protein-blender-mcp

fetch_structure

Download a protein structure by PDB ID or UniProt accession from RCSB or AlphaFold and load it into the Blender scene with an initial style, color, and material.

Instructions

Download a structure by ID and add it to the scene with an initial style.

pdb_id: a PDB code like "4HHB", or a UniProt accession when database is "alphafold". Use style="none" to load without any style and build it up with add_style.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "pdb_id": "<pdb_id>"
    },
    "name": "fetch_structure"
  }
}

Input Schema

Name	Required	Default
`color`	No	chain
`style`	No	cartoon
`pdb_id`	Yes
`database`	No	rcsb
`material`	No

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Nov 7, 2026

TDQS

A3.6/5.0

Behavior3/5

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

No annotations are supplied, so the description carries the full disclosure burden. It does reveal that the tool performs a network download and mutates the scene by adding the structure, but it says nothing about failure modes (invalid ID, no network), whether an existing structure is replaced, or what is returned.

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?

Two short paragraphs: the purpose is front-loaded, and the second paragraph is dedicated to the most confusing parameter. Slightly awkward placement of the pdb_id notes ahead of the style advice, but no wasted sentences.

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

Completeness3/5

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

For a five-parameter mutation tool with no annotations and no output schema, the description covers the essential path but leaves gaps around the three styling parameters (color, material) and side effects on the existing scene. Adequate to invoke correctly, incomplete for predicting behavior.

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 0%, so the description must compensate. It clarifies that pdb_id accepts a PDB code or a UniProt accession depending on database, and explains the special style="none" value, but leaves color, material, and the default database behavior undocumented beyond the raw enums.

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 opening sentence gives a specific verb and resource ('Download a structure by ID and add it to the scene with an initial style'), which clearly distinguishes it from load_file (local files) and add_style (styling only). It stops short of explicitly naming those siblings, so an agent must infer the boundary rather than read it.

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

Usage Guidelines4/5

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

It gives a concrete when-to-use pattern: load with style="none" and build up styling with add_style, which routes the agent to a specific sibling tool. It omits other relevant context, such as when to use load_file instead or what to do if a structure is already loaded.

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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