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Protocols

EMAN specifications

Information


Unique identifier OMICS_15596
Name EMAN
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

Subtool


  • MPSA

Download


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Versioning


No version available

Documentation


Maintainers


  • 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

 (815)
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

[…] TFFind3, 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× bin […]

call_split

Femtosecond X ray coherent diffraction of aligned amyloid fibrils on low background graphene

2018
Nat Commun
PMCID: 5943278
PMID: 29743480
DOI: 10.1038/s41467-018-04116-9
call_split See protocol

[…] rge-coupled device camera (F416, Tietz Video and Image Processing System, Gauting, Germany). Reference-free alignment was performed on manually selected fibril segments from recorded images using the EMAN2 image processing package. A total of 488 segments of 128 × 128 pixels were extracted from the micrographs, aligned, and classified by multivariate statistical analysis yielding eight class avera […]

call_split

Visualization of ligand induced transmembrane signaling in the full length human insulin receptor

2018
PMCID: 5940312
PMID: 29453311
DOI: 10.1083/jcb.201711047
call_split See protocol

[…] s connected by a density. For each sample, ∼10,000 particles (the exact numbers of images and selected particles are summarized in Table S1) were manually selected using the e2boxer.py command of the EMAN2 software package () and windowed into 180 × 180–pixel images. After image normalization and particle centering, the particle images were classified into 200 groups using K-means classification p […]

library_books

Structure and mechanism of the two component α helical pore forming toxin YaxAB

2018
Nat Commun
PMCID: 5935710
PMID: 29728606
DOI: 10.1038/s41467-018-04139-2

[…] on varied from ~5 Å in the head domains to 6–7 Å in the coiled-coil and foot domains. For validation, the final 3D map was projected in 2D for comparison with the experimental 2D class averages using EMAN2, imposing C10 symmetry and using 5° rotational steps. FSC between the model and the final map was computed using an online tool based on EMAN2 (https://www.ebi.ac.uk/pdbe/emdb/validation/fsc/), […]

library_books

Aggression in Women: Behavior, Brain and Hormones

2018
PMCID: 5942158
PMID: 29770113
DOI: 10.3389/fnbeh.2018.00081

[…] ndividuals should be perceived as more hostile following oxytocin administration. A recent study found support for the social salience hypothesis in a laboratory experiment of 28 men and 20 women (Ne’eman et al., ). Using a modified version of the PSAP, participants could behave selfishly, cooperatively, or aggressively. Relative to placebo, oxytocin selectively increased aggressive responses. The […]

library_books

Promotion of virus assembly and organization by the measles virus matrix protein

2018
Nat Commun
PMCID: 5928126
PMID: 29712906
DOI: 10.1038/s41467-018-04058-2

[…] nerated with SPIDER. All tomograms used for sub-volume averaging were collected at a pixel size of 2.94 Å, then binned by a factor of 2. Tomographic volumes were normalized using e2proc3d.py command (EMAN2) prior to iterative alignment and refinement in PEET (version 1.11.0 alpha). The parameters used for each structure are summarized in Supplementary Table . […]

Citations

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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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