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Protocols

EM-Bfactor specifications

Information


Unique identifier OMICS_26526
Name EM-Bfactor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some 3D maps, FSC curves.
Input format MRC,Spider,PIF,EM,Xmipp,Frealign,Bsoft
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Jose-Jesus Fernandez <>
  • person_outline Jose Fernandez <>

Publication for EM-Bfactor

EM-Bfactor citations

 (7)
library_books

Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo EM at 6 Å resolution

2016
PMCID: 5045269
PMID: 27704041
DOI: 10.1126/sciadv.1600058

[…] final reconstruction. for the final reconstruction, we used the “gold standard” procedure (), which involves computing two independent reconstructions in parallel. the final map was sharpened using em-bfactor (), which reweights the reconstruction transform based on the fourier shell correlation curve and then low-pass–filters it to a corresponding resolution to show each part’s structure., […]

library_books

A combined cryo EM and molecular dynamics approach reveals the mechanism of ErmBL mediated translation arrest

2016
PMCID: 4935803
PMID: 27380950
DOI: 10.1038/ncomms12026

[…] resolution of 3.6 å (0.143 fsc) and a local resolution extending towards 3.0 å for the core of the 30s and 50s subunits as computed using resmap (). the final maps were subjected to the programme em-bfactor in order to apply an automatically determined negative b-factor for sharpening of the map., initial models for the two ermbl-srcs were obtained by combining: (i) a model of the e. coli 70s […]

library_books

Structure of a human translation termination complex

2015
PMCID: 4605324
PMID: 26384426
DOI: 10.1093/nar/gkv909

[…] (truncation of frequencies higher than 8 å) refinement protocol was used to prevent potential over-fitting (). the final volume was subjected to b-factor sharpening using the program em-bfactor ()., the initial model of human erf1 was based on the crystal structure by cheng et al. () (pdb code: 3e1y-a). the missing minidomain herein was added from the nmr structure of the erf1 c […]

library_books

Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid

2015
PMCID: 4621102
PMID: 26311868
DOI: 10.1128/JVI.01353-15

[…] correlation (fsc) of 0.143 and a resolution of 8.97 å at an fsc of 0.5 (see fig. s1 in the supplemental material). the final map was sharpened by applying a b factor of −610.88, as calculated by em-bfactor (). densities corresponding to individual gp23 subunits were segmented with the segger extension of ucsf chimera (, ). local resolution estimation was prepared with the two half-maps […]

library_books

Structure of the Bacillus subtilis 70S ribosome reveals the basis for species specific stalling

2015
PMCID: 4423224
PMID: 25903689
DOI: 10.1038/ncomms7941

[…] the signal recognition particle bound to the ribosome (158,726 particles; 30%), which will be described elsewhere (beckert et al., unpublished). the final volumes were subjected to the program em-bfactor in order to apply an automatically determined negative b-factor for sharpening of the map., the b. subtilis 5s, 16s and 23s rrna sequences were taken from genebank; gene id 2914271, 936774 […]

library_books

Acetylcholine Binding Protein in the Hemolymph of the Planorbid Snail Biomphalaria glabrata Is a Pentagonal Dodecahedron (60 Subunits)

2012
PMCID: 3423370
PMID: 22916297
DOI: 10.1371/journal.pone.0043685

[…] least partially represent noise bias. the final density map (5.8 å resolution) was calculated from 8347 selected particles. a negative temperature factor of 375.84 å2 was applied using the software em-bfactor , . the resulting 3d reconstruction (see ) was low-pass filtered to 6 å., homology modeling with acachbp as template (pdb-id 2br7 ) and loop refinement were performed in modeller 9v9 ; […]


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EM-Bfactor institution(s)
Centro Nacional de Biotecnologia, CSIC. Campus Universidad Autonoma, Cantoblanco, Madrid, Spain; Department of Computer Architecture, University of Almeria, Almeria, Spain
EM-Bfactor funding source(s)
Supported by EU-FP6-LSHG-CT-2004-502828, MEC-TIN2005-00447, MEC-BFU2005-06487 and JA-P06-TIC1426.

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