Retrieve the amino-acid sequence for a specific PDB entry and chain ID (label_asym_id) to analyze protein structure composition.
Returns the amino-acid sequence for a specific PDB Entry and Chain ID (label_asym_id).
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | 4-character PDB id code. title: Pdb Id description: 4-character PDB id code. | |
| chain_id | Yes | PDB chain id. title: Chain Id description: PDB chain id. |
Changes observed during successful MCP inspections.
v1.1.10Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered without prose. The description adds real value by clarifying that chain_id means label_asym_id rather than a generic chain id, but it says nothing about return format (one-letter vs three-letter codes) or handling of modified residues.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
A single front-loaded sentence with zero filler. The core action and the two scoping identifiers appear immediately, and nothing is repeated from the schema.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a read-only, two-parameter retrieval with fully documented parameters, the description covers what is returned and how it is scoped. The absence of an output schema is largely compensated by 'returns the amino-acid sequence', though format details remain unspecified.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, so the baseline is 3, but the parenthetical '(label_asym_id)' genuinely disambiguates chain_id, which the schema only describes circularly as 'PDB chain id'. That distinction (label vs auth asymmetry) is a real footgun in PDB APIs, so it earns a step above baseline.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb (returns) and resource (amino-acid sequence) scoped to two identifiers (PDB Entry + Chain ID), so the agent knows exactly what it gets. It does not differentiate itself from sequence-oriented siblings such as seq_cuuscu_acc or seq_cescie_id, so it falls short of a 5.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
There is no when-to-use guidance, no prerequisites, and no alternatives named among the many sibling tools. The agent must infer from the name alone when this retrieval is preferable to the other sequence endpoints.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.