of aperiodic objects at atomic resolution using a conventional electron microscope. Philos. Trans. R. Soc. London Ser. B, 261, 71–94.
Hoppe, W., Bussler, P., Feltynowski, A., Hunsmann, N. & Hirt, A. (1973). Some experience with computerized image reconstruction methods. In Image Processing and Computer-Aided Design in Electron Optics, edited by R. W. Hawkes, pp. 92–126. London: Academic Press.
Hoppe, W. & Gassmann, J. (1968). Phase correction, a new method to solve partially known structures. Acta Cryst. B24, 97–107.
Horstmann, M. & Meyer, G. (1965). Messung der Elektronenbeugungs­intensitaten polykristalliner Aluminium schichten bei tiefer Temperatur und Vergleich mit der dynamischen Theorie. Z. Phys. 182, 380–397.
Hovmöller, S., Sjögren, A., Farrants, G., Sundberg, M. & Marinder, B. O. (1984). Accurate atomic positions from electron microscopy. Nature (London), 311, 238–241.
Howe, J. M., Sarikaya, M. & Gronsky, R. (1986). Space-group analyses of thin precipitates by different convergent-beam electron diffraction procedures. Acta Cryst. A42, 368–380.
Hu, H. H., Li, F. H. & Fan, H. F. (1992). Crystal structure determination of K2O·7Nb2O5 by combining high resolution electron microscopy and electron diffraction. Ultramicroscopy, 41, 387–397.
Huang, Z., Baldwin, P. R., Mullapudi, S. R. & Penczek, P. A. (2003). Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J. Struct. Biol. 144, 79–94.
Huang, Z. & Penczek, P. A. (2004). Application of template matching technique to particle detection in electron micrographs. J. Struct. Biol. 145, 29–40.
Huesman, R. H., Gullberg, G. T., Greenberg, W. L. & Budinger, T. F. (1977). RECLBL library users' manual – Donner algorithms for reconstruction tomography. University of California, Berkeley, USA.
Hurley, A. C. & Moodie, A. F. (1980). The inversion of three-beam intensities for scalar scattering by a general centrosymmetric crystal. Acta Cryst. A36, 737–738.
International Tables for Crystallography (2004). Vol. C. Mathematical, Physical and Chemical Tables, edited E. Prince, 3rd ed. Dordrecht: Kluwer Academic Publishers.
International Tables for Crystallography (2005). Vol. A. Space-Group Symmetry, edited by Th. Hahn, 5th ed. Heidelberg: Springer.
International Tables for X-ray Crystallography (1952). Vol. I. Symmetry Groups. Birmingham: Kynoch Press.
Ishizuka, K. (1982). Translation symmetries in convergent-beam electron-diffraction. Ultramicroscopy, 9, 255–258.
Ishizuka, K., Miyazaki, M. & Uyeda, N. (1982). Improvement of electron microscope images by the direct phasing method. Acta Cryst. A38, 408–413.
Jackson, J. I., Meyer, C. H., Nishimura, D. G. & Macovski, A. (1991). Selection of a convolution function for Fourier inversion using gridding. IEEE Trans. Med. Imaging, 10, 473–478.
Janner, A. & Janssen, T. (1980a). Symmetry of incommensurate crystal phases. I. Commensurate basic structures. Acta Cryst. A36, 399–408.
Janner, A. & Janssen, T. (1980b). Symmetry of incommensurate crystal phases. II. Incommensurate basic structure. Acta Cryst. A36, 408–415.
Jap, B. K. & Glaeser, R. M. (1980). The scattering of high-energy electrons. II. Quantitative validity domains of the single-scattering approximations for organic crystals. Acta Cryst. A36, 57–67.
Jap, B. K., Walian, P. J. & Gehring, K. (1991). Structural architecture of an outer membrane channel as determined by electron crystallography. Nature (London), 350, 167–170.
Jarić, M. Y. (1988). Editor. Introduction to Quasicrystals, Vol. 1. New York: Academic Press.
Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110–119.
Joyeux, L. & Penczek, P. A. (2002). Efficiency of 2D alignment methods. Ultramicroscopy, 92, 33–46.
Kaczmarz, S. (1993). Approximate solutions of systems of linear equations (Reprint of Kaczmarz, S., Angenäherte Auflösung von Systemen linearer Gleichunger, Bulletin International de l'Academie Polonaise des Sciences. Lett A, 355–357, 1937). Int. J. Control, 57, 1269–1271.
Kambe, K. (1982). Visualization of Bloch waves of high energy electrons in high resolution electron microscopy. Ultramicroscopy, 10, 223–228.
Karle, J. & Hauptman, H. (1956). A theory of phase determination for the four types of non-centrosymmetric space groups [1P222], [2P22], [3P_{1}2], [3P_{2}2]. Acta Cryst. 9, 635–651.
Kessel, M., Radermacher, M. & Frank, J. (1985). The structure of the stalk surface layer of a brine pond microorganism: correlation averaging applied to a double layered lattice structure. J. Microsc. 139, 63–74.
Kirkland, E. J., Siegel, B. M., Uyeda, N. & Fujiyoshi, Y. (1980). Digital reconstruction of bright field phase contrast images from high resolution electron micrographs. Ultramicroscopy, 5, 479–503.
Kiselev, N. A., Lerner, F. Ya. & Livanova, N. B. (1971). Electron microscopy of muscle phosphorylase B. J. Mol. Biol. 62, 537–549.
Klug, A. & Berger, J. E. (1964). An optical method for the analysis of periodicities in electron micrographs and some observations on the mechanism of negative staining. J. Mol. Biol. 10, 565–569.
Klug, A. & DeRosier, D. J. (1966). Optical filtering of electron micrographs: reconstruction of one-sided images. Nature (London), 212, 29–32.
Kossel, W. & Möllenstedt, G. (1938). Electron interference in a convergent beam. Nature (London), 26, 660.
