Gctf: Real-time CTF determination and correction
| Autor: | Kai Zhang |
|---|---|
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Logarithm Cryo-electron microscopy Computer science 02 engineering and technology computer.software_genre CTF contrast transfer function FFT Fast Fourier Transform Reduction (complexity) Software Structural Biology cryoEM cryo-electron microscopy Image Processing Computer-Assisted EPA equiphase averaging Background subtraction 0303 health sciences Computer program Resolution (electron density) NFS Network File System 021001 nanoscience & nanotechnology CTF determination Power (physics) LAS logarithmic amplitude spectra HAV hepatitis A virus Data mining 0210 nano-technology Algorithm Algorithms SSD Solid State Disk DQE detective quantum efficiency GPU program CCC cross-correlation coefficient Fast Fourier transform Image processing Article Acceleration 03 medical and health sciences Imaging Three-Dimensional Contrast transfer function GPU Graphic Processing Unit 1D (2D 3D) one(two three) dimensional 030304 developmental biology Micrograph business.industry SNR signal to noise ratio Cryoelectron Microscopy CCF cross-correlation function 030104 developmental biology business computer CCD Charge Coupled Device |
| Zdroj: | Journal of Structural Biology |
| ISSN: | 1047-8477 |
| DOI: | 10.1016/j.jsb.2015.11.003 |
| Popis: | Accurate estimation of the contrast transfer function (CTF) is critical for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction. Here, a GPU-accelerated computer program, Gctf, for accurate and robust, real-time CTF determination is presented. The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction. Novel approaches in Gctf improve both speed and accuracy. In addition to GPU acceleration (e.g. 10–50×), a fast ‘1-dimensional search plus 2-dimensional refinement (1S2R)’ procedure further speeds up Gctf. Based on the global CTF determination, the local defocus for each particle and for single frames of movies is accurately refined, which improves CTF parameters of all particles for subsequent image processing. Novel diagnosis method using equiphase averaging (EPA) and self-consistency verification procedures have also been implemented in the program for practical use, especially for aims of near-atomic reconstruction. Gctf is an independent program and the outputs can be easily imported into other cryoEM software such as Relion (Scheres, 2012) and Frealign (Grigorieff, 2007). The results from several representative datasets are shown and discussed in this paper. |
| Databáze: | OpenAIRE |
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