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Structure

structure
Read-onlyIdempotent

"PDB entry [1abc] details" / "fetch protein structure [pdb_id]" / "metadata for [PDB ID]" — full PDB entry record by ID (e.g. "1abc", "7BV2"). Returns experimental method (X-ray / cryo-EM / NMR), resolution, authors, deposition date, organism, ligands, related entities. Use after search to inspect a specific structure.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Annotations (readOnlyHint, idempotentHint) already communicate safety, so the description's burden is lower. The description adds value by specifying the output fields (experimental method, resolution, authors, deposition date, organism, ligands, related entities), which is useful context not present in annotations.

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?

The description begins with three redundant quoted variants ('"PDB entry [1abc] details" / "fetch protein structure [pdb_id]" / "metadata for [PDB ID]"'), which adds noise and length without new information. The core sentence is concise and front-loaded, but the redundancy hurts structure.

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

Completeness5/5

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

For a single-parameter tool with an output schema, the description provides sufficient context: what it does, what it returns, and when to use it. It does not need to explain return values since an output schema exists, and the usage guidance makes it complete for the given complexity.

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 schema has no description for pdb_id, and the description provides examples (1abc, 7BV2) plus the label 'PDB ID.' This gives basic semantics but does not explain format constraints, case sensitivity, or potential error cases. With 0% schema coverage, the description partially compensates but is not exhaustive.

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

Purpose5/5

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

The description clearly states the tool fetches a full PDB entry record by ID, listing specific return fields (method, resolution, authors, deposition date, organism, ligands, related entities). It distinguishes from sibling tools like search by providing a specific resource and verb, and the examples (1abc, 7BV2) clarify the input format.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It explicitly instructs to use this tool after `search` to inspect a specific structure, providing clear context for when to invoke it. This guidance implies it is not for discovery (use search instead), satisfying the explicit when/alternative criterion.

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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TDQS

A3.7/5.0
Disambiguation2/5

ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are nearly identical in purpose, and structure/summary both fetch PDB entries. The server name 'Rcsb Pdb' doesn't match most tools, which are Pipeworx data tools, compounding ambiguity.

Naming Consistency3/5

Mostly snake_case verb_noun, but verbs are inconsistent (ask, discover, generate, list, recall) and some names are noun phrases (entity_profile, polymarket_edges). No clear pattern unifies the set.

Tool Count2/5

37 tools is excessive for a server ostensibly about RCSB PDB; only 6 tools relate to PDB while 31 serve unrelated Pipeworx functionality. The count feels like a bundled grab-bag rather than a focused toolset.

Completeness3/5

The PDB-specific tools cover the core operations (search, fetch, assembly, ligand, polymer entity), so the structural biology surface is mostly complete. However, the server's overall purpose is muddled, and the Pipeworx tools are a separate domain that happens to be bundled in, making it unclear what 'completeness' even means for this server.