pymol-mcp

Add to Your Project

Copy this JSON into your .mcp.json to enable this server

Add to your .mcp.json:

{
  "mcpServers": {
    "pymol-mcp": {
      "command": "uv",
      "args": [
        "run",
        "${CLAUDE_PLUGIN_ROOT}/pymol_mcp_server.py"
      ],
      "env": {
        "PYTHONUNBUFFERED": "1"
      }
    }
  }
}

Security Considerations

Review these signals before enabling this server

Admin access level

This server has elevated permissions. Review the source code before enabling.

Details

Server configuration and connection parameters

Commanduv

Access Leveladmin

Arguments

Command-line arguments passed to the server process

run${CLAUDE_PLUGIN_ROOT}/pymol_mcp_server.py

Environment Variables

Environment variables set when the server starts

PYTHONUNBUFFERED=1

Stats

LanguagePython

Parent stars2

Parent forks1

MaintenanceGood

Last CommitMar 23, 2026

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