CTFFIND pipeline

CTFFIND specifications


Unique identifier OMICS_15823
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Fortran
License Other
Computer skills Advanced
Version 4.1
Stability Stable
Maintained Yes


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  • person_outline Nikolaus Grigorieff <>

Publications for CTFFIND

CTFFIND IN pipelines

PMCID: 5842316
PMID: 29499136
DOI: 10.1016/j.molcel.2018.02.008

[…] was 105,000x. motion correction and dose weighting was performed using motioncor2 (zheng et al., 2016). parameters of the contrast transfer function (ctf) of each micrograph were estimated with ctffind4 (rohou and grigorieff, 2015). in a first step, ∼20,000 particles were picked with the semi-automated swarm method using eman2 (tang et al., 2007). relion (scheres, 2012) was used […]

PMCID: 5906670
PMID: 29670100
DOI: 10.1038/s41467-018-03947-w

[…] of 50 e−1 per å2 at a pixel size of 0.785 å per pixel. the defocus range of the data set was set to a range of −1.5 – −3.5 μm., movie processing was performed using the software motioncor262 and ctffind463. after the particle picking performed with gautomatch (http://www.mrc-lmb.cam.ac.uk/kzhang/) for the particles with 200 å diameter, image processing was performed with relion264,65. […]

PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986

[…] received for each movie micrograph was 67 e-/å2. the nominal defocus range used was -1.5 to -4.0 μm., movie micrograph frames were aligned using motioncorr [57] and ctf models were calculated using ctffind3 [58]. the resulting motion-corrected and signal-integrated micrographs were subjected to automated difference-of-gaussian particle selection [59]. the resulting set of molecular […]

PMCID: 5344670
PMID: 28092267
DOI: 10.7554/eLife.24149.020

[…] 1 and 2)., the raw frame stacks were gain-normalized and then aligned and dose-compensated using unblur (grant and grigorieff, 2015) (table 1). ctf was estimated from the aligned frame sums using ctffind4 (rohou and grigorieff, 2015). to reduce the possibility of bias and capture every possible particle view, an initial set of 350,000 potential particles (referred to as ‘peaks’ in figure […]

PMCID: 5392032
PMID: 28439563
DOI: 10.1126/sciadv.1700325

[…] integrated with dose filter applied using motioncor2, and the integrated images were used for single-particle extraction and analysis. contrast transfer function (ctf) parameters were determined by ctffind3 and ctftilt (24) for untilted and tilted micrographs, respectively. the defocus value for each individual tilted particle was assigned according to its location in the corresponding […]

CTFFIND institution(s)
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA

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