invert_selection · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What invert_selection does on ChimeraX MCP Server

AI agents invoke invert_selection 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 invert_selection needs a policy

This tool triggers an action within the ChimeraX application (inverting the current atom/residue selection). It is not a pure read (it modifies application state), not a write to persistent data, not destructive, and not financial. It falls under Execute as it triggers an external operation in ChimeraX whose effect depends on the current selection context.

From the tool's definition Invert the current selection — triggers an operation in ChimeraX that changes the active selection state

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

invert_selection Rate-limited

invert_selection 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": {
    "invert_selection": {
      "limits": [
        {
          "counter": "invert_selection_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 invert_selection

What does the invert_selection tool do? +

Invert the current selection. 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 invert_selection? +

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

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

Can I rate-limit invert_selection? +

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

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

invert_selection 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.