Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

D M Belnap; A Kumar; J T Folk; T J Smith; T S Baker

doi:10.1006/jsbi.1999.4093

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Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

D M Belnap·A Kumar·J T Folk·T J Smith·T S Baker

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Abstract

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 A), 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.

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Algorithms Calibration Computer Graphics Cryoelectron Microscopy Crystallography, X-Ray Fourier Analysis Image Processing, Computer-Assisted Magnetic Resonance Spectroscopy Microscopy, Electron Microscopy, Phase-Contrast Models, Molecular Molecular Structure Viruses Journal Article Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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D M Belnap, A Kumar, J T Folk, T J Smith, T S Baker. Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".. https://doi.org/10.1006/jsbi.1999.4093

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