load_structure · Vmd MCP: Risk & Policy

WHAT IT DOES

What load_structure does on Vmd

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

WHY IT NEEDS A POLICY

Why load_structure needs a policy

Loading a structure file creates a new molecule object within VMD, which is a write/create operation with moderate blast radius. It does not delete or overwrite existing data, execute arbitrary code, or have financial implications. It is reversible (the molecule can be deleted). The severity is medium because it modifies the VMD session state and could load malicious or unintended files.

From the tool's definition Load a molecular structure file into VMD

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

load_structure Rate-limited

load_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": {
    "load_structure": {
      "limits": [
        {
          "counter": "load_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 Vmd, so you can run agents against it safely.

FAQ

Questions about load_structure

What does the load_structure tool do? +

Load a molecular structure file into VMD. It is categorised as a Write tool in the Vmd MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on load_structure? +

Register the Vmd MCP server in PolicyLayer and add a rule for load_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 Vmd. Nothing to install.

What risk level is load_structure? +

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

Can I rate-limit load_structure? +

Yes. Add a rate_limit block to the load_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 load_structure completely? +

Set action: deny in the PolicyLayer policy for load_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 load_structure? +

load_structure is provided by the Vmd MCP server (omararias-gaguancela/vmd-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.