Journal of Structural Biology, volume 193, issue 1, pages 1-12

Gctf: Real-time CTF determination and correction

Zhang Kai 1
1
 
Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge CB2 0QH, UK
Publication typeJournal Article
Publication date2016-01-01
Quartile SCImago
Q1
Quartile WOS
Q2
Impact factor3
ISSN10478477, 10958657
Structural Biology
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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Zhang K. Gctf: Real-time CTF determination and correction // Journal of Structural Biology. 2016. Vol. 193. No. 1. pp. 1-12.
GOST all authors (up to 50) Copy
Zhang K. Gctf: Real-time CTF determination and correction // Journal of Structural Biology. 2016. Vol. 193. No. 1. pp. 1-12.
RIS |
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RIS Copy
TY - JOUR
DO - 10.1016/j.jsb.2015.11.003
UR - https://doi.org/10.1016%2Fj.jsb.2015.11.003
TI - Gctf: Real-time CTF determination and correction
T2 - Journal of Structural Biology
AU - Zhang, Kai
PY - 2016
DA - 2016/01/01 00:00:00
PB - Elsevier
SP - 1-12
IS - 1
VL - 193
PMID - 26592709
SN - 1047-8477
SN - 1095-8657
ER -
BibTex |
Cite this
BibTex Copy
@article{2016_Zhang
author = {Kai Zhang},
title = {Gctf: Real-time CTF determination and correction},
journal = {Journal of Structural Biology},
year = {2016},
volume = {193},
publisher = {Elsevier},
month = {jan},
url = {https://doi.org/10.1016%2Fj.jsb.2015.11.003},
number = {1},
pages = {1--12},
doi = {10.1016/j.jsb.2015.11.003}
}
MLA
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MLA Copy
Zhang, Kai. “Gctf: Real-time CTF determination and correction.” Journal of Structural Biology, vol. 193, no. 1, Jan. 2016, pp. 1-12. https://doi.org/10.1016%2Fj.jsb.2015.11.003.
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