Resource for the Visualization of Biological Complexity (RVBC)

SPIDER and Web

SPIDER is an extensive software package designed for 3D reconstruction and image processing in electron microscopy (Frank, et al., 1996; Shaik, et al, 2008). Web is a graphics interface for displaying and interacting with image files created in SPIDER. SPIDER has been evolving in Dr. Frank's lab since the late 1970s and contains tools for single particle reconstruction, classification analysis, and electron tomography, as well as enhancing, analyzing, and segmenting 2-D and 3-D images. SPIDER and Web are available to outside users under the Open Source GPL license. Documentation of the over 500 operations in SPIDER and Web can be found on the SPIDER website. Recently we introduced SPIRE (SPIDER Reconstruction Engine), which consists of a graphical user interface for executing SPIDER procedure files.

Ramos

(Rapid motif search, Rath, et al., 2003) is a fast 3D search program used for finding a given motif in its various manifestations inside an EM density map, using the locally normalized cross-correlation function (CCF). It is implemented in SPIDER, and documented in the SPIDER webpages. The locally (i.e., under the footprint of the motif) normalized CCF performs superior to a globally normalized CCF since it optimizes the numerical scaling of the correlated objects. Ramos makes use of formulations proposed by Roseman (2003) that allow it to compute the locally-normalized CCF using Fourier techniques. Computation using Ramos is 50-100 times faster than real-space implementations of cross-correlation motif searching.

External software used at the RVBC

The visualization program: Amira is used to create surface-rendered models and animations from single-particle reconstructions and from electron tomographs.
The molecular modeling program: O is used for correlation and fitting of atomic maps to 3-D envelopes determined by EM.
NAMD is used for studying molecular dynamics.
The imaging program: Image J is used when sharing tomographic reconstructions with collaborators.

References

Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Yanghong, Ladjadj, M., and Leith, A. (1996). SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol., 116: 190-199.

Marko, M., Leith, A. (1996) Sterecon--three-dimensional reconstruction from stereoscopic contouring. J. Structural Biol. 116, 93-98.

Rath, B.K., Hegerl, R., Leith, A., Shaikh, T.R., Wagenknecht, T. and Frank, J. (2003) Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. J. Struct. Biol. 144: 95-103.

Roseman. A. (2003) Particle finding in electron micrographs using the fast local correlation algorithm. Ultramicroscopy 94:225-236 (2003).

Shaikh, T., Gao, H., Baxter, W., Asturias, F., Boisset, N., Leith, A., and Frank , J. (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nature Protocols 3: 1941-1974. PubMed