close_structure · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What close_structure does on ChimeraX MCP Server

AI agents use close_structure 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 close_structure needs a policy

Closing a model in ChimeraX is a reversible action—the underlying structure file remains intact and can be reopened. This is a modification of application state (the set of loaded models) rather than data deletion or destruction. It does not trigger code execution, financial operations, or irreversible data loss.

From the tool's definition Tool description states 'Close one or all open models', which removes or unloads visualization state from ChimeraX without permanently deleting underlying data files.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

close_structure Rate-limited

close_structure 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": {
    "close_structure": {
      "limits": [
        {
          "counter": "close_structure_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 close_structure

What does the close_structure tool do? +

Close one or all open models. 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 close_structure? +

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

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

Can I rate-limit close_structure? +

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

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

close_structure 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.