ChimeraX MCP Server

Control UCSF ChimeraX conversationally from Claude — load structures, mutate residues, color and render surfaces, measure geometry, and capture snapshots without typing ChimeraX commands.

   
Type MCP server
Supplier mahynotch
Availability GA
Pricing Free / OSS (MIT); UCSF ChimeraX is licensed separately (free for academic/non-profit) — review rbvi.ucsf.edu/chimerax
Capabilities Read/Write — Claude issues ChimeraX commands and runs arbitrary scripts against structures on your machine, writing snapshots and edited coordinate files
Verified works · 2026-07-27 — PyPI 0.1.1 resolves; chimerax-mcp entry point launch confirmed
Security caution · 2026-07-27 — provenance matches mahynotch, MIT, no OSV advisories, early v0.1.1 single-maintainer + runs arbitrary scripts

How to install

  1. Install UCSF ChimeraX separately, then install the MCP server (Python 3.10+): 
    pip install chimerax-mcp
  2. Register it:
    • Claude Code — direct MCP add (stdio): 
      claude mcp add -s user chimerax -- chimerax-mcp
    • Claude Desktop — stdio entry in claude_desktop_config.json: 
      {
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

The pip install step above provides the chimerax-mcp binary both registration snippets reference. Claude Code/Desktop launches the stdio process itself — there is no long-running server to keep open in another terminal, and ChimeraX is launched automatically when the first tool is called (no manual REST-API setup).

What it does

Exposes 39 tools that map onto ChimeraX operations:

  • Structure (6) — open_structure, close_structure, save_structure, list_models, get_sequence, run_script (arbitrary ChimeraX Python).
  • Editing (4) — mutate_residue, delete_atoms, add_hydrogen, minimize_energy.
  • Visualization (18) — surfaces (electrostatic, hydrophobicity, plain), cartoon/stick/atom representations, coloring, labels, zoom/view control, snapshots, and recording/spin.
  • Measurement (6) — measure_distance, measure_angle, align_and_rmsd, find_contacts, get_bfactors, measure_buried_area.
  • Selection (5) — select_atoms, select_near, select_chain, invert_selection, name_selection.

Primary use cases: interactive structural-biology sessions, residue mutation and energy minimization, publication figures and turntable movies, distance/angle/RMSD measurement and contact analysis.

Notes

Requires a local UCSF ChimeraX install (any version after 2024-03-18) and Python 3.10+; transport is stdio. Because it drives a full desktop application, it needs a graphical environment (ChimeraX auto-launches on first tool call). Complements the headless, GPU-free PyMOL skill (batch rendering) and the data-retrieval Protein MCP Server / PDB MCP Server (fetch structures first, then visualize/edit here). For AlphaFold/ESMFold prediction wired directly into ChimeraX, the sibling GDAmitha/chimerax-alphafold-mcp is an alternative packaging (not yet catalogued).

Sources

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