Example circos plot generated by ChimeraX CircosContacts
Example output from aggregated AlphaFold3 structure predictions.

Documentation

Detailed user docs are available for command semantics, interactive web controls, workflows, and troubleshooting.

Overview ChimeraX Command Web Interface Workflows Screenshot Capture Troubleshooting

Core Capabilities

  • Runs within ChimeraX via circoscontacts on open or selected models.
  • Supports contacts-style selection and restrict semantics.
  • Aggregates repeated contacts across models with Atom/Residue counting modes.
  • Merges DNA strands (including split/nicked cases) into a single logical arc.
  • Chain reordering and flipping, threshold filtering, and chain inclusion toggles.
  • Provides session save/load for reproducible annotation workflows.

Use Cases

  • Compare contact persistence across AlphaFold ensembles.
  • Inspect protein-DNA interaction hot spots under residue-range constraints.
  • Prepare figure-ready SVG with curated labels and sequence/comment callouts.
  • Export matching residue colors for ChimeraX surfaces and ribbons.
circoscontacts #1,2/S,T:100-120 restrict /S,T/C interModel false intramol false

Typical Workflow

1. Select

Choose open models (or subsets) using standard ChimeraX atom spec syntax.

2. Compute

Plugin runs ChimeraX contacts with your source/restrict settings.

3. Curate

Adjust chain order, orientation, thresholds, callouts, and region annotations.

4. Export

Save SVG, ChimeraX color script (.cxc), and session (.json).

Peter Carlton, www.carltonlab.org