Skip to main content
Glama
PDBe MCP Servers

PDBe MCP Servers

Official
by PDBeurope

ebi-pdbe-ent_rlerl_id_2439bcf6

Read-only

List all modelled and unmodelled residues for a PDB ID, excluding waters, with chain, residue number, component, modelled-atom fraction, and alternate-conformer details.

Instructions

List all residues in a PDB entry, excluding waters, including both modelled and unmodelled residues. For each residue, the response provides the entity ID, chain identifiers, mmCIF- and PDB-style residue numbers with insertion codes, chemical component names, the fraction of expected atoms that are modelled, and details of any alternate conformers present

Input Schema

NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered; the description nonetheless adds real behavioral context by disclosing that unmodelled residues are included, that waters are filtered out, and what per-residue details come back (numbering schemes, insertion codes, modelled-atom fraction, alternate conformers). It omits volume/size expectations and behavior for an unknown PDB id, which keeps it below a 5.

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

Conciseness4/5

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

One front-loaded sentence states the operation first and then enumerates the return fields; every clause carries information and nothing is repeated from the title. The return-field list is long but each item is substantive, so it stays readable.

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 the return shape and does so thoroughly for a one-parameter read tool, including the two numbering conventions and the modelling fraction. It lacks error/empty-result behavior and any sizing caveat for large entries, so it is not fully complete.

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 single pdb_id parameter is fully documented in the schema (100% coverage, including the 4-character format requirement), so the description does no parameter work and none is needed. Baseline 3 applies.

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 ('List all residues in a PDB entry') and immediately bounds the scope ('excluding waters, including both modelled and unmodelled residues'), which distinguishes it from a plain chain or entity listing. It does not explicitly name a sibling tool to contrast with, 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.

Usage Guidelines2/5

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 mention of alternatives such as the chain, entity, or interface-residue siblings. The only hint at a use case is implicit in the enumerated return fields (modelling fraction, alt conformers), which an agent must infer.

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

Deploy Server

Other Tools