chimerax-mcp 0.1.0

MCP server that connects AI coding tools to UCSF ChimeraX for natural-language protein editing

ChimeraX MCP Server

Talk to proteins in natural language. This MCP server connects AI coding tools (Claude Code, Cursor, VS Code, etc.) to UCSF ChimeraX, letting you load, edit, visualize, and analyze protein structures through conversation -- no manual ChimeraX commands needed.

Just say "open 6VXX, mutate A:501 to Lys, color by hydrophobicity, and take a screenshot" and watch ChimeraX do it in real time.

This project is in early development and actively looking for contributors. Bug reports, feature requests, and pull requests are very welcome -- check out the issues page or open a PR!

Demos

Load & Visualize

"Load 3LJ5, show only chain A, make it publication-ready with rainbow coloring and transparent surface"

Mutate Residue

"Open 6VXX, zoom to residue A:501, highlight it, mutate Thr to Lys, show nearby residues"

Electrostatic & Hydrophobicity Surfaces

"Load 1AKI, show surface, color by electrostatic potential, then switch to hydrophobicity"

Features

• 39 tools covering structure loading, editing, visualization, measurement, selection, and video recording
• Auto-launches ChimeraX -- no manual setup needed, just install and go
• Works with any MCP client -- Claude Code, Cursor, Windsurf, VS Code Copilot, Cline, OpenCode, Continue, Claude Desktop
• Built-in agent instructions -- AI agents automatically learn ChimeraX spec syntax and common workflows
• Security hardened -- command injection prevention, dangerous command blocking, script path validation
• Accepts flexible input -- both A:48 and /A:48 spec formats, both 1-letter and 3-letter amino acid codes
• Video recording -- capture sessions as MP4, record turntable spins
• Run custom scripts -- execute .cxc and .py scripts with path validation

Prerequisites

• UCSF ChimeraX installed (download)
• Python 3.10+

ChimeraX will be launched automatically when the first tool is called. No need to start it manually or enable the REST API yourself.

Manual setup (if auto-launch doesn't work)

Open ChimeraX and run in its command line:

remotecontrol rest start port 8765

To use a custom ChimeraX install location, set the CHIMERAX_BIN environment variable:

export CHIMERAX_BIN="/path/to/ChimeraX"

Installation

pip install git+https://github.com/mahynotch/chimerax-mcp.git

Other install methods

From PyPI (once published):

pip install chimerax-mcp

From source (development):

git clone https://github.com/mahynotch/chimerax-mcp.git
cd chimerax-mcp
pip install -e .

MCP Configuration

After installing, add the server to your AI coding tool:

Claude Code

claude mcp add -s user chimerax -- chimerax-mcp

Claude Desktop

Edit config file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
• Windows: %APPDATA%\Claude\claude_desktop_config.json
• Linux: ~/.config/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

Cursor

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project):

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

VS Code (Copilot)

Add to .vscode/mcp.json:

{
  "servers": {
    "chimerax": {
      "type": "stdio",
      "command": "chimerax-mcp"
    }
  }
}

Cline

Use the "Edit MCP Settings" button in the Cline panel, or edit directly:

• macOS: ~/Library/Application Support/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json
• Windows: %APPDATA%\Code\User\globalStorage\saoudrizwan.claude-dev\settings\cline_mcp_settings.json

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": [],
      "disabled": false
    }
  }
}

OpenCode

Add to ~/.config/opencode/opencode.json or project opencode.json:

{
  "mcp": {
    "chimerax": {
      "type": "local",
      "command": ["chimerax-mcp"],
      "enabled": true
    }
  }
}

Continue

Add to .continue/config.yaml:

mcpServers:
  - name: chimerax
    type: stdio
    command: chimerax-mcp

Quick Start

Once configured, just talk naturally:

"Open 6VXX, color by chain, show surface, zoom to residue A:501"

The AI will call MCP tools sequentially and ChimeraX renders each step in real time:

1. open_structure("6VXX") -- fetches the structure from RCSB
2. color_structure("#1", "chain") -- colors each chain differently
3. show_surface("#1") -- displays the molecular surface
4. zoom_to("/A:501") -- centers the view on residue 501 of chain A

Available Tools (39)

Structure (6)

Tool	Description
open_structure	Open PDB ID, file path, or URL
close_structure	Close one or all models
save_structure	Save to PDB/mmCIF/mol2
list_models	List all open models
get_sequence	Get amino acid sequence for a chain
run_script	Execute a .cxc or .py script

Editing (4)

Tool	Description
mutate_residue	Swap residue using Dunbrack rotamer library
delete_atoms	Delete atoms or residues
add_hydrogen	Add hydrogens (protonate)
minimize_energy	Run energy minimization

Visualization (18)

Tool	Description
color_structure	Color by scheme (chain, bfactor, rainbow) or named/hex color
show_electrostatic_surface	Coulombic ESP (red=negative, blue=positive)
show_hydrophobicity_surface	Molecular Lipophilicity Potential
show_surface	Show molecular surface with optional transparency
hide_surface	Hide molecular surface
show_cartoon	Show ribbon/cartoon
show_sticks	Show stick representation
hide_atoms	Hide atoms
zoom_to	Zoom camera to a selection
set_background	Set background color
label_residues	Add text labels to residues
clear_labels	Remove all labels
reset_view	Reset to default camera view
take_snapshot	Save PNG screenshot
start_recording	Begin recording session as video
stop_recording	Stop recording and save to MP4/WebM/MOV
spin	Rotate model around an axis
record_spin	Record a full turntable spin video

Measurement (6)

Tool	Description
measure_distance	Distance between two atoms (Angstroms)
measure_angle	Bond angle from three atoms (degrees)
align_and_rmsd	Structural alignment with RMSD
find_contacts	Residues within N Angstroms of selection
get_bfactors	B-factor values for selection
measure_buried_area	Buried solvent-accessible surface area

Selection (5)

Tool	Description
select_atoms	Select by ChimeraX specifier
select_near	Select within distance
select_chain	Select entire chain
invert_selection	Invert current selection
name_selection	Save selection under a reusable name

Security

Commands are sanitized before being sent to ChimeraX:

• Command injection blocked -- ; and newlines rejected (ChimeraX uses these as command separators)
• Dangerous commands blocked -- exec, shell, system are rejected
• Script execution validated -- run_script only accepts existing .cxc/.py files with path validation
• Local-only -- REST API listens on 127.0.0.1 only, not exposed to the network

Testing

Run the full test suite (53 tests) against a live ChimeraX instance:

pip install pytest
python -m pytest tests/test_live.py -v

Security tests run without ChimeraX. Live tests auto-skip if ChimeraX is not available.

Disclaimer

This project is not affiliated with, endorsed by, or sponsored by UCSF or the RBVI team. "ChimeraX" is a trademark of the University of California. This server communicates with ChimeraX through its public REST API and contains no ChimeraX source code.

Users are responsible for complying with ChimeraX's license terms. ChimeraX is free for academic and non-commercial use; commercial use requires a separate license from UCSF.

License

MIT -- see LICENSE