Participants in methodology and code development:
Dong Si, Kamal Al Nasr, Stephanie Zeil, Taylor Gerpheide, Devin Haslam, Dr. Willy Wriggers, Dr. Julio Kovacs and Dr. Jing He.

     Computer Science Department of Old Dominion University

SSETracer is a tool for detecting secondary structures in cryo-EM images.
It is capable of detecting helices and beta sheets in images of medium resolution.[1]

StrandTwister is a tool for determining beta strand locations from detected beta sheets.[2]

AxisComparison is a tool for evaluating the accuracy of detected helices and beta strands in lateral and longitudinal error.[3]

SSETracer, StrandTwister, and AxisComparison can now be used from within USCF Chimera. Necessary files are in the full download below.

SSE Tracer V 4.0, Strand Twister V 2.0, and AxisComparison V 1.0
        Full download

SSE Tracer V 4.0 for command line               Download     readMe
Strand Twister V 2.0 for command line         Download     readMe
Axis Comparison V 1.0 for command line     Download     readMe

Bundle Trac is a tool for tracing actin filament bundles in three-dimensional electron tomography density maps. [4]

Bundle Trac V 1.0 for Chimera         Download     readMe

This work is supported by NSF grant

1. Si, D., He, J. "Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps", Proceeding of ACM Conference on Bioinformatics Computational Biology and Biomedicine Workshops, Washington, D.C., September 22-25, 2013.

2. Si, D., He, J. "Tracing beta strands using StrandTwister from cryo-EM density maps at medium resolution", Structure, 22(11):1665-76, 2014.

3. Zeil, S., Kovacs, J., Wriggers, W., He, J. "Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix", Journal of Computational Biology, 24(1), 52-67, 2017.