Open a molecular structure from PDB ID, file path, or URL.
AI agents call open_structure to retrieve information from ChimeraX MCP Server without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool retrieves/loads molecular structure data from an external source (PDB, file, or URL) into ChimeraX for visualization. It is a read/fetch operation with no data modification or destructive side effects. Severity is low as the main risk is loading unintended or malicious structure files, but blast radius is minimal.
From the tool's definition Open a molecular structure from PDB ID, file path, or URL
Attacks that exploit this kind of access
Open a molecular structure from PDB ID, file path, or URL. It is categorised as a Read tool in the ChimeraX MCP Server MCP Server, which means it retrieves data without modifying state.
Register the ChimeraX MCP Server MCP server in PolicyLayer and add a rule for open_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.
open_structure is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the open_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.
Set action: deny in the PolicyLayer policy for open_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.
open_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.
Every MCP server has a record like this.
Type a name, get the same breakdown: verified identity, auth posture, risk grade, capabilities, recommended policy.
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