Molecule Visualization (ChimeraX, PyMOL)

by chatmol

68 stars

Not rated

GitHub

About

Connects AI systems to molecular visualization software like PyMol and ChimeraX, enabling direct command execution and image capture of molecular structures for scientific workflows.

Details

Author: chatmol
Repository: ChatMol/molecule-mcp
GitHub stars: 68
License: MIT License
Categories: Productivity, Developer Tools, Design, AI, Media, Infrastructure
Tags: #integration

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name Molecule Visualization (ChimeraX, PyMOL)

Command (node, npx, python, etc.) /path/to/mcp
Arguments
- Argument 1 run
- Argument 2 /path/to/molecule-mcp/pymol_server.py
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

JSON

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

From the repository

⚠️ 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:

{

  "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"

      ]

    },

    "gromacs_copilot": {

      "command": "/path/to/mcp",

      "args": [

        "run",

        "/path/to/molecule-mcp/mcp_server.py"

      ]

    }

  }

}

2. Install mcp and get the script

pip install "mcp[cli]" chatmol

pip install git+https://github.com/ChatMol/gromacs_copilot.git # optional, for running gromacs_copilot

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.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "molecule visualization (chimerax, pymol)": {
            "cwd": null,
            "env": {},
            "args": [
                "run",
                "/path/to/molecule-mcp/pymol_server.py"
            ],
            "shell": false,
            "command": "/path/to/mcp"
        }
    }
}

Linux

{
    "cwd": null,
    "env": [],
    "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
    ],
    "shell": false,
    "command": "/path/to/mcp"
}

Macos

{
    "cwd": null,
    "env": [],
    "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
    ],
    "shell": false,
    "command": "/path/to/mcp"
}

Windows

{
    "cwd": null,
    "env": [],
    "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
    ],
    "shell": false,
    "command": "/path/to/mcp"
}

Molecule-MCP

Molecule-MCP: A model-context-protocol server for molecules. Molecule-MCP connects molecule science releated tools to Claude AI through the Model Context Protocol (MCP), allowing Claude to directly interact with and control these tools and act as a co-scientist. This integration enables prompt assisted molecule modeling.

Molecule MCP

Installation

⚠️ 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:

{
  "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"
      ]
    },
    "gromacs_copilot": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/mcp_server.py"
      ]
    }
  }
}

2. Install mcp and get the script

pip install "mcp[cli]" chatmol
pip install git+https://github.com/ChatMol/gromacs_copilot.git # optional, for running gromacs_copilot
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.

Disclaimer

Molecule-MCP is provided "as is" without warranty of any kind, express or implied. The authors and contributors disclaim all warranties including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.

The authors bear no responsibility for any consequences arising from the use, misuse, or misinterpretation of this software or its outputs. Results obtained through Molecule-MCP should be independently validated prior to use in research, publications, or decision-making processes.

This software is intended for research and educational purposes only. Users are solely responsible for ensuring compliance with applicable laws, regulations, and ethical standards in their jurisdiction.

No reviews yet — be the first

Use Google, GitHub, or an email account so ratings stay tied to real people.

Email sign in

No reviews posted yet.

About

Details

Jump to

Setting up with Highlight

From the repository

Claude Desktop / Cursor

Linux

Macos

Windows

Molecule-MCP

Installation

Disclaimer

Install

More like this

Time

Sentry

Github

Git

GitLab

Context 7