run_script · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What run_script does on ChimeraX MCP Server

AI agents invoke run_script to trigger actions in ChimeraX MCP Server. 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_script needs a policy

This tool allows execution of arbitrary scripts (both ChimeraX commands and Python code), which can trigger complex computational operations, modify molecular structures in unpredictable ways, access files, or perform side effects beyond simple visualization. While the server is designed for protein structure analysis, script execution without strict input validation poses significant risk of unintended consequences.

From the tool's definition Tool description explicitly states 'Run a ChimeraX command script (.cxc) or Python script (.py)', indicating arbitrary code/script execution capability.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

run_script Rate-limited

run_script 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_script": {
      "limits": [
        {
          "counter": "run_script_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 ChimeraX MCP Server, so you can run agents against it safely.

FAQ

Questions about run_script

What does the run_script tool do? +

Run a ChimeraX command script (.cxc) or Python script (.py). It is categorised as a Execute tool in the ChimeraX MCP Server 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_script? +

Register the ChimeraX MCP Server MCP server in PolicyLayer and add a rule for run_script: 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 ChimeraX MCP Server. Nothing to install.

What risk level is run_script? +

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

Can I rate-limit run_script? +

Yes. Add a rate_limit block to the run_script 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_script completely? +

Set action: deny in the PolicyLayer policy for run_script. 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_script? +

run_script is provided by the ChimeraX MCP Server MCP server (mahynotch/chimerax-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.