Measure distance between two atoms in Angstroms with visual annotation.
AI agents call measure_distance 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 reads/computes a geometric measurement (distance) between two atoms and adds a visual annotation. It does not modify, delete, or create structural data — it only queries spatial information and annotates the view, which is a reversible display operation. Closest to Read category.
From the tool's definition Measure distance between two atoms in Angstroms with visual annotation
Attacks that exploit this kind of access
Measure distance between two atoms in Angstroms with visual annotation. 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 measure_distance: 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.
measure_distance 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 measure_distance 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 measure_distance. 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.
measure_distance 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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