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mahynotch

ChimeraX MCP Server

by mahynotch

measure_distance

Calculate the distance between two atoms in Angstroms and display a visual annotation in the structure.

Instructions

Measure distance between two atoms in Angstroms with visual annotation. Aliases: distance, how far, length between.

Example: measure_distance("/A:501@CA", "/A:31@CA")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
atom1Yes
atom2Yes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description must disclose behavioral traits. It mentions 'visual annotation' but does not explain side effects, safety (e.g., read-only nature), or whether it modifies the structure. This is insufficient.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise: a single functional sentence, alias list, and example. Every element is relevant and front-loaded.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a simple measurement tool with an output schema (not provided), the description covers the key points: what is measured, units, and visual feedback. Could be more complete by noting return value format or additional constraints.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema has two string parameters with 0% description coverage. The description adds an example showing the atom selection format ('/A:501@CA'), which hints at the parameter semantics, but does not fully explain the required pattern or acceptable values.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's action: 'Measure distance between two atoms in Angstroms with visual annotation.' It also includes aliases and an example, making it specific and distinct from sibling tools like measure_angle.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use this tool versus alternatives such as measure_angle or find_contacts. There are no explicit when-not or prerequisite conditions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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