Abstract
We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO2R, has been used for the refinement of several virus structures, including those of the 500 Å diameter dengue virus (to 9.5 Å resolution), the 850 Å mammalian reovirus (to better than 7 Å), and the 1800 Å paramecium bursaria chlorella virus (to 15 Å).
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1-19 |
| Number of pages | 19 |
| Journal | Journal of Structural Biology |
| Volume | 154 |
| Issue number | 1 |
| DOIs | |
| State | Published - Apr 2006 |
Bibliographical note
Funding Information:We express our thanks to M. G. Rossmann for many helpful discussions, to S. B. Walker for the initial 3D model of reovirus, and to R. E. Lynch and M. Sherman for their comments. We appreciate the detailed and constructive suggestions of the anonymous reviewers and the editors. The research was partially supported by National Science Foundation Grants DBI0296107 to D.C.M. and T.S.B., ACI0296035 and EIA0296179 to D.C.M., and NIH Grants GM33050 and AI45976 to T.S.B.
Keywords
- 3D reconstruction
- Cluster of PCs
- CryoTEM
- Electron cryo-microscopy
- Orientation and origin refinement
- Parallel algorithm
- Virus structure determination