Kosykh, V. P., Pustovskikh, A. I., Kirichuk, V. S., Kühne, T., Orlova, E. V., Tsuprun, V. L. & Kiselev, N. A. (1983). Use of digital storage methods to recover images of monocrystalline layers of virus particles. Sov. Phys. Crystallogr. 28, 637–643.
Krämer, S., Mayer, J., Witt, C., Weikenmeier, A. & Rühle, M. (2000). Ultramicroscopy, 81, 245–262.
Kühlbrandt, W., Wang, D. N. & Fujiyoshi, Y. (1994). Atomic model of plant light-harvesting complex by electron crystallography. Nature (London), 367, 614–621.
Kutateladze, T. G., Ogburn, K. D., Watson, W. T., de Beer, T., Emr, S. D., Burd, C. G. & Overduin, M. (1999). Phosphatidylinositol 3-phosphate recognition by the FYVE domain. Mol. Cell, 3, 805–811.
Kuwabara, S. (1978). Nearly aberration-free crystal images in high voltage electron microscopy. J. Electron Microsc. 27, 161–169.
Langer, R., Frank, J., Feltynowski, A. & Hoppe, W. (1970). Anwendung des Bilddifferenzverfahrens auf die Untersuchung von Struktur­änderungen dünner Kohlefolien bei Elektronenbestrahlung. Ber. Bunsenges Phys. Chem. 74, 1120–1126.
Langs, D. A. & DeTitta, G. T. (1975). A flexible and rapid phase determination and refinement procedure. Acta Cryst. A31, S16.
Lanzavecchia, S. & Bellon, P. L. (1994). A moving window Shannon reconstruction for image interpolation. J. Visual Comm. Image Repres. 3, 255–264.
Lanzavecchia, S. & Bellon, P. L. (1998). Fast computation of 3D Radon transform via a direct Fourier method. Bioinformatics, 14, 212–216.
Lanzavecchia, S., Bellon, P. L. & Scatturin, V. (1993). SPARK, a kernel of software programs for spatial reconstruction in electron microscopy. J. Microsc. 171, 255–266.
Lanzavecchia, S., Tosoni, L. & Bellon, P. L. (1996). Fast sinogram computation and the sinogram-based alignment of images. Comp. Appl. Bio. Sci. 12, 531–537.
Lata, K. R., Penczek, P. & Frank, J. (1995). Automatic particle picking from electron micrographs. Ultramicroscopy, 58, 381–391.
Laurette, I., Zeng, G. L., Welch, A., Christian, P. E. & Gullberg, G. T. (2000). A three-dimensional ray-driven attenuation, scatter and geometric response correction technique for SPECT in inhomogeneous media. Phys. Med. Biol. 45, 3459–3480.
Lawrence, M. C. (1992). Least-squares method of alignment using markers. In Electron Tomography, edited by J. Frank, pp. 197–204. New York: Plenum Press.
Lawton, J. A. & Prasad, B. V. V. (1996). Automated software package for icosahedral virus reconstruction. J. Struct. Biol. 116, 209–215.
Levine, D. & Steinhardt, P. J. (1984). Quasicrystals – a new class of ordered structures. Phys. Rev. Lett. 53, 2477–2480.
Lewitt, R. M. (1990). Multidimensional digital image representations using generalized Kaiser–Bessel window functions. J. Opt. Soc. Am. A, 7, 1834–1846.
Lewitt, R. M. (1992). Alternatives to voxels for image representation in iterative reconstruction algorithms. Phys. Med. Biol. 37, 705–716.
Li, D. X. & Hovmöller, S. (1988). The crystal structure of Na3Nb12O31F determined by HREM and image processing. J. Solid State Chem. 73, 5–10.
Li, F. H. (1991). Crystal structures from high-resolution electron microscopy. In Electron Crystallography of Organic Molecules, edited by J. R. Fryer & D. L. Dorset, pp. 153–167. Dordrecht: Kluwer Academic Publishers.
Liang, Y. Y., Ke, E. Y. & Zhou, Z. H. (2002). IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database. J. Struct. Biol. 137, 292–304.
Liebman, G. (1955). A unified representation of magnetic electron lens properties. Proc. Phys. Soc. London Sect. B, 68, 737–745.
Liu, Y.-W., Fan, H.-F. & Zheng, C.-D. (1988). Image processing in high-resolution electron microscopy using the direct method. III. Structure-factor extrapolation. Acta Cryst. A44, 61–63.
Lobachev, A. N. & Vainshtein, B. K. (1961). An electron diffraction study of urea. Sov. Phys. Crystallogr. 6, 313–317.
Ludtke, S. J., Baldwin, P. R. & Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97.
Lynch, D. F. & Moodie, A. F. (1972). Numerical evaluation of low energy electron diffraction intensity. I. The perfect crystal with no upper layer lines and no absorption. Surf. Sci. 32, 422–438.
Lynch, D. F., Moodie, A. F. & O'Keefe, M. A. (1975). n-Beam lattice images. V. The use of the charge-density approximation in the interpretation of lattice images. Acta Cryst. A31, 300–307.
Mackay, A. L. (1982). Crystallography and the Penrose pattern. Physica (Utrecht), 114A, 609–613.
McLachlan, D. (1958). Crystal structure and information theory. Proc. Natl Acad. Sci. USA, 44, 948–956.
Mallick, S. P., Carragher, B., Potter, C. S. & Kriegman, D. J. (2005). ACE: automated CTF estimation. Ultramicroscopy, 104, 8–29.
Mao, Y., Nickitenko, A., Duan, X., Lloyd, T. E., Wu, M. N., Bellen, H. & Quiocho, F. A. (2000). Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction. Cell, 100, 447–456.
Marabini, R. & Carazo, J. M. (1996). On a new computationally fast image invariant based on bispectral projections. Pattern Recognit. Lett. 17, 959–967.
Marabini, R., Herman, G. T. & Carazo, J. M. (1998). 3D reconstruction in electron microscopy using ART with smooth spherically symmetric volume elements (blobs). Ultramicroscopy, 72, 53–65.
