hide_surface · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What hide_surface does on ChimeraX MCP Server

AI agents use hide_surface 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 hide_surface needs a policy

The action hides (toggles visibility of) a molecular surface in ChimeraX, which is a reversible write operation on the visualization state—not permanent data deletion, not code execution, and not destructive. The user can unhide the surface at any time.

From the tool's definition Tool name is 'hide_surface' with description 'Hide molecular surface.' This modifies the visualization state of a molecular structure by hiding its surface representation, which is a reversible display operation.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

hide_surface Rate-limited

hide_surface 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": {
    "hide_surface": {
      "limits": [
        {
          "counter": "hide_surface_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 hide_surface

What does the hide_surface tool do? +

Hide molecular surface. 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 hide_surface? +

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

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

Can I rate-limit hide_surface? +

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

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

hide_surface 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.