What is Chimerax Alphafold Mcp

ChimeraX-AlphaFold-MCP is an integration of ChimeraX and its AlphaFold Tool with Claude AI through the Model Context Protocol (MCP), enabling natural language interaction for structural biology, molecular visualization, and structure prediction.

Use cases

Use cases include conversational structural biology, molecular visualization, structure prediction, and analysis, allowing researchers to manipulate and analyze molecular structures using natural language.

How to use

To use ChimeraX-AlphaFold-MCP, install the required software including ChimeraX, Claude for Desktop, and Python. Follow the installation guide to set up the environment, clone the repository, and install dependencies. Once set up, you can interact with the system using natural language commands.

Key features

Key features include two-way communication via REST API, intelligent command parsing for Chimera and AlphaFold, molecular visualization control, structural analysis capabilities, code execution in ChimeraX, and direct execution of AlphaFold & ESMFold commands.

Where to use

ChimeraX-AlphaFold-MCP is used in fields such as structural biology, bioinformatics, and molecular modeling, where understanding protein structures and interactions is crucial.

ChimeraX-AlphaFold-MCP: Integrating ChimeraX and AlphaFold with Claude AI

ChimeraX-AlphaFold-MCP connects ChimeraX and its AlphaFold Tool to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful integration allows for conversational structural biology, molecular visualization, and structure prediction and analysis capabilities through natural language.

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Features

• Two-way communication: Connect Claude AI to ChimeraX through a REST API.
• Intelligent command parsing: Natural language processing for Chimera and AlphaFold commands
• Molecular visualization control: Manipulate representations, colors, and views
• Structural analysis: Perform measurements, alignments, and other analyses
• Code execution: Run arbitrary Python code in ChimeraX from Claude
• Protein Structure Prediction: Directly run AlphaFold & ESMFold Commands by typing your workflow.

Installation Guide

Prerequisites

• ChimeraX installed on your system (Any Version After March 18th 2024)
• Claude for Desktop
• Python 3.10 or newer
• Git

Step 1: Install the UV Package Manager

On macOS:

brew install uv

On Windows:

powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
set Path=C:\Users\[YourUsername]\.local\bin;%Path%

For other platforms, visit the UV installation guide.

Step 2: Clone the Repository

git clone https://github.com/GDAmitha/chimerax-alphafold-mcp.git
cd pymol-mcp

Step 3: Set Up the Environment

Create and activate a Python virtual environment:

python -m venv venv

On macOS/Linux:

source venv/bin/activate

On Windows:

venv\Scripts\activate

Step 4: Install Dependencies

With the virtual environment activated:

pip install mcp

Step 5: Configure Claude Desktop

1. Open Claude Desktop
2. Go to Claude > Settings > Developer > Edit Config
3. This will open the claude_desktop_config.json file
4. Add the MCP server configuration:

{
  "mcpServers": {
    "pymol": {
      "command": "[Full path to your venv python]",
      "args": [
        "[Full path to pymol_mcp_server.py]"
      ]
    }
  }
}

For example:

{
  "mcpServers": {
    "pymol": {
      "command": "/Users/username/chimerax-alphafold-mcp/venv/bin/python",
      "args": [
        "/Users/username/chimerax-alphafold-mcp/mcp_direct_chimerax.py"
      ]
    }
  }
}

Note: Use the actual full paths on your system. On Windows, use forward slashes (/) instead of backslashes.

Step 6: Start listening on ChimeraX

1. Open ChimeraX
2. Type “remotecontrol rest start” into the command line.

Usage

Starting the Connection

In Claude Desktop:

• You should see a hammer icon in the tools section when chatting
• Click it to access the ChimeraX & AlphaFold tools

Example Commands

Here are some examples of what you can ask Claude to do:

• “Load PDB 1UBQ and display it as cartoon”
• “Color the protein by secondary structure”
• “Highlight the active site residues with sticks representation”
• “Align two structures and show their differences”
• “Calculate the distance between these two residues”
• “Save this view as a high-resolution image”

Troubleshooting

• Connection issues: Make sure the REST connection plugin is listening at http://127.0.0.1:63269/cmdline.html
• Command errors: Check the ChimeraX output window for any error messages
• AlphaFold Collab not appearing: Restart ChimeraaX and check that the connection was established.
• Claude not connecting: Verify the paths in your Claude configuration file are correct

Limitations & Notes

• Some complex operations may need to be broken down into simpler steps
• Always save your work before using experimental features
• Join our Bio-MCP Community to troubleshoot, provide feedback & improve Bio-MCPS! https://join.slack.com/t/bio-mcpslack/shared_invite/zt-31z4pho39-K5tb6sZ1hUvrFyoPmKihAA

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.