Markham, R., Frey, S. & Hills, G. J. (1963). Methods for the enhancement of image detail and accentuation of structure in electron microscopy. Virology, 20, 88–102.
Matej, S. & Lewitt, R. M. (1996). Practical considerations for 3-D image reconstruction using spherically symmetric volume elements. IEEE Trans. Med. Imaging, 15, 68–78.
Matsuda, T., Tonomura, A. & Komada, T. (1978). Observation of lattice images with a field emission electron microscope. Jpn. J. Appl. Phys. 17, 2073–2074.
Midgley, P. A., Sleight, M. E. & Vincent, R. (1996). The structure of a metastable Au–Sn phase determined by convergent beam electron diffraction. J. Solid State Chem. 124, 132–142.
Mindell, J. A. & Grigorieff, N. (2003). Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347.
Ming, D. M., Kong, Y. F., Lambert, M. A., Huang, Z. & Ma, J. P. (2002). How to describe the movement of protein without amino acids sequence and coordinates. Proc. Natl Acad. Sci. USA, 13, 8620–8625.
Mitra, K., Schaffitzel, C., Shaikh, T., Tama, F., Jenni, S., Brooks, C. L. III, Ban, N. & Frank, J. (2005). Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature (London), 438, 318–324.
Miyake, S., Takagi, S. & Fujimoto, F. (1960). The extinction rule for reflexions in symmetrical spot patterns of electron diffraction by crystals. Acta Cryst. 13, 360–361.
Mo, Y. D., Cheng, T. Z., Fan, H. F., Li, J. Q., Sha, B. D., Zheng, C. D., Li, F. H. & Zhao, Z. X. (1992). Structural features of the incommensurate modulation in the Pb-doped Bi-2223 high-Tc phase by defect method electron diffraction analysis. Supercond. Sci. Technol. 5, 69–72.
Moodie, A. F. (1965). Some structural implications of n-beam interactions. International Conference on Electron Diffraction and Crystal Defects, Melbourne, Australia, paper ID-1.
Morniroli, J. P. (2002). Large-Angle Convergent Beam Electron Diffraction. Paris: French Society of Microscopy.
Moss, B. & Dorset, D. L. (1982). Effect of crystal bending on direct phasing of electron diffraction data from cytosine. Acta Cryst. A38, 207–211.
Mouche, F., Boisset, N. & Penczek, P. A. (2001). Lumbricus terrestris hemoglobin – the architecture of linker chains and structural variation of the central toroid. J. Struct. Biol. 133, 176–192.
Nagasawa, T. (1983). Master of Physics Thesis, Tohoku University, Japan.
Natterer, F. & Wübbeling, F. (2001). Mathematical Methods in Image Reconstruction. Philadelphia: SIAM.
Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920–930.
Nowacki, W. (1967). Crystal Data. ACA Monograph No. 6. Washington: American Crystallographic Association.
Ogawa, T. (1985). On the structure of a quasicrystal 3-dimensional Penrose transformation. J. Phys. Soc. Jpn, 54, 3205–3208.
Ogawa, T., Moriguchi, S., Isoda, S. & Kobayashi, T. (1994). Application of an imaging plate to electron crystallography at atomic resolution. Polymer, 35, 1132–1136.
Ogata, Y., Tsuda, K., Akishige, Y. & Tanaka, M. (2004). Refinement of the crystal structural parameters of the intermediate phase of h-BaTiO3 using convergent-beam electron diffraction. Acta Cryst. A60, 525–531.
Okabe, A., Boots, B., Sugihara, K. & Chiu, S. N. (2000). Spatial Tessellations: Concepts and Applications of Voronoi Diagrams. New York: John Wiley & Sons.
Orlov, S. S. (1976). Theory of three-dimensional reconstruction 1. Conditions for a complete set of projections. Sov. Phys. Crystallogr. 20, 312–314.
O'Sullivan, J. D. (1985). A fast sinc function gridding algorithm for Fourier inversion in computer tomography. IEEE Trans. Med. Imaging, 4, 200–207.
Ottensmeyer, F. P., Andrews, J. W., Basett-Jones, D. P., Chan, A. S. & Hewitt, J. (1977). Signal to noise enhancement in dark field electron micrographs of vasopressin: filtering of arrays of images in reciprocal space. J. Microsc. 109, 256–268.
Pan, M. & Crozier, P. A. (1993). Quantitative imaging and diffraction of zeolites using a slow-scan CCD camera. Ultramicroscopy, 52, 487–498.
Parlett, B. N. (1980). A new look at the Lanczos-algorithm for solving symmetric-systems of linear-equations. Linear Algebr. Its Appl. 29, 323–346.
Paul, D., Patwardhan, A., Squire, J. M. & Morris, E. P. (2004) Single particle analysis of filamentous and highly elongated macromolecular assemblies. J. Struct. Biol. 148, 236–250.
Penczek, P. (1998). Measures of resolution using Fourier shell correlation. J. Mol. Biol. 280, 115–116.
Penczek, P., Ban, N., Grassucci, R. A., Agrawal, R. K. & Frank, J. (1999). Haloarcula marismortui 50S subunit – complementarity of electron microscopy and X-ray crystallographic information. J. Struct. Biol. 128, 44–50.
Penczek, P., Marko, M., Buttle, K. & Frank, J. (1995). Double-tilt electron tomography. Ultramicroscopy, 60, 393–410.
Penczek, P., Radermacher, M. & Frank, J. (1992). Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy, 40, 33–53.
Penczek, P. A. (2002). Three-dimensional spectral signal-to-noise ratio for a class of reconstruction algorithms. J. Struct. Biol. 138, 34–46.
Penczek, P. A., Chao, Y., Frank, J. & Spahn, C. M. T. (2006). Estimation of variance in single particle reconstruction using the bootstrap technique. J. Struct. Biol. 154, 168–183.
Penczek, P. A. & Frank, J. (2006). Resolution in electron tomography. In Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell, 2nd ed., edited by J. Frank, pp. 307–330. Berlin: Springer.
Penczek, P. A., Frank, J. & Spahn, C. M. T. (2006a). A method of focused classification, based on the bootstrap 3-D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol. 154, 184–194.
Penczek, P. A., Frank, J. & Spahn, C. M. T. (2006b). Conformational analysis of macromolecules analyzed by cryo-electron microscopy. In Microscopy and Microanalysis, edited by P. Kotula, M. Marko, J.-H. Scott et al., p. CD386. Chicago: Cambridge University Press.
Penczek, P. A., Grassucci, R. A. & Frank, J. (1994). The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy, 53, 251–270.
Penczek, P. A., Renka, R. & Schomberg, H. (2004). Gridding-based direct Fourier inversion of the three-dimensional ray transform. J. Opt. Soc. Am. A, 21, 499–509.
Penczek, P. A., Zhu, J. & Frank, J. (1996). A common-lines based method for determining orientations for N > 3 particle projections simultaneously. Ultramicroscopy, 63, 205–218.
Penczek, P. A., Zhu, J., Schröder, R. & Frank, J. (1997). Three-dimensional reconstruction with contrast transfer function compensation from defocus series. Scan. Microsc. Suppl. 11, 1–10.
Penrose, R. (1974). The role of aesthetics in pure and applied mathematical research. Bull. Inst. Math. Appl. 10, 266–271.
Pérez, S. & Chanzy, H. (1989). Electron crystallography of linear polysaccharides. J. Electron Microsc. Tech. 11, 280–285.
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). UCSF Chimera – a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612.
Picture Processing and Digital Filtering (1975). Edited by T. S. Huang. Berlin: Springer-Verlag.
Pinsker, Z. G. (1953). Electron Diffraction. London: Butterworth.
Pinsker, Z. G., Zvyagin, B. B. & Imamov, R. M. (1981). Principal results of electron-diffraction structural investigations. Sov. Phys. Crystallogr. 26, 669–674.
Pogany, A. P. & Turner, P. S. (1968). Reciprocity in electron diffraction and microscopy. Acta Cryst. A24, 103–109.
Portier, R. & Gratias, D. (1981). Diffraction symmetries for elastic scattering. In Electron Microscopy and Analysis. Inst. Phys. Conf. Ser. No. 61, pp. 275–278. Bristol, London: Institute of Physics.
Powell, M. J. D. (1973). On search directions for minimization algorithm. Math. Program. 4, 193–201.
Provencher, S. W. & Vogel, R. H. (1988). Three-dimensional reconstruction from electron micrographs of disordered specimens. I. Method. Ultramicroscopy, 25, 209–221.
Pullan, L., Mullapudi, S., Huang, Z., Baldwin, P. R., Chin, C., Sun, W., Tsujimoto, S., Kolodziej, S., Stoops, J. K., Lee, J. C., Waxham, M. N., Bean, A. J. & Penczek, P. A. (2006). The endosome-associated protein Hrs is hexameric and controls cargo sorting as a `master molecule'. Structure, 14, 661–671.
Radermacher, M. (1992). Weighted back-projection methods. In Electron Tomography, edited by J. Frank, pp. 91–115. New York: Plenum.
Radermacher, M. (1994). Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms. Ultramicroscopy, 53, 121–136.
Radermacher, M. (2000). Three-dimensional reconstruction of single particles in electron microscopy. In Image Analysis: Methods and Applications, edited by D.-P. Häder, pp. 295–328. Boca Raton: CRC Press.
Radermacher, M., Wagenknecht, T., Verschoor, A. & Frank, J. (1986). A new 3-D reconstruction scheme applied to the 50S ribosomal subunit of E. coli. J. Microsc. 141, RP1–RP2.
Radermacher, M., Wagenknecht, T., Verschoor, A. & Frank, J. (1987). Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146, 113–136.
Radi, G. (1970). Complex lattice potentials in electron diffraction calculated for a number of crystals. Acta Cryst. A26, 41–56.
Renka, R. J. (1997). Algorithm 772. STRIPACK: Delaunay triangulation and Voronoi diagram on the surface of a sphere. ACM Trans. Math. Software, 23, 416–434.
Revol, J. F. (1991). Electron crystallography of radiation-sensitive polymer crystals. In Electron Crystallography of Organic Molecules, edited by J. R. Fryer & D. L. Dorset, pp. 169–187. Dordrecht: Kluwer Academic Publishers.
Revol, J. F. & Manley, R. St. J. (1986). Lattice imaging in polyethylene single crystals. J. Mater. Sci. Lett. 5, 249–251.
Rez, P. (1978). In Electron Diffraction 1927–1977, edited by P. J. Dobson, J. B. Pendry & C. J. Humphreys, pp. 61–67. Inst. Phys. Conf. Ser. No. 41. Bristol, London: Institute of Physics.
Roseman, A. M. (2003). Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy, 94, 225–236.
Roseman, A. M., Chen, S., White, H., Braig, K. & Saibil, H. R. (1996). The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL. Cell, 87, 241–251.
Rossouw, C. J., Gibson, M. A. & Forwood, C. T. (1996). Dynamical electron diffraction analysis of lattice parameters, Debye–Waller factors and order in Ti–Al and Ti–Ga alloys. Ultramicroscopy, 66, 193–209.
Rozenfeld, A. (1969). Picture Processing by Computer. New York: Academic Press.
Ruiz, T., Mechin, I., Bar, J., Rypniewski, W., Kopperschlager, G. & Radermacher, M. (2003). The 10.8-A structure of Saccharomyces cerevisiae phosphofructokinase determined by cryoelectron microscopy: localization of the putative fructose 6-phosphate binding sites. J. Struct. Biol. 143, 124–134.
