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J Struct Biol. 2016 Jan;193(1):1-12. doi: 10.1016/j.jsb.2015.11.003. Epub 2015 Nov 19.

Gctf: Real-time CTF determination and correction.

Author information

1
Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: kzhang@mrc-lmb.cam.ac.uk.

Abstract

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.

KEYWORDS:

CTF determination; Contrast transfer function; Cryo-electron microscopy; GPU program

PMID:
26592709
PMCID:
PMC4711343
DOI:
10.1016/j.jsb.2015.11.003
[Indexed for MEDLINE]
Free PMC Article

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