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Three dimensional electron microscopy of macromolecular assemblies Visualization of biological molecules 2nd Edition by Joachim Frank ISBN 9781429415217 1429415215

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Three dimensional electron microscopy of macromolecular assemblies Visualization of biological molecules 2nd Edition Joachim Frank Digital Instant Download

Author(s): Joachim Frank
ISBN(s): 9781429415217, 1429415215
Edition: 2
File Details: PDF, 8.55 MB
Year: 2006
Language: english
SKU: EB-1006108 Category: Tag:

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Product details: 

ISBN 10:   1429415215

ISBN 13: 9781429415217

Author: Joachim Frank

Cryoelectron microscopy of biological molecules is among the hottest growth areas in biophysics and structural biology at present, and Frank is arguably the most distinguished practitioner of this art. CryoEM is likely over the next few years to take over much of the structural approaches currently requiring X-ray crystallography, because one can now get good and finely detailed images of single molecules down to as little as 200,000 MW, covering a substantial share of the molecules of greatest biomedical research interest. This book, the successor to an earlier work published in 1996 with Academic Press, is a natural companion work to our forthcoming book on electron crystallography by Robert Glaeser, with contributions by six others, including Frank. A growing number of workers will employ CryoEM for structural studies in their own research, and a large proportion of biomedical researchers will have a growing interest in understanding what the capabilities and limits of this approach are.
 

Table of contents: 

CHAPTER 1. Introduction

  1. The Electron Microscope and Biology
     1.1 General Remarks
     1.2 Three-Dimensional Electron Microscopy

  2. Single-Particle Versus Crystallographic Analysis

  3. Crystallography without Crystals

  4. Toward a Unified Approach to Structural Analysis of Macromolecules

  5. Single-Particle Reconstruction, Macromolecular Machines, and Structural Proteomics

  6. The Electron Microscope and the Computer

CHAPTER 2. Electron Microscopy of Macromolecular Assemblies

  1. Principle of the Transmission Electron Microscope

  2. Specimen Preparation Methods
     2.1 Introduction
     2.2 Negative Staining
     2.3 Glucose Embedment
     2.4 Use of Tannic Acid
     2.5 Ice-Embedded Specimens
     2.6 Hybrid Techniques: Cryo-Negative Staining
     2.8 Support Grids

  3. Principle of Image Formation in the Transmission Electron Microscope
     3.1 Introduction
     3.2 The Weak-Phase Object Approximation
     3.3 The Contrast Transfer Theory
     3.4 Amplitude Contrast
     3.5 Formulation of Bright-Field Image Formation Using Complex Atomic Scattering Amplitudes
     3.6 Optical and Computational Diffraction Analysis – The Power Spectrum
     3.7 Determination of the Contrast Transfer Function
     3.8 Instrumental Correction of the Contrast Transfer Function
     3.9 Computational Correction of the Contrast Transfer Function
     3.10 Locally Varying CTF and Image Quality

  4. Special Imaging Techniques and Devices
     4.1 Low-Dose Electron Microscopy
     4.2 Spot Scanning
     4.3 Energy Filtration
     4.4 Direct Image Readout and Automated Data Collection

CHAPTER 3. Two-Dimensional Averaging Techniques

  1. Introduction
     1.1 The Different Sources and Types of Noise
     1.2 Principle of Averaging: Historical Notes
     1.3 Equivalence between Averaging and Quasi-Optical Fourier Filtration
     1.4 A Discourse on Terminology: Views Versus Projections
     1.5 The Role of Two-Dimensional Averaging in the Three-Dimensional Analysis of Single Molecules
     1.6 Origins of Orientational Preferences

  2. Digitization and Selection of Particles
     2.1 Hardware for Digitization
     2.2 The Sampling Theorem
     2.3 Interactive Particle Selection
     2.4 Automated Particle Selection

  3. Alignment Methods
     3.1 Quantitative Definitions of Alignment
     3.2 Homogeneous Versus Heterogeneous Image Sets
     3.3 Translational and Rotational Cross-Correlation
     3.4 Reference-Based Alignment Techniques
     3.5 Reference-Free Alignment Techniques
     3.6 Alignment Using the Radon Transform

CHAPTER 4. Classification and Multivariate Statistical Analysis

4.8 Nonlinear Mapping
4.9 Self-Organized Maps
4.10 Supervised Classification: Use of Templates
4.11 Inference from Two to Three Dimensions

CHAPTER 5. Three-Dimensional Reconstruction

  1. Introduction

  2. General Mathematical Principles
     2.1 The Projection Theorem and Radon’s Theorem
     2.2 Object Boundedness, Shape Transform, and Resolution
     2.3 Definition of Eulerian Angles, and Special Projection Geometries: Single-Axis and Conical Tilting

  3. The Rationales of Data Collection: Reconstruction Schemes
     3.1 Introduction
     3.2 Cylindrically Averaged Reconstruction
     3.3 Compatibility of Projections
     3.4 Relating Projections to One Another Using Common Lines
     3.5 The Random-Conical Data Collection Method
     3.6 Comparison of Common Lines Versus Random-Conical Methods
     3.7 Reconstruction Schemes Based on Uniform Angular Coverage

  4. Overview of Existing Reconstruction Techniques
     4.1 Preliminaries
     4.2 Weighted Back-Projection
     4.3 Fourier Reconstruction Methods
     4.4 Iterative Algebraic Reconstruction Methods

  5. The Random-Conical Reconstruction in Practice
     5.1 Overview
     5.2 Optical Diffraction Screening
     5.3 Interactive Tilted/Untilted Particle Selection
     5.4 Optical Density Scaling
     5.5 Processing of Untilted-Particle Images
     5.6 Processing of Tilted-Particle Images
     5.7 Carrying Out the Reconstruction

  6. Common-Lines Methods (or “Angular Reconstitution”) in Practice

  7. Reference-Based Methods and Refinement
     7.1 Introduction
     7.2 Three-Dimensional Projection Matching
     7.3 Numerical Aspects
     7.4 Three-Dimensional Radon Transform Method
     7.5 The Size of Angular Deviations
     7.6 Model Dependence of the Reconstruction
     7.7 Consistency Check by Reprojection

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