Saad, A., Ludtke, S. J., Jakana, J., Rixon, F. J., Tsuruta, H. & Chiu, W. (2001). Fourier amplitude decay of electron cryomicroscopic images of single particles and effects on structure determination. J. Struct. Biol. 133, 32–42.
Saito, M., Tanaka, M., Tsai, A. P., Inoue, A. & Masumoto, T. (1992). Space group determination of decagonal quasi-crystals of an Al70Ni15Fe15 alloy using convergent-beam electron-diffraction. Jpn. J. Appl. Phys. 31, L109–L112.
Saitoh, K., Tanaka, M. & Tsai, A. P. (2001). Structural study of an Al73Ni22Fe5 decagonal quasicrystal by high-angle annular dark-field scanning transmission electron microscopy. J. Electron Microsc. 50, 197–203.
Saitoh, K., Tsuda, K., Tanaka, M., Kaneko, K. & Tsai, A. P. (1997). Structural study of an Al72Ni20Co8 decagonal quasicrystal using the high-angle annular dark-field method. Jpn. J. Appl. Phys. 36, L1400–L1402.
Saitoh, K., Tsuda, K., Tanaka, M. & Tsai, A. P. (1999). Structural study of an Al70Ni15Fe15 decagonal quasicrystal using high-angle annular dark-field scanning transmission electron microscopy. Jpn. J. Appl. Phys. 38, L671–L674.
Saitoh, K., Tsuda, K., Terauchi, M. & Tanaka, M. (2001). Distinction between space groups having principal rotation and screw axes, which are combined with twofold rotation axes, using the coherent convergent-beam electron diffraction method. Acta Cryst. A57, 219–230.
Sander, B., Golas, M. M. & Stark, H. (2003). Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. J. Struct. Biol. 142, 392–401.
Saunders, M., Bird, D. M., Zaluzee, N. J., Burgess, W. G., Preston, A. R. & Humphreys, C. J. (1995). Measurement of the low-order structure factors for silicon from zone-axis CBED pattern. Ultramicroscopy, 60, 311–323.
Saxton, W. O. (1978). Computer Techniques for Image Processing of Electron Microscopy. New York: Academic Press.
Saxton, W. O. & Baumeister, W. (1982). The correlation averaging of a regularly arranged bacterial envelope protein. J. Microsc. 127, 127–138.
Sayre, D. (1952). The squaring method: a new method for phase determination. Acta Cryst. 5, 60–65.
Sayre, D. (1980). Phase extension and refinement using convolutional and related equation systems. In Theory and Practice of Direct Methods in Crystallography, edited by M. F. C. Ladd & R. A. Palmer, pp. 271–286. New York: Plenum Press.
Scaringe, R. P. (1992). Crystallography in two dimensions: comparison of theory and experiment for molecular layers. Trans. Am. Crystallogr. Assoc. 28, 11–23.
Schatz, M. & van Heel, M. (1990). Invariant classification of molecular views in electron micrographs. Ultramicroscopy, 32, 255–264.
Schatz, M. & van Heel, M. (1992). Invariant recognition of molecular projections in vitreous ice preparations. Ultramicroscopy, 45, 15–22.
Scherzer, O. (1949). The theoretical resolution limit of the electron microscope. J. Appl. Phys. 20, 20–29.
Schiske, P. (1968). Zur Frage der Bildrekonstruktion durch Fokusreihen. 1 Y Eur. Reg. Conf. Electron Microsc. Rome, 1, 145–146.
Schomberg, H. (2002). Notes on direct and gridding-based Fourier inversion methods. In Proceedings of the IEEE International Symposium on Biomedical Imaging, Washington, DC, edited by M. Unser & Z. P. Liang, pp. 645–648.
Schomberg, H. & Timmer, J. (1995). The gridding method for image reconstruction by Fourier transformation. IEEE Trans. Med. Imaging, 14, 596–607.
Schüler, M., Connell, S. R., Lescoute, A., Giesebrecht, J., Dabrowski, M., Schroeer, B., Mielke, T., Penczek, P. A., Westhof, E. & Spahn, C. M. T. (2006). Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nature Struct. Mol. Biol. 13, 1092–1096.
Sezan, M. I. (1992). An overview of convex projections theory and its application to image recovery problems. Ultramicroscopy, 40, 55–67.
Sezan, M. I. & Stark, H. (1982). Image restoration by the method of convex projections. II. Applications and numerical results. IEEE Trans. Med. Imaging, 1, 95–101.
Sha, B.-D., Fan, H.-F. & Li, F.-H. (1993). Correction for the dynamical electron diffraction effect in crystal structure analysis. Acta Cryst. A49, 877–880.
Shannon, C. E. (1949). Communication in the presence of noise. Proc. Inst. Radio Eng. 37, 10–21.
Shechtman, D., Blech, I., Gratias, D. & Cahn, J. W. (1984). Metallic phase with long-range orientational order and no translational symmetry. Phys. Rev. Lett. 53, 1951–1953.
Shoemaker, V. & Glauber, R. (1952). The Born approximation in electron diffraction. Nature (London), 170, 290–291.
Sigworth, F. J. (2004). Classical detection theory and the cryo-EM particle selection problem. J. Struct. Biol. 145, 111–122.
Sorzano, C. O. S., Marabini, R., Velazquez-Muriel, J., Bilbao-Castro, J. R., Scheres, S. H. W., Carazo, J. M. & Pascual-Montano, A. (2004). XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 148, 194–204.
Spahn, C. M. T., Penczek, P., Leith, A. & Frank, J. (2000). A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome. Struct. Fold. Des. 8, 937–948.
Spence, J. C. H. (1993). On the accurate measurement of structure-factor amplitudes and phases by electron diffraction. Acta Cryst. A49, 231–260.
Spence, J. C. H. (2003). High-Resolution Electron Microscopy. New York: Oxford University Press.
Spence, J. C. H. & Cowley, J. M. (1978). Lattice imaging in STEM. Optik, 50, 129–142.
