PyMOL MCP server

This PyMOL-Claude integration enables direct communication between PyMOL and Claude Desktop, allowing you to control PyMOL through natural language commands via Claude's interface.

Installation and Setup

Install PyMOL Plugin

Copy the claude_plugin directory to your PyMOL plugins directory:

cp -r claude_plugin ~/.pymol/plugins/claude_integration

Configure Claude Desktop

1. Locate your Claude Desktop configuration file:

   ~/Library/Application Support/Claude/claude_desktop_config.json
   

2. Add the MCP server configuration:

   {
     "mcpServers": {
       "pymol": {
         "command": "python3",
         "args": [
           "/path/to/pymol_mcp.py"
         ]
       }
     }
   }
   

   Make sure to replace /path/to/pymol_mcp.py with the actual full path to where you've placed the pymol_mcp.py file on your system.

Launch the Integration

To start using the integration:

1. Open PyMOL first (the Claude plugin should automatically activate)
2. Launch Claude Desktop
3. Both applications should now be able to communicate with each other

Using the Integration

Basic Commands

Once the integration is running, you can send PyMOL commands directly through Claude. For example, try typing these commands in Claude:

fetch 1cbs
show cartoon
color spectrum

PyMOL should respond by fetching the protein structure with ID 1cbs, displaying it in cartoon representation, and coloring it with a spectrum color scheme.

Command Examples

You can use any standard PyMOL commands through Claude, such as:

• Loading structures: load /path/to/structure.pdb
• Visualization changes: show surface, show sticks, organic
• Coloring: color cyan, chain A, util.cbaw
• Selections: select binding_site, resi 100-120
• View manipulation: zoom, rotate y, 90

Troubleshooting

If you encounter issues with the integration:

1. Verify that PyMOL is running with the plugin active
2. Ensure Claude Desktop is properly configured with the correct path to pymol_mcp.py
3. Check terminal output for any error messages
4. Try restarting both applications (start PyMOL first, then Claude)
5. Confirm that file paths in your Claude configuration are correct and accessible

If problems persist, check for any firewall or permission issues that might be preventing communication between the applications.

How to install this MCP server

For Claude Code

To add this MCP server to Claude Code, run this command in your terminal:

claude mcp add-json "pymol" '{"command":"python3","args":["/path/to/pymol_mcp.py"]}'

See the official Claude Code MCP documentation for more details.

For Cursor

There are two ways to add an MCP server to Cursor. The most common way is to add the server globally in the ~/.cursor/mcp.json file so that it is available in all of your projects.

If you only need the server in a single project, you can add it to the project instead by creating or adding it to the .cursor/mcp.json file.

Adding an MCP server to Cursor globally

To add a global MCP server go to Cursor Settings > Tools & Integrations and click "New MCP Server".

When you click that button the ~/.cursor/mcp.json file will be opened and you can add your server like this:

{
    "mcpServers": {
        "pymol": {
            "command": "python3",
            "args": [
                "/path/to/pymol_mcp.py"
            ]
        }
    }
}

Adding an MCP server to a project

To add an MCP server to a project you can create a new .cursor/mcp.json file or add it to the existing one. This will look exactly the same as the global MCP server example above.

How to use the MCP server

Once the server is installed, you might need to head back to Settings > MCP and click the refresh button.

The Cursor agent will then be able to see the available tools the added MCP server has available and will call them when it needs to.

You can also explicitly ask the agent to use the tool by mentioning the tool name and describing what the function does.

For Claude Desktop

To add this MCP server to Claude Desktop:

1. Find your configuration file:

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

2. Add this to your configuration file:

{
    "mcpServers": {
        "pymol": {
            "command": "python3",
            "args": [
                "/path/to/pymol_mcp.py"
            ]
        }
    }
}

3. Restart Claude Desktop for the changes to take effect