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mahynotch

ChimeraX MCP Server

by mahynotch

get_sequence

Retrieve the amino acid sequence for a specified protein chain. Input a chain identifier to get its residue sequence.

Instructions

Return amino acid sequence for a chain. Aliases: sequence, residues, chain sequence.

Example: get_sequence("/A")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
chain_specYes

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 fully disclose behavior. It only states the function, omitting details like error handling (e.g., missing chain), output format (e.g., one-letter codes), or any side effects. Minimal transparency.

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, with two short lines and an example. Every word adds value, and the purpose is front-loaded. No wasted text.

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?

Given the tool's simplicity (one parameter, no annotations, but an output schema exists), the description is largely sufficient. It explains the core function and provides an example. Minor gaps like chain specification format do not significantly impair understanding.

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 schema has 0% description coverage for the single parameter 'chain_spec.' The description adds meaning via the example '/A' and the aliases 'sequence, residues, chain sequence,' indicating the parameter specifies a chain. However, it does not fully define the format or constraints.

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 returns 'amino acid sequence for a chain,' specifying the verb and resource. Among siblings, no other tool retrieves sequences, so it is well-distinguished.

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 provides an example and aliases but no explicit guidance on when to use this tool vs alternatives. Usage is implied by the purpose, but no when-not or exclusion criteria are given.

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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