Spence, J. C. H., O'Keefe, M. A. & Kolar, H. (1977). Image interpretation in crystalline germanium. Optik (Stuttgart), 49, 307–323.
Spence, J. C. H. & Zuo, J. M. (1992). Electron Microdiffraction. New York: Plenum Press.
Steeds, J. W., Bird, D. M., Eaglesham, D. J., Mckernen, S., Vincent, R. & Withers, R. L. (1985). Study of modulated structures by transmission electron microscopy. Ultramicroscopy, 18, 97–110.
Steeds, J. W. & Evans, N. S. (1980). Practical examples of point and space group determination in convergent beam diffraction. Proc. Electron Microsc. Soc. Am. pp. 188–191.
Steeds, J. W., Rackham, G. M. & Shannon, M. D. (1978). On the observation of dynamically forbidden lines in two and three dimensional electron diffraction. In Electron Diffraction 1927–1977. Inst. Phys. Conf. Ser. No. 41, pp. 135–139.
Steinkilberg, M. & Schramm, H. J. (1980). Eine verbesserte Dreh­korrelations Methode für die Strukturbestimmung biologischer Macro­moleküle durch Mittelung elektronenmikroskopischer Bilder. Hoppe–Seyler's Z. Physiol. Chem. 361, 1363–1369.
Stereochemical Applications of Gas-Phase Electron Diffraction (1988). Part A, edited by I. Hargittai & M. Hargittai. New York: VCH.
Steurer, W. (2004). Twenty years of structure research on quasicrystals. Part 1. Pentagonal, octagonal, decagonal and dodecagonal quasicrystals. Z. Kristallogr. 219, 391–446.
Taftø, T. & Spence, J. C. H. (1982). A simple method for the determination of structure-factor phase relationships and crystal polarity using electron diffraction. J. Appl. Cryst. 15, 60–64.
Tanaka, M. (1986). Conventional transmission-electron-microscopy techniques in convergent-beam electron diffraction. J. Electron Microsc. 35, 314–323.
Tanaka, M. (1989). Symmetry analysis. J. Electron Microsc. Tech. 13, 27–39.
Tanaka, M., Saito, R. & Sekii, H. (1983). Point-group determination by convergent-beam electron diffraction. Acta Cryst. A39, 357–368.
Tanaka, M., Saito, P., Ueno, K. & Harada, Y. (1980). Large angle convergent-beam electron diffraction. J. Electron. Microsc. 29, 408–412.
Tanaka, M., Sekii, H. & Nagasawa, T. (1983). Space group determination by dynamic extinction in convergent beam electron diffraction. Acta Cryst. A39, 825–837.
Tanaka, M., Takayoshi, H., Ishida, M. & Endoh, Y. (1985). Crystal chirality and helicity of the helical spin-density wave in MnSi. 1. Convergent-beam electron diffraction. J. Phys. Soc. Jpn, 54, 2970–2974.
Tanaka, M. & Terauchi, M. (1985). Convergent-Beam Electron Diffraction. Tokyo: JEOL Ltd.
Tanaka, M., Terauchi, M. & Kaneyama, T. (1988). Convergent-Beam Electron Diffraction II. Tokyo: JEOL Ltd.
Tanaka, M., Terauchi, M. & Sekii, H. (1987). Observation of dynamic extinction due to a glide plane perpendicular to an incident beam by convergent-beam electron diffraction. Ultramicroscopy, 21, 245–250.
Tanaka, M., Terauchi, M., Suzuki, S., Hiraga, K. & Hirabayashi, M. (1987). Convergent-beam and small-area-parallel-beam electron diffraction patterns of icosahedral quasicrystals of an Al74Mn20Si6 alloy. Acta Cryst. B43, 494–501.
Tanaka, M., Terauchi, M. & Tsuda, K. (1994). Convergent-Beam Electron Diffraction III. Tokyo: JEOL–Maruzen.
Tanaka, M., Terauchi, M., Tsuda, K. & Saitoh, K. (2002). Convergent-Beam Electron Diffraction IV, p. 13. Tokyo: JEOL.
Tanaka, M. & Tsuda, K. (1990). Determination of positional parameters by convergent-beam electron diffraction. Proc. XIIth Int. Congr. Electron Microsc., Seattle, edited by L. D. Peachy & D. B. Williams, Vol. 2, pp. 518–519. San Francisco: San Francisco Press.
Tanaka, M. & Tsuda, K. (1991). Microbeam Analysis, edited by D. G. Howitt, pp. 145–146. San Francisco: San Francisco Press.
Tanaka, M., Tsuda, K. & Saitoh, K. (1996). Convergent-beam electron diffraction and electron microscope studies of decagonal quasicrystals. Sci. Rep. RITU, A42, 199–205.
Tanaka, M., Tsuda, K., Terauchi, M., Fujiwara, A., Tsai, A. P., Inoue, A. & Masumoto, T. (1993). Electron diffraction and electron microscope study on decagonal quasicrytals of Al–Ni–Fe alloys. J. Non-Cryst. Solids, 153&154, 98–102.
Terauchi, M., Takahashi, M. & Tanaka, M. (1994). Convergent-beam electron diffraction study of incommensurately modulated crystals. II. (3+1)-dimensional space groups. Acta Cryst. A50, 566–574.
Terauchi, M. & Tanaka, M. (1993). Convergent-beam electron diffraction study of incommensurately modulated crystals. I. (3+1)-dimensional point groups. Acta Cryst. A49, 722–729.
Thon, F. (1966). On the defocusing dependence of phase contrast in electron microscopical images. Z. Naturforsch. Teil A, 21, 476–478.
Tinnappel, A. (1975). PhD Thesis, Technische Universität Berlin, Germany.
Tivol, W. F., Dorset, D. L., McCourt, M. P. & Turner, J. N. (1993). Voltage-dependent effect on dynamical scattering and the electron diffraction structure analysis of organic crystals: copper perchloro­phthalocyanine. Microsc. Soc. Am. Bull. 23, 91–98.
