Segger is a tool for segmenting 3D density maps obtained using cryo-electron microscopy (Cryo-EM). It allows users to determine and further analyze the molecular composition and structure of nanomachines imaged using Cryo-EM. 


  • Segger is a plugin for UCSF Chimera.
  • The main UI for Segger is the Segment Map dialog which can be launched from Tools - Volume Data.
  • Segger also includes several tools which can be launched from the 'Shortcuts' tab on the Segment Map dialog, under Other Tools:
    • The Fit to Segments dialog which allows rigid fitting of atomic structures to segmented regions. This can also be launched from the Tools menu, under Volume Data.
    • Extract dialog - for extracting and (soft-) masking maps with segmented regions
    • iSeg - radial/icosahedral segmentation
    • ProMod - probabilistic modeling of multiple conformations obtained from flexible fitting
    • ModelZ - asessment of features in the map (e.g. side chains) using a fitted model. More details here.
  • Download and installation instructions: GitHub
  • Tutorials
  • For more information or to provide feedback, please contact Greg


Documentation at UCSF Chimera site:



Segger and related tools are described in the following publications. Thank you for citing the appropriate one in your papper!

  • 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.
    • Tools and concepts: rSeg, Extract, SegLoop, ProMod
  • 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
    • Tools and concepts: Fit to Segments, Rigid Fitting, Z-Scores
  • 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.
    • Tools and Concepts: Segment Map, Fit to Segments, Watershed Segmentation, Hierarchical Groupings
  • 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.