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Bsoft specifications

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Unique identifier OMICS_15606
Name Bsoft
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++
Computer skills Medium
Version 1.9.4
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Bsoft

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  • person_outline Bernard Heymann

Publications for Bsoft

Bsoft citations

 (100)
library_books

Cryo EM reveals the structural basis of microtubule depolymerization by kinesin 13s

2018
Nat Commun
PMCID: 5916938
PMID: 29695795
DOI: 10.1038/s41467-018-04044-8

[…] (eman1 pdb2mrc) low-pass filtering and thresholding them as indicated above. the same mask was used for the two nmmt maps. local resolution was also estimated from the two raw half maps using the bsoft (v. 1.9.5) function blocres with a kernel size of 10 pixel (supplementary fig. )., step 7. map post-processing. the two independently refined raw half maps were averaged, corrected […]

library_books

Robo1 Forms a Compact Dimer of Dimers Assembly

2018
PMCID: 5807052
PMID: 29307485
DOI: 10.1016/j.str.2017.12.003

[…] object scale (a). a semi-automatic particle selection with the eman boxer routine () led to an extraction of a total of ∼68,500 subframes of 80x80 pixels that were ctf-corrected with ctffind3 () and bsoft (), and low-path filtered at 15 å. this data set was subjected to multivariate statistical analysis and classification with imagic-5 (), which led to a removal of ∼11% of the images. […]

library_books

Hexameric and pentameric complexes of the ExbBD energizer in the Ton system

2018
eLife
PMCID: 5903867
PMID: 29661272
DOI: 10.7554/eLife.35419.035

[…] the gold standard fsc 0.143 criteria () were measured to be 6.69 å for the hexamer at ph 8.0 and 7.11 å for the pentamer at ph 5.4. local resolution was estimated using resmap () and blocres in the bsoft package () from unfiltered half maps. both programs gave similar estimates, but the latter values appeared to be of slightly lower resolution. details related to cryo-em spa are summarized […]

library_books

Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80α and SaPI1 Capsids

2017
Viruses
PMCID: 5744158
PMID: 29258203
DOI: 10.3390/v9120384

[…] subjected to real-space refinement in coot, followed by one cycle of refmac5 refinement., all maps were sharpened with an empirically determined inverse b factor using the program bfilter from the bsoft suite []. map display and density operations were done in ucsf chimera []., to assess the role of cleavage of cp and sp by prp in the 80α assembly process, we generated mutant phages […]

library_books

Tubulin isoform composition tunes microtubule dynamics

2017
Mol Biol Cell
PMCID: 5706985
PMID: 29021343
DOI: 10.1091/mbc.E17-02-0124

[…] microtubule reconstruction was assessed for overfitting during refinement using a high-resolution noise-substitution test (). using local resolution estimates determined with the blocres program in bsoft, the reconstruction was sharpened with a bfactor of −180 up to a resolution of 5.5 or 4 å for visualization of kinesin or tubulin densities respectively., α1b/βi tubulin was built directly […]

library_books

CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

2017
Nat Commun
PMCID: 5648754
PMID: 29051543
DOI: 10.1038/s41467-017-01241-9

[…] 100 × 100 pixel images (pixel size of 4.29 å). each particle image was corrected for contrast transfer function (ctf) by phase-flipping with the corresponding defocus and astigmatism values using bsoft. the particles from un-tilted micrographs were subjected to reference-free 2d classification using eman. particles in good classes with well-defined and interpretable features were selected […]


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Bsoft institution(s)
Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA; Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
Bsoft funding source(s)
This research was supported in part by the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health and by start-up funds provided by the BYU Department of Chemistry and Biochemistry.

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