Preprint: Please note that this article has not completed peer review.
Method Article

Beginner's Guide to THUNDER

Mingxu Hu
DOI: 10.1038/protex.2018.060

Abstract

Electron cryo-microscopy (cryoEM) is now a powerful tool in determining atomic structures of biological macromolecules under nearly natural conditions. THUNDER is a particle-filter algorithm based cryoEM image processing software. Here, we describe a protocol for using THUNDER to analysis cryoEM images in purpose of achieving a 3D model. A JSON file is used for setting parameters in THUNDER. Meaning of each attribute is discussed in this protocol. The .thu file format is defined for storing information of each particle image, including CTF parameters, rotation, translation, defocus adjustment and grading weight. The definition of this .thu file is introduced in this protocol. Finally, the procedure of running THUNDER and examining the output of THUNDER is contained in this protocol.

Keywords
cryoEM, image processing, THUNDER

Figures

Introduction

Equipment

Procedure

Anticipated Results

References

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Preprint: Please note that this article has not completed peer review.
Method Article

Beginner's Guide to THUNDER

Mingxu Hu

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Abstract

Electron cryo-microscopy (cryoEM) is now a powerful tool in determining atomic structures of biological macromolecules under nearly natural conditions. THUNDER is a particle-filter algorithm based cryoEM image processing software. Here, we describe a protocol for using THUNDER to analysis cryoEM images in purpose of achieving a 3D model. A JSON file is used for setting parameters in THUNDER. Meaning of each attribute is discussed in this protocol. The .thu file format is defined for storing information of each particle image, including CTF parameters, rotation, translation, defocus adjustment and grading weight. The definition of this .thu file is introduced in this protocol. Finally, the procedure of running THUNDER and examining the output of THUNDER is contained in this protocol.

Figures

Introduction

Equipment

Procedure

Anticipated Results

References

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