Molecule-MCP

Bundle of three MCP servers that turn Claude into a natural-language driver for molecular visualization (PyMOL, ChimeraX) and molecular dynamics (GROMACS).


Type	MCP server (bundle of three)
Supplier	chatmol (community OSS)
Availability	GA
Pricing	Free / OSS (MIT)
Capabilities	Read/Write

How to install

pip install "mcp[cli]" chatmol
git clone https://github.com/chatmol/molecule-mcp

Register three entries in claude_desktop_config.json pointing at the bundled scripts (replace /path/to/molecule-mcp with the absolute path of your clone — e.g., /Users/you/repos/molecule-mcp):

{
  "mcpServers": {
    "pymol":            { "command": "python", "args": ["/path/to/molecule-mcp/pymol_server.py"] },
    "chimerax":         { "command": "python", "args": ["/path/to/molecule-mcp/ChimeraX_server.py"] },
    "gromacs_copilot":  { "command": "python", "args": ["/path/to/molecule-mcp/mcp_server.py"] }
  }
}

For Claude Code, the equivalent registrations are (run all three):

claude mcp add --transport stdio pymol           -- python /path/to/molecule-mcp/pymol_server.py
claude mcp add --transport stdio chimerax        -- python /path/to/molecule-mcp/ChimeraX_server.py
claude mcp add --transport stdio gromacs_copilot -- python /path/to/molecule-mcp/mcp_server.py

What it does

PyMOL server — visualization commands driven from chat (load, color, select, render).
ChimeraX server — same shape for ChimeraX.
GROMACS Copilot — MD setup, solvation, equilibration, and production runs from natural language.

Primary use cases: Conversational molecular visualization, agent-driven MD setup and execution, structural-biology demos and teaching.

Notes

Requires local PyMOL, ChimeraX, and (optionally) GROMACS installations. stdio transport. Research-use disclaimer (no warranty) — validate results independently before drawing conclusions from the simulations.

Sources

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