Rcsb Pdb Skill

Community

makabaka007x

rcsb-pdb-skill

Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.

Overview

Publisher	makabaka007x
Repository	`cadd-skill`
Skill name	`rcsb-pdb-skill`
Stars	54
Forks	6
Bundled files	2
Links	Skill source Repository

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
2 bundled files
Scripts, templates, and references the model can read while it works. Files are read-only and never executed.
Open source
Published by makabaka007x on GitHub. Read the source before you install it.

Installation

Install the Rcsb Pdb Skill AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/makabaka007x/cadd-skill/tree/main/skills/rcsb-pdb-skill
Enable the skill in any chat where you want it available.

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/makabaka007x/cadd-skill.git /tmp/cadd-skill
mkdir -p .claude/skills
cp -r /tmp/cadd-skill/skills/rcsb-pdb-skill .claude/skills/rcsb-pdb-skill

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Rcsb Pdb Skill in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Rcsb Pdb Skill on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Rcsb Pdb Skill is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

Operating rules

Use scripts/rest_request.py for all RCSB PDB and Search API calls.
Use base_url=https://data.rcsb.org/rest/v1 for core metadata, https://search.rcsb.org/rcsbsearch/v2 for Search API, and https://www.rcsb.org for FASTA downloads.
Core entry or assembly lookups usually do not need max_items; Search API results are better with query pager rows around 10 and max_items=10.
Re-run requests in long conversations instead of relying on older tool output.
Treat displayed ... in tool previews as UI truncation, not literal request content.

Execution behavior

Return concise markdown summaries from the script JSON by default.
Prefer core metadata endpoints for focused lookups and Search API POST requests for discovery.
For FASTA downloads, use response_format=text so the script returns a short text_head unless raw output is requested.

Input

Read one JSON object from stdin.
Required fields: base_url, path
Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
Common RCSB patterns:
- {"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}
- {"base_url":"https://search.rcsb.org/rcsbsearch/v2","path":"query","method":"POST","json_body":{"query":{"type":"terminal","service":"full_text","parameters":{"value":"hemoglobin"}},"return_type":"entry","request_options":{"pager":{"start":0,"rows":10}}},"record_path":"result_set","max_items":10}
- {"base_url":"https://www.rcsb.org","path":"fasta/entry/4HHB/download","response_format":"text"}

Output

Success returns ok, source, path, method, status_code, warnings, and either compact records, a compact summary, or text_head.
Use raw_output_path when save_raw=true.
Failure returns ok=false with error.code and error.message.

Execution

bash
echo '{"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}' | python scripts/rest_request.py

References

No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.

Bundled files

The model reads these on demand while the skill is loaded. They are exposed as readable files and are never executed.

agents/openai.yaml1 KB
scripts/rest_request.py10 KB

Frequently asked questions

What does the Rcsb Pdb Skill AI skill do?

Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.

Why use Rcsb Pdb Skill on TypingMind?

Because you install it once and use it with any model. Rcsb Pdb Skill is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Rcsb Pdb Skill in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/makabaka007x/cadd-skill/tree/main/skills/rcsb-pdb-skill. TypingMind reads its SKILL.md and bundles its files and installs it as a skill you can enable per chat.

Which AI models can use Rcsb Pdb Skill?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Rcsb Pdb Skill?

As many as you like. As long as a model supports skills, you can use Rcsb Pdb Skill with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Rcsb Pdb Skill AI skill free?

It is published on GitHub by makabaka007x. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

Operating rules

Execution behavior

Input

Output

Execution

References

Bundled files

Frequently asked questions

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