Low-resolution density maps from atomic models: How stepping 'back' can be a step 'forward'

David M. Belnap, Abhinav Kumar, Jon T. Folk, Thomas J. Smith, Timothy S. Baker

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 Å), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates, editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

Original languageEnglish (US)
Pages (from-to)166-175
Number of pages10
JournalJournal of Structural Biology
Issue number2-3
StatePublished - Apr 1999
Externally publishedYes


  • Correlation of cryoelectron microscopy and X-ray crystallography
  • Cryoelectron microscopy
  • Modeling
  • Scanning transmission electron microscopy
  • Three-dimensional image reconstruction
  • Truncation of resolution
  • X-ray crystallography

ASJC Scopus subject areas

  • Structural Biology


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