Tournaire, M. (1962). Recent developments of the matrical and semi-reciprocal formulation in the field of dynamical theory. J. Phys. Soc. Jpn, 17, Suppl. B11, 98–100.
Tsai, A. P. (2003). `Back to the future' – An account of the discovery stable quasicrystals. Acc. Chem. Res. 36, 31–38.
Tsai, A. P., Inoue, A. & Masumoto, T. (1987). A stable quasi-crystal in Al–Cu–Fe system. Jpn. J. Appl. Phys. Lett. 26, L1505–L1507.
Tsai, A. P., Inoue, A. & Masumoto, T. (1989a). A stable decagonal quasicrystal in the Al–Cu–Co system. Mater. Trans. Jpn. Inst. Met. 30, 300–304.
Tsai, A. P., Inoue, A. & Masumoto, T. (1989b). Stable decagonal Al–Co–Ni and Al–Co–Cu quasicrystals. Mater. Trans. Jpn. Inst. Met. 30, 463–473.
Tsai, A. P., Inoue, A. & Masumoto, T. (1989c). New decagonal Al–Ni–Fe and Al–Ni–Co alloys prepared by liquid quenching. Mater. Trans. Jpn. Inst. Met. 30, 150–154.
Tsipursky, S. I. & Drits, V. A. (1977). Efficiency of electronometric intensity registration at electron diffraction structural studies. Izv. Akad. Nauk SSSR Ser. Fiz. 41, 2263–2271.
Tsuda, K., Ogata, Y., Takagi, K., Hashimoto, T. & Tanaka, M. (2002). Refinement of crystal structural parameters and charge density using convergent-beam electron diffraction – the rhombohedral phase of LaCrO3. Acta Cryst. A58, 514–525.
Tsuda, K., Saito, M., Terauchi, M., Tanaka, M., Tsai, A. P., Inoue, A. & Masumoto, K. (1993). Electron microscope study of decagonal quasicrystals of Al70Ni15Fe15. Jpn. J. Appl. Phys. 32, 129–134.
Tsuda, K., Saitoh, K., Terauchi, M., Tanaka, M. & Goodman, P. (2000). Distinction of space groups (I23 and I213) and (I222 and I212121) using coherent convergent-beam electron diffraction. Acta Cryst. A56, 359–369.
Tsuda, K. & Tanaka, M. (1995). Refinement of crystal structure parameters using convergent-beam electron diffraction: the low-temperature phase of SrTiO3. Acta Cryst. A51, 7–19.
Tsuda, K. & Tanaka, M. (1999). Refinement of crystal structural parameters using two-dimensional energy-filtered CBED patterns. Acta Cryst. A55, 939–954.
Tsuji, M. (1989). Electron microscopy. In Comprehensive Polymer Science, Vol. 1. Polymer Characterization, edited by C. Booth & C. Price, pp. 785–840. Oxford: Pergamon Press
Turner, P. S. & Cowley, J. M. (1969). The effects of n-beam dynamical diffraction on electron diffraction intensities from polycrystalline materials. Acta Cryst. A25, 475–481.
Unser, M., Trus, B. L. & Steven, A. C. (1987). A new resolution criterion based on spectral signal-to-noise ratios. Ultramicroscopy, 23, 39–51.
Unwin, P. N. T. & Henderson, R. (1975). Molecular structure determination by electron microscopy of unstained crystalline specimens. J. Mol. Biol. 94, 425–440.
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.
Vainshtein, B. K. (1952). Dependence of electron scattering on the atomic number. Dokl. Akad. Nauk SSSR, 85, 1239–1242.
Vainshtein, B. K. (1954). On the studies of crystal lattice potential by electron diffraction. Tr. Inst. Krist. Akad. Nauk SSSR, 9, 259–276.
Vainshtein, B. K. (1955). Elektronograficheskoe issledovanie diketopiperazina. Zh. Fiz. Khim. 29, 327–344.
Vainshtein, B. K. (1956). Structure Analysis by Electron Diffraction. Moscow: Akad. Sci. USSR.
Vainshtein, B. K. (1964). Structure Analysis by Electron Diffraction. Oxford: Pergamon Press.
Vainshtein, B. K. (1971). Finding the structure of objects from projections. Sov. Phys. Crystallogr. 15, 781–787.
Vainshtein, B. K., D'yakon, I. A. & Ablov, A. V. (1971). Electron diffraction determination of the structure of copper DL-alaninate. Sov. Phys. Dokl. 15, 645–647.
Vainshtein, B. K. & Klechkovskaya, V. V. (1993). Electron diffraction by Langmuir–Blodgett films. Proc. R. Soc. London Ser. A, 442, 73–84.
Vilkov, L. V., Mastryukov, V. S. & Sadova, N. I. (1978). Determination of Geometrical Structure of Free Molecules. Leningrad: Khimiya.
Vincent, R., Bird, D. M. & Steeds, J. W. (1984a). Structure of AuGeAs determined by convergent-beam electron-diffraction. 1. Derivation of basic structure. Philos. Mag. A, 50, 745–763.
Vincent, R., Bird, D. M. & Steeds, J. W. (1984b). Structure of AuGeAs determined by convergent-beam electron-diffraction. 2. Refinement of structural parameters. Philos. Mag. A, 50, 765–786.
Vincent, R. & Exelby, D. R. (1991). Structure of metastable Al–Ge phases determined from HOLZ Patterson transforms. Philos. Mag. Lett. 63, 31–38.
Vincent, R. & Exelby, D. R. (1993). Structure of a metastable Al–Ge phase determined from large angle CBED patterns. Philos. Mag. B, 68, 513–528.
Vincent, R. & Midgley, P. A. (1994). Double conical beam rocking system for measurement of integrated electron diffraction intensities. Ultramicroscopy, 53, 271–282.
Vine, W. J., Vincent, R., Spellward, P. & Steeds, J. W. (1992). Observation of phase contrast in convergent-beam electron diffraction. Ultramicroscopy, 41, 423–428.
