SPIDER

SPIDER performs image processing, single-particle averaging, and three-dimensional reconstruction of biological macromolecules from single-particle electron micrographs.

Key Features:

• CTF operations: Determination, modeling, and correction of the contrast transfer function (CTF) for electron microscopy images.
• Single-particle averaging and reconstruction: Implementation of single-particle averaging and 3D reconstruction algorithms for macromolecular structure determination.
• Initial model generation: Support for initial reconstruction using random-conical tilt and common lines approaches.
• Reference-based alignment and iterative refinement: Reference-based alignment of particles combined with iterative refinement of orientations and reconstructions.
• Supervised classification: Supervised classification methods to identify homogeneous subsets and separate multiple conformations.

Scientific Applications:

• Single-particle 3D reconstruction: Reconstruction of biological macromolecules from single-particle electron micrographs.
• CTF correction: Contrast transfer function correction to improve image quality and downstream reconstructions.
• Ab initio model generation: Generation of preliminary models via random-conical tilt and common lines for initial model building.
• Conformational heterogeneity analysis: Identification and separation of distinct conformational states using supervised classification.

Methodology:

Operations explicitly include CTF determination, modeling and correction; initial reconstruction via random-conical tilt and common lines; reference-based alignment with iterative refinement; and supervised classification.