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Frealign specifications

Information


Unique identifier OMICS_15608
Name Frealign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Shell (Bash)
Computer skills Advanced
Version 9.11
Stability Stable
Source code URL http://grigoriefflab.janelia.org/sites/default/files/frealign_v9.11_151031.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Nikolaus Grigorieff

Publications for Frealign

Frealign citations

 (97)
call_split

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
call_split See protocol

[…] ts were used to get an estimate of the resolution to which the new reference was filtered for the next refinement cycle. Refinement was done in two stages. The first using Spider and the second using Frealign. An exhaustive search of the Euler angles and displacements corresponding to each particle-image was performed by multi-reference alignment against projection images of the reference model (S […]

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

[…] object because of the Ewald sphere effect. To account for the Ewald sphere effect, one way to perform the projection match was to calculate the projection with Ewald sphere correction as embedded in Frealign or jspr program, which in principle works but has not been proven using real data. Since we used block-based single-particle reconstruction where the protein complex was divided into several […]

library_books

Ewald sphere correction using a single side band image processing algorithm

2018
Ultramicroscopy
PMCID: 5862657
PMID: 29413409
DOI: 10.1016/j.ultramic.2017.11.001

[…] s only an approximation. Wan et al. restate the proposals of DeRosier with slightly different mathematics. Wolf et al. implemented two practical procedures to account for Ewald sphere curvature in Frealign. Their first procedure used a single side-band correction to insert the structure factor twice, each at the correct location in the 3D transform. Still, since no subsequent masking of the sin […]

library_books

Nucleotide– and Mal3 dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics

2017
Nat Commun
PMCID: 5727398
PMID: 29235477
DOI: 10.1038/s41467-017-02241-5

[…] th 13_3 architecture were selected. The final 3D reconstruction contained 12763 segments, and was calculated using a semiautomated single-particles approach for pseudohelical assemblies in SPIDER and FREALIGN. To avoid model bias, the reference was filtered in each refinement iteration (15 Å in the first and second iteration, to 12 Å in the third and fourth iteration and to 10 Å in the final itera […]

library_books

Tubulin isoform composition tunes microtubule dynamics

2017
Mol Biol Cell
PMCID: 5706985
PMID: 29021343
DOI: 10.1091/mbc.E17-02-0124

[…] straight kinesin-3–decorated 14pf microtubules were manually boxed in Eman Boxer, serving as input for a set of custom-designed semi-automated single-particle processing scripts utilizing Spider and Frealign as described previously () with minor modifications. The final 14pf microtubule reconstruction was assessed for overfitting during refinement using a high-resolution noise-substitution test ( […]

library_books

Quenching protein dynamics interferes with HIV capsid maturation

2017
Nat Commun
PMCID: 5701193
PMID: 29176596
DOI: 10.1038/s41467-017-01856-y

[…] xels using iterative helical real space reconstruction. The refined helical parameters corresponded to a rise of 13.46 Å and a rotation angle of 128.88°. The preliminary map was further refined using Frealign without binning. During the refinement, helical symmetry and full-CTF correction were applied. A total of 14,000 helical segments were included in the final reconstruction. The FSC curve was […]

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

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