Vogel, R. H. & Provencher, S. W. (1988). Three-dimensional reconstruction from electron micrographs of disordered specimens. II. Implementation and results. Ultramicroscopy, 25, 223–239.
Voronova, A. A. & Vainshtein, B. K. (1958). An electron diffraction study of CuCl2·3Cu(OH)2. Sov. Phys. Crystallogr. 3, 445–451.
Walz, J., Typke, D., Nitsch, M., Koster, A. J., Hegerl, R. & Baumeister, W. (1997). Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification. J. Struct. Biol. 120, 387–395.
Watanabe, D., Uyeda, R. & Kogiso, M. (1968). An apparent variation of structure factors for electrons with accelerating voltage. An observation through Kikuchi patterns. Acta Cryst. A24, 249–250.
Welch, P. D. (1967). The use of fast Fourier transform for the estimation of power spectra: a method based on time averaging over short modified periodograms. IEEE Trans. Audio Electroacoust. AU-15, 70–73.
Wenk, H.-R., Downing, K. H., Ho, M.-S. & O'Keefe, M. A. (1992). 3D structure determination from electron-microscope images: electron crystallography of staurolite. Acta Cryst. A48, 700–716.
Wolff, P. M. de (1974). The pseudo-symmetry of modulated crystal structures. Acta Cryst. A30, 777–785.
Wolff, P. M. de (1977). Symmetry operations for displacively modulated structures. Acta Cryst. A33, 493–497.
Wolff, P. M. de, Janssen, T. & Janner, A. (1981). The superspace groups for incommensurate crystal structures with a one-dimensional modulation. Acta Cryst. A37, 625–636.
Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004). Model-based particle picking for cryo-electron microscopy. J. Struct. Biol. 145, 157–167.
Xiang, S.-B., Fan, H.-F., Wu, X.-J., Li, F.-H. & Pan, Q. (1990). Direct methods in superspace. II. The first application to an unknown incommensurate modulated structure. Acta Cryst. A46, 929–934.
Yamamoto, A. (1982). Structure factor of modulated crystal structures. Acta Cryst. A38, 87–92.
Yamamoto, A. (1996). Crystallography of quasiperiodic crystals. Acta Cryst. A52, 509–560.
Yamamoto, A. & Ishihara, K. N. (1988). Penrose patterns and related structures. II. Decagonal quasicrystals. Acta Cryst. A44, 707–714.
Yamamoto, A., Janssen, T., Janner, A. & de Wolff, P. M. (1985). A note on the superspace groups for one-dimensionally modulated structures. Acta Cryst. A41, 528–530.
Yamamoto, N. (1988). Electron microscope study of incommensurate phases. Kotaibutsui, 23, 547.
Yang, C., Ng, E. G. & Penczek, P. A. (2005). Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm. J. Struct. Biol. 149, 53–64.
Yao, J.-X. (1981). On the application of phase relationships to complex structures. XVIII. RANTAN – random MULTAN. Acta Cryst. A37, 642–644.
Yin, Z. H., Zheng, Y. L., Doerschuk, P. C., Natarajan, P. & Johnson, J. E. (2003). A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction. J. Struct. Biol. 144, 24–50.
Yin, Z. Y., Zheng, Y. L. & Doerschuk, P. C. (2001). An ab initio algorithm for low-resolution 3-D reconstructions from cryoelectron microscopy images. J. Struct. Biol. 133, 132–142.
Youla, D. C. & Webb, H. (1982). Image restoration by the method of convex projections. 1. Theory. IEEE Trans. Med. Imaging, 1, 81–94.
Yuen, C. K. & Fraser, D. (1979). Digital Spectral Analysis. Adelaide: CSIRO Pitman.
Zemlin, F., Reuber, E., Beckmann, E., Zeitler, E. & Dorset, D. L. (1985). Molecular resolution electron micrographs of monolamellar paraffin crystal. Science, 229, 461–462.
Zhu, J., Penczek, P. A., Schröder, R. & Frank, J. (1997). Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. J. Struct. Biol. 118, 197–219.
Zhu, Y., Carragher, B., Glaeser, R. M., Fellmann, D., Bajaj, C., Bern, M., Mouche, F., de Haas, F., Hall, R. J., Kriegman, D. J., Ludtke, S. C., Mallick, S. P., Penczek, P. A., Roseman, A. M., Sigworth, F. J., Volkmann, N. & Potter, C. S. (2004). Automatic particle selection: results of a comparative study. J. Struct. Biol. 145, 3–14.
Zhukhlistov, A. P., Avilov, A. S., Ferraris, G., Zvyagin, B. B. & Plotnikov, V. P. (1997). Statistical distribution of hydrogen over three positions in the brucite Mg(OH)2 structure from electron diffractometry data. Crystallogr. Rep. 42, 774–777.
Zhukhlistov, A. P. & Zvyagin, B. B. (1998). Crystal structure of lizardite 1T from electron diffractometry data. Crystallogr. Rep. 43, 950–955.
Zuo, J. M., Kim, M., O'Keeffe, M. & Spence, J. C. H. (1999). Observation of d holes and Cu–Cu bonding in cuprite. Nature (London), 401, 49–52.
Zvyagin, B. B. (1967). Electron-Diffraction Analysis of Clay Mineral Structures. New York: Plenum.
Zvyagin, B. B., Vrublevskaya, Z. V., Zhukhlistov, A. P., Sidorenko, S. V., Soboleva, A. F. & Fedotov, A. F. (1979). High-Voltage Electron Diffraction Investigations of Layered Minerals. Moscow: Nauka.
Zvyagin, B. B., Zhukhlistov, A. P. & Plotnikov, A. P. (1996). Development of the electron diffractometry of minerals. Structural studies of crystals. (Coll. Works 75th Anniversary Acad. B. K. Vainshtein.) Nauka-Physmathlit, pp. 225–234.