mutate_residue · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What mutate_residue does on ChimeraX MCP Server

AI agents invoke mutate_residue 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 mutate_residue needs a policy

'mutate_residue' implies modifying a residue in a protein structure, which is a write/execute operation on structural data. Given the server's editing context and sibling tools like 'delete_atoms' (Destructive) and 'add_hydrogen' (Write), mutating a residue likely alters the model in a way that may or may not be reversible depending on session state.

From the tool's definition Tool name 'mutate_residue' on a server for protein structure 'editing' — the server description explicitly mentions 'editing' as a capability.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

mutate_residue Rate-limited

mutate_residue 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": {
    "mutate_residue": {
      "limits": [
        {
          "counter": "mutate_residue_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 mutate_residue

What does the mutate_residue tool do? +

mutate_residue. 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 mutate_residue? +

Register the ChimeraX MCP Server MCP server in PolicyLayer and add a rule for mutate_residue: 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 mutate_residue? +

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

Can I rate-limit mutate_residue? +

Yes. Add a rate_limit block to the mutate_residue 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 mutate_residue completely? +

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

mutate_residue 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.