# molecule-mcp

> MCP Server

Molecule-MCP connects molecule science tools to Claude AI via the Model Context Protocol, enabling Claude to interact with and control these tools, acting as a co-scientist for prompt-assisted molecule modeling.

## Overview

- **Category:** AI
- **Language:** Python
- **Stars:** 96
- **Forks:** 4
- **Owner:** ChatMol
- **GitHub:** https://github.com/ChatMol/molecule-mcp
- **Created:** 2025-03-19T12:54:09+00:00
- **Updated:** 2025-03-28T19:27:48+00:00
- **Source:** https://model-context-protocol.com/servers/molecule-model-context-protocol-server

## Setup

## Setup

⚠️ **Note**: Molecule-MCP requires Claude Desktop to be installed and running.
1. Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following:
```json
{
  "mcpServers": {
    "pymol": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
      ]
    },
	"chimerax": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/chimerax_server.py"
      ]
    }
  }
}
```
2. Install mcp and get the script
```bash
pip install mcp chatmol
which mcp
```
the path to mcp will be displayed. Copy this path for the next step and replace `/path/to/mcp` with the path to mcp.
```
git clone https://github.com/ChatMol/molecule-mcp.git
cd molecule-mcp
pwd
```
the path to molecule-mcp will be displayed. Copy this path for the next step and replace `/path/to/molecule-mcp` with the path to molecule-mcp.

## Tools

## Available Tools

1.  Model-Context-Protocol server (connects molecule science tools to Claude AI).
2.  Integration with Claude AI (enables prompt assisted molecule modeling).
3.  PyMOL server (allows Claude to interact with PyMOL).
4.  ChimeraX server (allows Claude to interact with ChimeraX).