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Protocols

CTFFIND specifications

Information


Unique identifier OMICS_15823
Name CTFFIND
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

Versioning


No version available

Documentation


Maintainer


  • person_outline Nikolaus Grigorieff

Publications for CTFFIND

CTFFIND citations

 (410)
library_books

Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

2018
Nat Commun
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] dose in the em data collection was 32.6 e−/å2. the nominal defocus range used was −1.5 to −3.5 μm., all of the collected frames were aligned prior to processing. ctf estimation was carried out using ctffind3, and particles were picked using an automated particle-picking program implemented in the appion software package. particles were stacked using a box size of 256 × 256 pixels at 1.31 å/pix […]

call_split

Structural and immunologic correlates of chemically stabilized HIV 1 envelope glycoproteins

2018
PLoS Pathog
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986
call_split See protocol

[…] 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 [] and ctf models were calculated using ctffind3 []. the resulting motion-corrected and signal-integrated micrographs were subjected to automated difference-of-gaussian particle selection []. the resulting set of molecular projection-image […]

call_split

Cryo EM of nucleosome core particle interactions in trans

2018
Sci Rep
PMCID: 5935684
PMID: 29728587
DOI: 10.1038/s41598-018-25429-1
call_split See protocol

[…] remove inconsistent particles. the resulting useful particles were then used for semi-automatic and automatic particle picking in xmipp. the contrast transfer function parameters were determined by ctffind4. the 2d class averages were generated with the relion software package. bad class averages were removed from further data analysis. the 3d refinements and classifications were subsequently […]

library_books

Structural basis for energy transduction by respiratory alternative complex III

2018
Nat Commun
PMCID: 5928083
PMID: 29712914
DOI: 10.1038/s41467-018-04141-8

[…] particles were picked manually using eman boxer or automatically by template matching in gautomatch (by kai zhang, mrc-lmb cambridge, uk), and the micrograph-based ctf was determined using ctffind4 on drift-corrected, non-dose-weighted images. automatically picked particles were subjected to a first round of reference-free two-dimensional classification with isac within sphire, […]

library_books

Cryo EM reveals the structural basis of microtubule depolymerization by kinesin 13s

2018
Nat Commun
PMCID: 5916938
PMID: 29695795
DOI: 10.1038/s41467-018-04044-8

[…] of klp10a nm construct in complex with curved tubulin protofilaments in the presence of amp-pnp (supplementary fig. ) were aligned and classified using relion (v 2.0). ctf was estimated using ctffind4. first 10,016 ring-like structures were picked manually from 464 cryo-em images by marking their centers and masking them with a circular mask of 540 å. this set of particles was subjected […]

library_books

Pushing the resolution limit by correcting the Ewald sphere effect in single particle Cryo EM reconstructions

2018
Nat Commun
PMCID: 5908801
PMID: 29674632
DOI: 10.1038/s41467-018-04051-9

[…] complexes by taking the depth of field effect into account (supplementary information). the reconstructions of these simulated images were calculated using the defocus values measured by the program ctffind4 and the known orientation information. the resolution of the reconstructed map was then calculated by comparing the map and the corresponding 3d model using a fsc threshold of 0.5. since […]


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

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