align_and_rmsd · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What align_and_rmsd does on ChimeraX MCP Server

AI agents invoke align_and_rmsd 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 align_and_rmsd needs a policy

Aligning a structure modifies its coordinates/orientation in ChimeraX (not purely read), making it an Execute-level operation with side effects. It is reversible in principle but triggers an external operation in the visualization environment. The blast radius is medium since it affects the displayed structure state but doesn't delete or overwrite persisted data irreversibly.

From the tool's definition Align one selection to another and report RMSD — performs a structural alignment operation (modifies the position/orientation of a structure) and computes a metric

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

align_and_rmsd Rate-limited

align_and_rmsd 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": {
    "align_and_rmsd": {
      "limits": [
        {
          "counter": "align_and_rmsd_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 align_and_rmsd

What does the align_and_rmsd tool do? +

Align one selection to another and report RMSD. 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 align_and_rmsd? +

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

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

Can I rate-limit align_and_rmsd? +

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

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

align_and_rmsd 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.