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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

export_for_pymol

Export protein structure data from AlphaFold MCP Server in PyMOL-compatible format for visualization, with optional confidence score coloring.

Instructions

Export structure data formatted for PyMOL visualization

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": {
      "uniprotId": "<uniprotId>"
    },
    "name": "export_for_pymol"
  }
}

Input Schema

NameRequiredDescriptionDefault
includeConfidenceNoInclude confidence score coloring (default: true)
uniprotIdYesUniProt accession

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.0.0

TDQS

C2.9/5.0
Behavior2/5

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

With no annotations provided, the description carries full burden for behavioral disclosure. It states the tool exports formatted data but doesn't describe what format is produced (e.g., PDB file, script), whether it's a file download or data return, authentication requirements, rate limits, or potential side effects. This leaves significant behavioral gaps for a tool that presumably generates output.

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

Conciseness5/5

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

The description is a single, efficient sentence that communicates the core purpose without unnecessary words. It's appropriately sized for a straightforward export tool and front-loads the essential information.

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

Completeness2/5

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

For an export tool with no annotations and no output schema, the description is insufficient. It doesn't explain what format the output takes, whether it's downloadable data or a visualization script, or what the agent should expect as a result. Given the complexity of structure data export and lack of structured metadata, more behavioral context is needed.

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%, so the schema already documents both parameters thoroughly. The description adds no additional parameter information beyond what the schema provides - it doesn't explain how 'includeConfidence' affects PyMOL visualization or provide context about UniProt IDs. Baseline 3 is appropriate when schema does the heavy lifting.

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 clearly states the verb ('Export') and resource ('structure data') with specific formatting purpose ('formatted for PyMOL visualization'). It distinguishes from obvious sibling 'export_for_chimerax' by specifying the target visualization tool, though doesn't explicitly differentiate from other export/download tools like 'download_structure' or 'batch_download'.

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?

No explicit guidance on when to use this tool versus alternatives is provided. The description implies usage for PyMOL visualization needs, but doesn't specify when to choose this over 'export_for_chimerax' or other structure retrieval tools, nor does it mention prerequisites or constraints beyond what's in the schema.

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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