ChimeraX CircosContacts

A ChimeraX plugin that converts predicted contact sets into interactive circos-style maps for analysis and visualization.

ChimeraX command plugin Interactive HTML output Export: SVG + ChimeraX colors
Example circos plot generated by ChimeraX CircosContacts
Example output from aggregated AlphaFold3 structure predictions.

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