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JOURNAL OF STRUCTURAL BIOLOGY Volume 144, Numbers 1/2, October/November 2003 CONTENTS Editorial Bridget Carragher and Pawel A. Penczek. Analytical Methods and Software Tools for Macromolecular Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
Regular Articles Ansgar Philippsen, Andreas D. Schenk, Henning Stahlberg, and Andreas Engel. Iplt—image processing library and toolkit for the electron microscopy community . . . . . . . . . . . . . . . . . . . . . . . . Jorge Navaza.
4
On the three-dimensional reconstruction of icosahedral particles . . . . . . . . . . . . . . . . .
13
Zhye Yin, Yili Zheng, Peter C. Doerschuk, Padmaja Natarajan, and John E. Johnson. A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24
Yao Cong, Julio A. Kovacs, and Willy Wriggers. 2D fast rotational matching for image processing of biophysical data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
51
Kristian Sandberg, David N. Mastronarde, and Gregory Beylkin. A fast reconstruction algorithm for electron microscope tomography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
Steven J. Ludtke and Wah Chiu.
Focal pair merging for contrast enhancement of single particles
73
Zhong Huang, Philip R. Baldwin, Srinivas Mullapudi, and Pawel A. Penczek. Automated determination of parameters describing power spectra of micrograph images in electron microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
79
B.K. Rath, R. Hegerl, A. Leith, T.R. Shaikh, T. Wagenknecht, and J. Frank. Fast 3D motif search of EM density maps using a locally normalized cross-correlation function . . . . . . . . . . . . . . . . . . . .
95
N. Jim enez-Lozano, M. Chagoyen, J. Cuenca-Alba, and J.M. Carazo. FEMME database: topologic and geometric information of macromolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 Wen Jiang, Matthew L. Baker, Qiu Wu, Chandrajit Bajaj, and Wah Chiu. Applications of a bilateral denoising filter in biological electron microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 Stefan Birmanns and Willy Wriggers. Interactive fitting augmented by force-feedback and virtual reality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 Chandrajit Bajaj, Zeyun Yu, and Manfred Auer. Volumetric feature extraction and visualization of tomographic molecular imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 James Z. Chen, Johannes F€ urst, Michael S. Chapman, and Nikolaus Grigorieff. Low-resolution structure refinement in electron microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 Jos e-Jes us Fern andez and Sam Li. An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 Shixin Yang, Xiong Yu, Vitold E. Galkin, and Edward H. Egelman. Issues of resolution and polymorphism in single-particle reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162 Andrew Ward, Michael F. Moody, Brian Sheehan, Ronald A. Milligan, and Bridget Carragher. Windex: a toolset for indexing helices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Continued
Koji Yonekura, Chikashi Toyoshima, Saori Maki-Yonekura, and Keiichi Namba. GUI programs for processing individual images in early stages of helical image reconstruction—for high-resolution structure analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 Michael F. Schmid. Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals: application to the Limulus acrosomal bundle . . . . . . . 195 J.C.H. Spence, U. Weierstall, T.T. Fricke, R.M. Glaeser, and K.H. Downing. Three-dimensional diffractive imaging for crystalline monolayers with one-dimensional compact support . . . . . . . . 209 G. Huldt, A. Sz} oke, and J. Hajdu.
Diffraction imaging of single particles and biomolecules . . . . . 219
K. Henrick, R. Newman, M. Tagari, and M. Chagoyen. EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228 Wei Dai, Yuyao Liang, and Z. Hong Zhou. Web portal to an image database for high-resolution three-dimensional reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238 H.D. White, K. Thirumurugan, M.L. Walker, and J. Trinick. A second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray . . . . . . . . . . . . . . . 246
1
Regular Articles Ansgar Philippsen, Andreas D. Schenk, Henning Stahlberg, and Andreas Engel. Iplt—image processing library and toolkit for the electron microscopy community . . . . . . . . . . . . . . . . . . . . . . . . Jorge Navaza.
4
On the three-dimensional reconstruction of icosahedral particles . . . . . . . . . . . . . . . . .
13
Zhye Yin, Yili Zheng, Peter C. Doerschuk, Padmaja Natarajan, and John E. Johnson. A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24
Yao Cong, Julio A. Kovacs, and Willy Wriggers. 2D fast rotational matching for image processing of biophysical data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
51
Kristian Sandberg, David N. Mastronarde, and Gregory Beylkin. A fast reconstruction algorithm for electron microscope tomography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
Steven J. Ludtke and Wah Chiu.
Focal pair merging for contrast enhancement of single particles
73
Zhong Huang, Philip R. Baldwin, Srinivas Mullapudi, and Pawel A. Penczek. Automated determination of parameters describing power spectra of micrograph images in electron microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
79
B.K. Rath, R. Hegerl, A. Leith, T.R. Shaikh, T. Wagenknecht, and J. Frank. Fast 3D motif search of EM density maps using a locally normalized cross-correlation function . . . . . . . . . . . . . . . . . . . .
95
N. Jim enez-Lozano, M. Chagoyen, J. Cuenca-Alba, and J.M. Carazo. FEMME database: topologic and geometric information of macromolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 Wen Jiang, Matthew L. Baker, Qiu Wu, Chandrajit Bajaj, and Wah Chiu. Applications of a bilateral denoising filter in biological electron microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 Stefan Birmanns and Willy Wriggers. Interactive fitting augmented by force-feedback and virtual reality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 Chandrajit Bajaj, Zeyun Yu, and Manfred Auer. Volumetric feature extraction and visualization of tomographic molecular imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 James Z. Chen, Johannes F€ urst, Michael S. Chapman, and Nikolaus Grigorieff. Low-resolution structure refinement in electron microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 Jos e-Jes us Fern andez and Sam Li. An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 Shixin Yang, Xiong Yu, Vitold E. Galkin, and Edward H. Egelman. Issues of resolution and polymorphism in single-particle reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162 Andrew Ward, Michael F. Moody, Brian Sheehan, Ronald A. Milligan, and Bridget Carragher. Windex: a toolset for indexing helices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Continued
Koji Yonekura, Chikashi Toyoshima, Saori Maki-Yonekura, and Keiichi Namba. GUI programs for processing individual images in early stages of helical image reconstruction—for high-resolution structure analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 Michael F. Schmid. Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals: application to the Limulus acrosomal bundle . . . . . . . 195 J.C.H. Spence, U. Weierstall, T.T. Fricke, R.M. Glaeser, and K.H. Downing. Three-dimensional diffractive imaging for crystalline monolayers with one-dimensional compact support . . . . . . . . 209 G. Huldt, A. Sz} oke, and J. Hajdu.
Diffraction imaging of single particles and biomolecules . . . . . 219
K. Henrick, R. Newman, M. Tagari, and M. Chagoyen. EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228 Wei Dai, Yuyao Liang, and Z. Hong Zhou. Web portal to an image database for high-resolution three-dimensional reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238 H.D. White, K. Thirumurugan, M.L. Walker, and J. Trinick. A second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray . . . . . . . . . . . . . . . 246