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pdb_structure_summary

Retrieve a protein structure summary from PDB by ID, including title, resolution, method, organism, deposition date, and chain sequence. Use it for structural biology and drug design queries.

Instructions

Get protein structure summary from PDB. 按 PDB ID 获取蛋白质结构摘要:title/resolution/method/organism/deposition date and chain sequence. 标题/分辨率/实验方法/物种/沉积日期及指定链序列,for structural biology and drug design. 用于结构生物学、药物设计的结构查询。

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes
chain_idNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

With no annotations, the description carries the burden of explaining behavior. It does disclose what the tool returns (title, resolution, method, organism, deposition date, chain sequence), which is useful. However, it does not describe error behavior, input validation, rate limits, or explicitly confirm read-only semantics beyond the verb 'Get'.

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

Conciseness2/5

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

The description is front-loaded with the main purpose, but it repeats nearly the same content in English and Chinese across multiple clauses. The field list and intended use case each appear twice, so not every sentence earns its place.

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

Completeness3/5

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

The tool is simple, has an output schema, and the description covers both parameters at a basic level. An agent could likely call it correctly, but the lack of usage guidance, input format specifics, and behavioral details leaves moderate gaps for a tool with no annotations.

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?

Schema description coverage is 0%, so the description must compensate. It does explain pdb_id as a PDB identifier and hints at chain_id through 'specified chain sequence' / '指定链序列', but it does not clarify format constraints or what 'default chain' means. The schema provides the default but not the underlying semantics.

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

Purpose4/5

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

The description opens with a specific verb and resource ('Get protein structure summary from PDB') and enumerates the returned fields: title, resolution, method, organism, deposition date, and chain sequence. It is clear and unambiguous, but it does not explicitly distinguish itself from sibling tools like alphafold_structure or emdb_structure_lookup.

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 gives a domain context ('for structural biology and drug design') but provides no guidance on when to choose this tool over alternatives. There are no exclusions, no mention of when another PDB-related or structure tool would be more appropriate, and no prerequisites are stated.

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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