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. 

Overview

• 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. 
• For more information or to provide feedback, please contact Greg gregp@slac.stanford.edu

Tutorials

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

Documentation at UCSF Chimera site:

• Segment Map
• Fit To Segments

References

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.

Examples

• Gallery

Highlights

• May 2019 - Added iSeg dialog for improved segmentation of icosahedral geometries (e.g. SGIV).
• March 2019 - Segger updated to v2.0 to include "grouping by connectivity"; presentation at S2C2 Training Workshop.
• February 2018 - Segger was used to segment CryoEM map of Ebola nucleocapsid-like assembly.
• November 2017 - Paper in Nature uses Segger to segment proteins and RNA in a DNA-binding transcription complex.
• April 2017 - Paper in Elife on AAA+ unfoldase cites Segger. Cryo-EM is shedding light on amazing molecular mechanisms.
• May 2017 - Paper in Science uses Segger to segment conformations of the cardiac ryanodine receptor.
• June 2016 - Poster on SGIV, a large virus with multiple icosahedral layers, segmented using Segger, presented at Gordon Research Conference in Hong Kong.
• May 2016 - A paper in Nature on how neurotransmitters work - nice segmentations using Segger.
• February 2016 - We published a paper on a new P22 virion asymmetric reconstruction, analyzed using Segger and probabilistic modeling of fitted models.
• November 2015 - Segger was presented at the NCMI 2015 Workshop.
• October 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). See tutorials below for more information on how to use them.
• September 2015 - Segger is cited in a Nature paper on eIF3, where segmented densities are used for focused classification.
• March 2015 - We used Segger to segment a nuclear receptor complex. Challenging at low resolutions, had to use many maps and antibodies to identify various parts with certainty.
• June 2014 - Poster at Gordon Research Conference on Cryo-EM, Girona, Spain.
• January 2013 - Paper introducing Segger is one of the top cited papers between 2009-2013 in Journal of Structural Biology. Number of citations now at ~150 and counting. Thank you for citing Segger!
• October 2013 - Segger presented at NCMI workshop on Cryo-EM methods.
• August 2012 - Segger presented at The 6th Brazil School for Single Particle Cryo-EM, Socorro, Brazil.