PHOELIX protocols

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PHOELIX specifications

Information


Unique identifier OMICS_15603
Name PHOELIX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Shell (Bash)
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bridget Carragher <>

Publications for PHOELIX

PHOELIX in pipeline

2012
PMCID: 3384419
PMID: 22734002
DOI: 10.1083/jcb.201201132

[…] without binning on a 4,000 × 4,000 charge-coupled device camera (ultrascan 895; gatan) with the resulting pixel size corresponding to 3.8 å on the specimen., helical processing was performed using phoelix essentially as described previously (). in brief, each microtubule was computationally straightened, and layer-line information was extracted. layer-line data from a large number […]


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PHOELIX in publications

 (7)
PMCID: 5479445
PMID: 28193500
DOI: 10.1016/j.jsb.2017.02.003

[…] programs for fourier-bessel analysis were first developed in the mrc image processing package (), and have since been adapted in many other packages, such as the brandeis helical package (), phoelix () and for objects with a break in helical symmetry known as a seam in ruby-helix (). fourier-bessel analysis of helices is often considered laborious and difficult, as small inaccuracies […]

PMCID: 3544905
PMID: 23342004
DOI: 10.1371/journal.pone.0053792

[…] mts with fifteen protofilaments. using imod , fifteen-protofilament/two-start helical mts were extracted from the images and rotated to lie horizontally. helical processing was carried out using phoelix as described previously . in brief, each mt was computationally straightened and layer-line information was extracted. layer-line data from a large number of mts were shifted to a common […]

PMCID: 3482196
PMID: 23110214
DOI: 10.1371/journal.pone.0048204

[…] on a gatan us4000 ccd camera at a ∼2 µm defocus. the pixel size of images acquired under these conditions is 2.24 å., micrographs were screened for helical, 15-protofilament microtubules using the phoelix software package . for 3d reconstructions of microtubule-fab complexes, we selected filaments with strong signal at the 1/8 nm layerline in the 2d power spectra, indicative of high levels […]

PMCID: 3384419
PMID: 22734002
DOI: 10.1083/jcb.201201132

[…] without binning on a 4,000 × 4,000 charge-coupled device camera (ultrascan 895; gatan) with the resulting pixel size corresponding to 3.8 å on the specimen., helical processing was performed using phoelix essentially as described previously (). in brief, each microtubule was computationally straightened, and layer-line information was extracted. layer-line data from a large number […]

PMCID: 3003314
PMID: 20974813
DOI: 10.1083/jcb.201007081

[…] a 4,000 × 4,000 charge-coupled device (gatan, inc.) calibrated using tobacco mosaic virus. the dimer axial repeat was derived from the height of the 8-nm layer line in power spectra computed using phoelix ()., fig. s1 shows data that dcx–mts have a b lattice 13-pf architecture and the fsc of the asymmetric map. fig. s2 shows the fsc of the symmetrized structure and defines the specificity […]


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PHOELIX institution(s)
Beckman Institute and Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
PHOELIX funding source(s)
This work was supported by Grants AR39155, GM44932, and GM52468 from the National Institutes of Health.

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