Frealign protocols

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Frealign statistics

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Frealign specifications


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
Maintained Yes


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  • person_outline Nikolaus Grigorieff <>

Publications for Frealign

Frealign in pipelines

PMCID: 5458492
PMID: 28580912
DOI: 10.1107/S2059798317004181

[…] for example a 3.4 å resolution alcohol oxidase structure obtained using a jeol 3200fsc microscope (vonck et al., 2016), a 1.8 å resolution glutamate dehydrogenase structure obtained using the frealign software package (merk et al., 2016) and a 2.5 å resolution trypanosoma cruzi 60s ribosomal subunit structure (liu et al., 2016) obtained using a falcon ii camera. furthermore, competitors […]

PMCID: 5584162
PMID: 28652389
DOI: 10.1083/jcb.201612195

[…] were generated using eman2 multi-model refinement () with models of 12, 13, 14, and 15 pf mts () low-pass filtered to 20-å resolution, followed by ihrsr to obtain initial 3d reconstructions. frealign () was then used to further process the dominant pf number for each mt condition to obtain better alignment parameters. finally, we applied in-house scripts to determine the seam location […]

PMCID: 5589491
PMID: 28741611
DOI: 10.1038/nsmb.3439

[…] 3.2 å resolution were further manually inspected for good areas and power-spectra quality. automatic particle picking was performed using signature and single particles were processed using the frealign software package. initial alignment was performed with 116,212 particles using e. coli 70s ribosome as a reference structure. subsequently, particles were subjected to 3d-classification […]

PMCID: 5607000
PMID: 28931821
DOI: 10.1038/s41467-017-00782-3

[…] in a freely available, open source program called cryoef. the program takes as input the euler angles assigned to a particle set from any of the popular 3d reconstruction programs, including frealign, eman and relion–., we defined the efficiency, somewhat arbitrarily, to have four properties useful for data assessment. first, the efficiency is linearly related to the amount of solid […]

PMCID: 5655137
PMID: 29027901
DOI: 10.7554/eLife.28560.031

[…] generating a density map, low-pass filtered to 20 å, from our initial atomic models of rnap with or without s1 (rnap mask was used for 30sδs1•rnap data). the mask was applied to reference volumes in frealign, with the volume outside of the mask weighted by a factor of 1.0 (). a five-pixel cosine edge was used on the mask and the masking filter function. this classification for the 30s•rnap data […]

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Frealign in publications

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

[…] 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 […]

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 […]

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

[…] 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 […]

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

[…] 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 […]

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 […]

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

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