RAPTOR statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RAPTOR
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Tool usage distribution map

This map represents all the scientific publications referring to RAPTOR per scientific context
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Protocols

RAPTOR specifications

Information


Unique identifier OMICS_15668
Name RAPTOR
Alternative name Robust Alignment and Projection Estimation for Tomographic Reconstruction
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mark Horowitz

Publication for Robust Alignment and Projection Estimation for Tomographic Reconstruction

RAPTOR citations

 (13)
library_books

Evolution of higher torque in Campylobacter type bacterial flagellar motors

2018
Sci Rep
PMCID: 5758724
PMID: 29311627
DOI: 10.1038/s41598-017-18115-1

[…] tomated data-collection software,. Images were collected at a nominal magnification of 25,000x to a final pixel size of 0.81 nm from a cumulative dose of ∼ 120e−/Å2.Tomograms were reconstructed using RAPTOR and the IMOD package (IMOD v4.8.41, PEET v1.10.1, eTomo v4.8.41). Flagellar motors were manually picked and aligned from tomograms using PEET. FSC curves were determined from the final averages […]

library_books

Mutations in the Borrelia burgdorferi Flagellar Type III Secretion System Genes fliH and fliI Profoundly Affect Spirochete Flagellar Assembly, Morphology, Motility, Structure, and Cell Division

2015
MBio
PMCID: 4436065
PMID: 25968649
DOI: 10.1128/mBio.00579-15

[…] otal of 45 cell tomograms from WT 5A18NP1, its fliH and fliI mutants, and their complemented clones (see ). Tilt series were automatically aligned and reconstructed using a combination of IMOD () and RAPTOR (). […]

library_books

Griffithsin tandemers: flexible and potent lectin inhibitors of the human immunodeficiency virus

2015
Retrovirology
PMCID: 4419512
PMID: 25613831
DOI: 10.1186/s12977-014-0127-3

[…] −70 μm underfocus. Tilt series spanned an angular range of +/− 65° with 2° tilt increments and were acquired at −2.5 μm underfocus with a per-tilt dose of 1 – 2 e−/Å2. Tilt series were aligned using RAPTOR as implemented in IMOD [,], and tomograms were reconstructed using R-weighted back projection as implemented in IMOD. […]

call_split

Architecture of the ring formed by the tubulin homologue FtsZ in bacterial cell division

2014
eLife
PMCID: 4383033
PMID: 25490152
DOI: 10.7554/eLife.04601.030
call_split See protocol

[…] Tomographic reconstructions from tilt series were calculated using RAPTOR () and the IMOD tomography reconstruction package, followed by SIRT reconstruction with the PRIISM software or the TOMO3D package (; ; ). Measurements of distances between structures were carri […]

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Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ

2013
Nat Commun
PMCID: 3847603
PMID: 24292151
DOI: 10.1038/ncomms3856
call_split See protocol

[…] lt-series was 180-220 e−/Å2. UCSF Tomo was used for automatic acquisition of tilt-series and 2D projection images. Three-dimensional reconstructions were calculated using the IMOD software package or Raptor. Tomograms were visualized using 3dMOD. Density profiles were generated using ImageJ. […]

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The structure of the COPII transport vesicle coat assembled on membranes

2013
eLife
PMCID: 3778437
PMID: 24062940
DOI: 10.7554/eLife.00951.018
call_split See protocol

[…] Tomograms were aligned based on the positions of gold fiducials and reconstructed by weighted back-projection, using the IMOD () and raptor () software packages. Visual analysis and segmentation of reconstructed tomograms were performed with Amira (Visualisation Sciences Group, an FEI company) and Chimera (). Sub-tomogram averaging […]


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RAPTOR institution(s)
Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
RAPTOR funding source(s)
This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

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