Find residues within N Angstroms of a selection.
AI agents call find_contacts 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 is a read-only analysis tool that queries protein structure geometry to identify nearby residues. It has no side effects, does not modify the structure, and poses minimal risk. The operation is purely informational retrieval of spatial proximity data.
From the tool's definition Tool description states 'Find residues within N Angstroms of a selection' - a query operation that retrieves/identifies spatial relationships without modifying data or executing arbitrary code.
Attacks that exploit this kind of access
Find residues within N Angstroms of a selection. 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 find_contacts: 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.
find_contacts 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 find_contacts 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 find_contacts. 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.
find_contacts 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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