A package for sharpening high resolution information in single particle
electron cryomicroscopy

J.J. Fernández (1), D. Luque (1), J.R. Castón (1), J.L. Carrascosa (1),
P.B. Rosenthal (2), R. Henderson (2)

(1)  Centro Nacional de Biotecnologia - CSIC, Madrid 28049, Spain.
(2)  MRC Laboratory of Molecular BiologyCambridge CB2 2QH, UK.

Contact: jjfernandez.software @ gmail.com


This package allows sharpening of high resolution information in 3D maps obtained by electron cryomicroscopy according to the approach by Rosenthal and Henderson (JMB 333:721-745, 2003). The program allows automatic determination of the Bfactor for maps at a resolution higher than 10 Angstroms. The program also allows application of the Bfactor found, or a Bfactor value provided by the user, to sharpen the map and compensate the decay of the amplitudes. Before sharpening, the map is weighted in Fourier space by Cref, a function computed from the FSC that represent the correlation between the map and a perfect reference, in order to avoid noise amplification. Furthermore, the program also places the structure factor amplitudes of the map on an absolute scale. The program accepts 3D maps in any format common in EM (e.g. MRC, Spider, Xmipp, PIF, EM, etc) and also accepts FSC curves in the format of most common packages for single particles cryoEM (Frealign, Spider, EMAN, Xmipp, Bsoft). As output, the program produces the sharpened map and a Guinier plot that allows assessment of the sharpening.

A detailed description of the procedures implemented in the package is in the following articles:

Optimal Determination of Particle Orientation, Absolute Hand and Contrast Loss in Single-particle Electron Cryomicroscopy
P.B. Rosenthal and R. Henderson
Journal of Molecular Biology 333:721-745, 2003.

Sharpening high resolution information in single particle electron cryomicroscopy
J.J. Fernandez, D. Luque, J.R. Caston, J.L. Carrascosa
Journal of Structural Biology 164:170-175, 2008.

Please, cite these articles if you use EM-BFACTOR in your works.

Current version: May 2014

Available material:
  • Documentation in PDF:  embfactor.pdf

  • Binaries for 64-bits x86-based platforms under linux
  • Binaries for 64-bits Intel-based Macs under OSX (10.6 and onwards)

The development of embfactor has been supported by the Spanish MEC and MCI, European Molecular Biology Organization and the 3DEM Network of Excellence.

Copyright by the authors.