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chains_ent_chains_id_entity_id_200017f6

Read-only

Fetches chain-level details for a PDB entity, listing polymer chains, residue ranges, per-residue validation data, and chain identifiers like Best Chain ID.

Instructions

Returns detailed chain-level annotations for a specified PDB Entity ID, including all of their polymer chains, their residue ranges, and per-residue validation information, along with metadata such as Best Chain ID and author-provided chain identifiers (Obs: chainId in additionalData response refers to struct_asym_id not the author-provided auth_asym_id).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idYesEntity id (molecule number in mmcif-speak). type: string pattern: ^[0-9]+$ title: Entity Id description: Entity id (molecule number in mmcif-speak).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

B3.4/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds genuine value by disclosing the response caveat that chainId in additionalData is struct_asym_id rather than auth_asym_id, a subtlety an agent could not otherwise anticipate.

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

Conciseness3/5

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

It is a single sentence, so there is no wasted padding, but it is dense and the parenthetical struct_asym_id caveat is tacked onto the end rather than front-loaded. The key routing information is present but buried.

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?

With no output schema, the description carries the burden of explaining returns and does so reasonably well by enumerating chains, residue ranges, validation data, and metadata. Missing only pagination/response-size behavior, which is a minor gap for a per-entity lookup.

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 100% and both parameters (pdb_id, entity_id) are documented in the schema, so the baseline of 3 applies. The description reinforces that entity_id is an entity/molecule identifier but adds no format or constraint detail beyond the schema.

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 states a specific verb ('Returns') and resource ('detailed chain-level annotations for a specified PDB Entity ID') and enumerates the returned content (polymer chains, residue ranges, per-residue validation, Best Chain ID). It is clear on its own but never distinguishes itself from the many sibling entity-level tools (e.g. annot_ent, molecules_ent, seq_cescie).

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?

There is no explicit when-to-use or when-not-to-use guidance and no alternatives are named, despite a large set of similar per-entity sibling tools. Usage must be inferred entirely from the return-content description.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.