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e2boxer.py specifications

Information


Unique identifier OMICS_27769
Name e2boxer.py
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some micrograph filenames.
Output data Some particles, either as boxed particle images or coordinates list.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Additional information


http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2boxer

e2boxer.py citations

 (79)
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

[…] from them or two nanodiscs 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 usin […]

call_split

Mutations in VP1 and 5′ UTR affect enterovirus 71 virulence

2018
Sci Rep
PMCID: 5923339
PMID: 29703921
DOI: 10.1038/s41598-018-25091-7
call_split See protocol

[…] oltage of 120 kV. All digital images were acquired with a Gatan, Inc. Ultrascan 4000 4 k × 4 k CCD Camera System (Model 895). Virions harvested from RD and Vero cells were selected manually using the e2boxer.py package in EMAN2. ML2D, an image classification algorithm package included in Xmipp 3.1, was used to classify the selected particles as empty or full. The crystal structure of the EV-VP1 pr […]

call_split

Granule stored MUC5B mucins are packed by the non covalent formation of N terminal head to head tetramers

2018
PMCID: 5900763
PMID: 29440393
DOI: 10.1074/jbc.RA117.001014
call_split See protocol

[…] EMAN2 (version 2.12) (). Defocus, particle separation, and amplitude contrast were evaluated with e2evalimage.py. Single particles, 4456, in different orientations were selected from the images using e2boxer.py in swarm mode. False positives, such as aggregated particles and stain artifacts, were discarded. For each image, the contrast transfer function parameters were estimated on boxed-out regio […]

library_books

Structure and function of urea amidolyase

2018
Biosci Rep
PMCID: 5770610
PMID: 29263142
DOI: 10.1042/BSR20171617

[…] e operating at 200 kV. Micrographs were recorded by SO 163 films at a nominal magnification of 50000×, and scanned at 2000 dpi with a pixel size of 2.54 Å. 4495 particles were manually selected using e2boxer.py []. Alignment and 2D classification were performed by RELION []. […]

library_books

Two classes of protective antibodies against Pseudorabies virus variant glycoprotein B: Implications for vaccine design

2017
PLoS Pathog
PMCID: 5754140
PMID: 29261802
DOI: 10.1371/journal.ppat.1006777

[…] us range of—(1–3) μm. Images were recorded with a 4k×4k BM-Eagle CCD camera with a calibrated pixel size of 1.36 Å.A total of ~8000 particles were semi-automatically picked from 200 micrographs using e2boxer.py in EMAN2 [] package. The contrast transfer function (CTF) parameters were estimated by e2ctffit.py [] and applied to correct the images by phase-flipping [] method. All the subsequent class […]

call_split

Bri2 BRICHOS client specificity and chaperone activity are governed by assembly state

2017
Nat Commun
PMCID: 5727130
PMID: 29234026
DOI: 10.1038/s41467-017-02056-4
call_split See protocol

[…] ) for further processing. Defocus, particle separation and amplitude contrast were evaluated with e2evalimage.py. Single particles, 3000, in different orientations were selected from the images using e2boxer.py in swarm or manual mode. False positives, such as aggregated particles and stain artifacts were discarded. For each image, the contrast transfer function (CTF) parameters were estimated on […]

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