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EMAN specifications


Unique identifier OMICS_15596
Alternative names EMAN2, EMAN2.1
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Python
Parallelization CUDA
License GNU General Public License version 3.0
Computer skills Medium
Version 2.21a
Stability Stable
Registration required Yes
Maintained Yes


  • MPSA




No version available



  • person_outline Steven Ludtke <>
  • person_outline Team MPSA <>

Additional information

http://blake.bcm.edu/emanwiki/EMAN2 Download also includes SPHIRE and SPARK software.

Publications for EMAN

EMAN citations


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

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

[…] 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 in eman boxer.py via appion. three rounds of reference-free 2d classification were carried out using msa/mra with a binning factor of 2, to remove amorphous particles. after 2d classification, the 2× […]


Structural basis for energy transduction by respiratory alternative complex III

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

[…] between −0.6 and −4.0 μm., a set of 2479 movies was collected. whole-image drift correction and dose weighting of each movie were performed using motioncor2. 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 […]


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

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

[…] and selection. atomic models of microtubules ranging from 11 to 16 protofilaments of type r or l (right or left handed protofilament twist) were generated, and converted to densities with eman1 pdb2mrc with a voxel step size of 4 å/voxel. the densities were low passed filtered to 15 å and the spider operation pj 3q was used to generate 200 reference projections per microtubule type. […]


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

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

[…] e enough to contain a block. the full image size of a whole virus is 1536×1536 pixels. thus a 3d volume data requires 13.5 gb memory, which becomes a major issue for reconstruction. for instance, the eman software cannot handle any map larger than 1290×1290×1290 pixels because of the limitation of the size of array used in eman when the programs in eman were compiled. besides, the hsv (1.38 å/pixe […]


Enhanced stability of a chimeric hepatitis B core antigen virus like particle (HBcAg VLP) by a C terminal linker hexahistidine peptide

PMCID: 5897928
PMID: 29653575
DOI: 10.1186/s12951-018-0363-0

[…] on kodak so-163 film sheets. images were digitized at 1.5 å per pixel and particles were selected manually. the dataset was divided into two separate groups and image analysis was carried out using eman []. when no further resolution improvement was seen, both half datasets were compared for resolution determination. subsequently the two half-datasets were combined for the final structural […]


Automated tracing of helical assemblies from electron cryo micrographs

PMCID: 5847486
PMID: 29191673
DOI: 10.1016/j.jsb.2017.11.013

[…] () libraries. the required input parameters are summarized in and listed for three different test cases. finally, michelixtrace outputs either a text file containing coordinate traces in the common eman box format or writes out the coordinates in an sqlite3 database file spring.db for further usage inside the spring software suite. in addition, we added an option to generate relion readable […]

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EMAN institution(s)
National Center for Macromolecular Imaging, The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
EMAN funding source(s)
Supported by NIH grants R01GM080139 and P41GM103832.

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