Bsoft protocols

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Bsoft specifications

Information


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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Maintainer


  • person_outline Bernard Heymann <>

Publications for Bsoft

Bsoft in pipelines

 (28)
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. […]

2018
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 […]

2017
PMCID: 5279940
PMID: 28109158
DOI: 10.7554/eLife.23006.013

[…] random particles were extracted from the final dataset and 3d refined separately with a 60 å low-pass filtered initial reference. the local resolution distributions were calculated with blocres from bsoft ()., for the motiocor2 () based reconstruction, the movies were gain-normalized and aligned using 9 × 9 patches, 2x downsampling, first two frames discarded and dose-weighting with 1.0 e−/ […]

2017
PMCID: 5490006
PMID: 28643783
DOI: 10.1038/ncomms15720

[…] apo mcm sample, 191 for atpγs-mcm, 155 for apo cdt1–mcm and 608 for atpγs–cdt1–mcm. contrast transfer function estimation was performed with ctffind3 (ref. ) and micrographs were phase-flipped with bsoft. particles were selected semi-automatically using the e2boxer programme from the eman2 package. particles (33,862) were collected for the apo mcm sample, 38,924 for atpγs-mcm, 41,013 for apo […]

2017
PMCID: 5565971
PMID: 28830949
DOI: 10.1128/mBio.01268-17

[…] dose of approximately 70 e−/å2 per tilt series. the nominal defocus was −4 μm, corresponding to a first contrast transfer function zero at 3.7 nm−1., tilt series were reconstructed with the bsoft package (). individual gb molecules were located on microvesicles or pseudotyped particles denoised with an anisotropic nonlinear diffusion filter () and were extracted from the corresponding […]


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Bsoft in publications

 (90)
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 […]

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. […]

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 […]

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 […]

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 […]


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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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