run_command · Pymol Cursor MCP: Risk & Policy

WHAT IT DOES

What run_command does on Pymol Cursor

AI agents invoke run_command to trigger actions in Pymol Cursor. What it does depends on the arguments the agent supplies, and its effects often reach beyond the immediate call — builds kicked off, notifications sent, workflows started.

WHY IT NEEDS A POLICY

Why run_command needs a policy

The tool executes PyMOL commands, which are programming constructs capable of causing side effects beyond simple data retrieval. PyMOL's command language permits arbitrary Python execution (via the 'python' command and similar), file I/O, and manipulation of molecular data and rendering state.

From the tool's definition Tool description states 'Run a single PyMOL command' and server description confirms it 'execute[s] PyMOL commands through XML-RPC'. PyMOL commands can invoke arbitrary Python code, modify molecular structures, write files, and trigger external operations.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

run_command Rate-limited

run_command stays usable, but rate-capped — a runaway agent can't fire it dozens of times a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "run_command": {
      "limits": [
        {
          "counter": "run_command_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

RATE-LIMIT THIS TOOL →

Instant setup, no code required.

PolicyLayer is an MCP gateway: every tool call is checked against your rule before it reaches Pymol Cursor, so you can run agents against it safely.

FAQ

Questions about run_command

What does the run_command tool do? +

Run a single PyMOL command. It is categorised as a Execute tool in the Pymol Cursor MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on run_command? +

Register the Pymol Cursor MCP server in PolicyLayer and add a rule for run_command: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Pymol Cursor. Nothing to install.

What risk level is run_command? +

run_command is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit run_command? +

Yes. Add a rate_limit block to the run_command rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block run_command completely? +

Set action: deny in the PolicyLayer policy for run_command. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides run_command? +

run_command is provided by the Pymol Cursor MCP server (truong128/pymol-cursor-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.