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Welcome to the segger wiki!

Segger is a tool for segmenting 3D density maps obtained using cryo-electron microscopy (CryoEM).

• Overview
• Highlights
• Documentation / Tutorials

To cite Segger:

• Resolution and Probabilistic Structural Models of Subcomponents Derived from CryoEM Maps of Mature P22 Bacteriophage.
  G. Pintilie, D.H. Chen, C.A. Haase-Pettingell, J.A. King, W. Chiu Biophys. J., vol. 110, no. 4, pp. 827-839, Feb. 2016. PubMed.
  This paper describes the application of Segger, Extract, rSeg, SegLoop, and ProMod for the analysis of an asymmetric reconstruction of the P22 Bacteriophage, leading to some new insights into the structure and function of its various subcomponents - tail, hub, portal, coat, DNA.

• Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps.
  G. Pintilie, W. Chiu.
  Biopolymers, vol 97(9), Sep. 2012, pp. 742-60 Pubmed

• Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
  G. Pintilie, J. Zhang, T. Goddard, W. Chiu, D. Gossard.
  Journal of Structural Biology, vol. 170, Jun. 2010, pp. 427-438. Pubmed.

• Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation
  G. Pintilie, J. Zhang, W. Chiu, D. Gossard.
  In Life Science Systems and Applications Workshop, IEEE/NIH, pp. 44-47, 2009, Pubmed.

Examples:

• Gallery 1