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Gctf: Real-time CTF determination and correction

Open access
Zhang, Kai·2016·Journal of Structural Biology
DOI 10.1016/j.jsb.2015.11.003

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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.

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Metadata

Authors
Zhang, K.
Venue
Journal of Structural Biology
Publisher
Elsevier BV
Published
2016-01
Volume
193
Issue
1
Pages
1-12
ISSN
1047-8477 (ISSN-L)
DOI
10.1016/j.jsb.2015.11.003
OpenAlex
W2950967305
Cited by
3,537
References
2
FWCI
61.11
Type
journal article
Language
en
Open access
hybrid
Licence
Funders
  • Medical Research Council (MC_UP_A025_1011)
  • Wellcome Trust New Investigator Award (WT100387)

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Zhang, K. (2016). Gctf: Real-time CTF determination and correction. Journal of Structural Biology. https://doi.org/10.1016/j.jsb.2015.11.003

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