Retrieve the amino-acid sequence for a specific PDB entry and chain ID to analyze protein chain 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.
v2.0.1Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already cover the safety profile (readOnlyHint=true, destructiveHint=false), so the description only needs to add context. It does add one valuable clarification: chain_id is a label_asym_id. It does not explain the idempotentHint=false on what is semantically a pure lookup, nor the return format.
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 resource, the scope, and the key identifier convention all land immediately.
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 two-parameter read with no output schema, the definition covers what is needed to invoke it correctly and identifies the identifier convention. The remaining minor gap is the return format (one-letter vs three-letter codes, plain text vs FASTA), which is not stated.
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% and the schema itself only says "PDB chain id." The description earns credit above the baseline by specifying that the chain identifier is label_asym_id, which resolves real ambiguity against auth_asym_id usage elsewhere in PDB APIs.
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?
The description states a specific verb and resource ("Returns the amino-acid sequence") scoped to a specific PDB Entry and Chain ID, so the agent knows exactly what comes back. It does not differentiate itself from the many sibling sequence-style tools (seq_cescie_id, seq_cuuscu_acc, ent_chain_seq), leaving the agent to infer which sequence endpoint applies.
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?
No when-to-use or when-not-to-use guidance is given, and no alternative is named despite a crowded set of sibling tools that also deal with sequences, chains, and entities. The only implicit guidance is that the caller must already know a pdb_id and chain_id.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.