label_residues · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What label_residues does on ChimeraX MCP Server

AI agents use label_residues to create or update resources in ChimeraX MCP Server — usually the action step of a workflow, after the agent has gathered context. Every call changes real data in your ChimeraX MCP Server environment.

WHY IT NEEDS A POLICY

Why label_residues needs a policy

The tool adds visual annotations (labels) to residues in a ChimeraX structure. This is a Write operation because it creates/modifies display data (labels) reversibly—labels can be removed or changed without affecting the protein structure itself. It is not Read (no data retrieval), Destructive (reversible and does not delete atoms or data), Execute (not running arbitrary code/commands), Financial, or Other.

From the tool's definition Tool description: 'Add text labels to residues' — this modifies the visualization state of the protein structure by adding labels, which is a reversible operation that does not delete or permanently alter the underlying structural data.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

label_residues Rate-limited

label_residues stays usable, but capped — an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "label_residues": {
      "limits": [
        {
          "counter": "label_residues_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

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 label_residues

What does the label_residues tool do? +

Add text labels to residues. Default shows residue name + number. It is categorised as a Write tool in the ChimeraX MCP Server MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on label_residues? +

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

label_residues is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit label_residues? +

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

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

label_residues 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.