save_structure · ChimeraX MCP Server MCP: Risk & Policy

WHAT IT DOES

What save_structure does on ChimeraX MCP Server

AI agents use save_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 save_structure needs a policy

The tool writes/exports molecular structure data to files, which is a reversible operation (files can be modified or deleted afterward). It does not execute arbitrary code, delete existing files, move money, or perform irreversible destructive actions.

From the tool's definition Tool name and description: 'save_structure' which 'Save a model to PDB, mmCIF, or mol2 file' — this creates or writes data to files in molecular structure formats.

Attacks that exploit this kind of access

Recommended rule Ready

Verdict

save_structure Rate-limited

save_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": {
    "save_structure": {
      "limits": [
        {
          "counter": "save_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 save_structure

What does the save_structure tool do? +

Save a model to PDB, mmCIF, or mol2 file. 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 save_structure? +

Register the ChimeraX MCP Server MCP server in PolicyLayer and add a rule for save_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 save_structure? +

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

Can I rate-limit save_structure? +

Yes. Add a rate_limit block to the save_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 save_structure completely? +

Set action: deny in the PolicyLayer policy for save_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 save_structure? +

save_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.

// THE FULL RECORD

save_structure is one line of ChimeraX MCP Server's registry record.

The record carries the whole server: verified identity, auth posture, risk grade, every tool classified, recommended policy — re-checked continuously.

Teams ship this data inside their own products. See what a licence covers →