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mahynotch

ChimeraX MCP Server

by mahynotch

measure_angle

Measures the bond angle in degrees defined by three atoms in a protein structure. Input atom specifiers for accurate angle calculation.

Instructions

Measure bond angle defined by three atoms in degrees. Aliases: angle, bond angle.

Example: measure_angle("/A:501@N", "/A:501@CA", "/A:501@C")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
atom1Yes
atom2Yes
atom3Yes

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 carries full burden for behavioral traits. It only states it measures an angle and gives an example, but does not disclose read-only nature, side effects, or limitations.

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

Conciseness4/5

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

The description is very concise and front-loaded with the main action. The example is useful, but the description could be more structured (e.g., bullet points) without adding length.

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

Completeness2/5

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

Given the complexity (3 required parameters, no schema descriptions, and many sibling tools), the description lacks completeness: no usage guidance, no parameter explanation, and minimal behavioral context. Output schema exists but is not described.

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

Parameters2/5

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

Input schema has 0% description coverage for parameters; they are just type 'string'. The description provides an example showing atom specification format, but no explicit explanation of the syntax or semantics for the three atom parameters.

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 explicitly states 'Measure bond angle defined by three atoms in degrees', providing a clear verb and resource. It includes aliases and an example, distinguishing it from sibling tools like measure_distance.

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

Usage Guidelines3/5

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

The description implies usage through the example but does not explicitly state when to use this tool versus alternatives, nor does it provide any exclusion criteria or prerequisites.

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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