SPARX pipeline

SPARX specifications

Information


Unique identifier OMICS_15602
Name SPARX
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL http://sparx-em.org/sparxwiki/Downloads?action=AttachFile&do=view&target=eman2.sparx.2016.09.07.linux64.tar.gz
Maintained Yes

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Versioning


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Maintainer


  • person_outline Steven Ludtke <>

Publication for SPARX

SPARX IN pipelines

 (3)
2017
PMCID: 5666345
PMID: 28937604
DOI: 10.3390/toxins9100298

[…] and constant rotation during formation yielded smaller nanodiscs within the expected diameter range (100–150 å) containing a single pa pore (figure 1b)., initial classification analysis using sparx [27] revealed heterogeneity in the dataset with one, two, or three lfn bound to pa pores (figure 2a–c). the release of lfn-pa-nanodisc complexes from the bead surface into solution also […]

2015
PMCID: 4385409
PMID: 25751425
DOI: 10.1038/nsmb.2996

[…] for 3d reconstruction. we used a 60å low pass filtered negative stain reconstruction of dynactin (emd-2716) 19 as our initial model for 3d refinement by iterative projection matching using eman2 and sparx libraries 34,35. refinement of the initial model began generating forward projections at an angular increment of 20°, which decreased incrementally to 1°. the refinement would not proceed […]

2014
PMCID: 4239666
PMID: 25411884
DOI: 10.1038/nchem.2107

[…] of the original particle images resulted in a final pixel size of 4.1 å. image alignment and classification were carried out using the iterative stable alignment and clustering (isac) program in the sparx software package48., atc-hl3 protein samples were analyzed by small-angle x-ray scattering in eight different buffer conditions (see supplementary methods) at the 12.3.1 beamline […]

SPARX funding source(s)
This research has been supported by NIH Grant P01GM064692 and by the US Department of Energy under Contract No. DE-AC02-05CH11231.

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