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

  • The main UI for Segger is the Segment Map dialog which can be launched from Tools - Volume Data.
    • The segmentation approach is based on watershed method, a non-parametric clustering technique related to mean-shift clustering.
    • While this method produces many small regions in noisy and high-resolution maps, grouping to form larger regions is possible using scale-space filtering.
    • Grouping information is stored hierarchically, so grouped regions can be interactively ungrouped and regrouped to adjust the results.
  • The Fit to Segments dialog allows the use of segmentations to rigidly dock atomic structures into a density map, and can also show docking statistics such as Z-score for determining confidence of fit.

Recent Updates:

  • Nov 2, 2015 - Segger was presented in a session at the NCMI 2015 Workshop
  • Oct 20, 2015 - Update to v.1.9.2 in Chimera Daily Build Oct 20 or later) includes some new tools: radial segmentation (rSeg), loop modeling using segmented regions (SegLoop), probabilistic modeling from multiple flexible fitting results (ProMod)
  • A new entry under Segment Map dialog -> File, Associate Selected, allows you to associate a map with a segmentation file. The path to the map is stored in the segmentation file, so moving these files to a different path breaks the association, making it hard to then do further processing with the segmentation. Now you can re-associate the segmentation & map using this command.


  1. Segment Map
  2. Fit to Segments
  3. Segmenting with Fitted Models
  4. Docking Scores
  5. Resolution of Subcomponents (Extract)
  6. Radial/Icosahedral Segmentation (rSeg)
  7. Loop modeling (SegLoop)
  8. Probabilistic Modeling (ProMod)

Documentation at Chimera site:



  • 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
    • To appear: Biophysical Journal, 2015
    • This paper describes the application of Segger, Extract, rSeg, SegLoop, and ProMod for the analysis of an asymmetric reconstruction of the P22 Bacteriophage, shedding 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

  • 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, IEEExplore DSpace



As of June 16, 2010, Segger is automatically included in daily builds of Chimera.

Thus downloading it from the links below is not necessary if you instead just get the latest daily build.

For questions, corrections, comments, suggestions, etc., email

© Baylor College of Medicine 2018
CryoEM Center
N420, Alkek Building, One Baylor Plaza, Houston, Texas 77030
(713) 798-6989