Structure File Prep

Organization

ai4protein

structure_file_prep

Structure/sequence file preparation with VenusFactory file tools. Use for FASTA parsing, PDB chain extraction, PDB↔mmCIF conversion (MAXIT), apo checks, batch PDB→FASTA, and UniProt ID from RCSB metadata. Do NOT use for structure prediction (protein_structure_pipeline) or homology search.

Overview

Publisher	ai4protein
Repository	`VenusFactory2`
Skill name	`structure_file_prep`
Stars	255
Forks	37
Bundled files	Instructions only
License	Apache-2.0
Links	Skill source Repository Homepage

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.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by ai4protein on GitHub. Read the source before you install it.

Installation

Install the Structure File Prep 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/ai4protein/VenusFactory2/tree/main/src/agent/skills/structure_file_prep
Enable the skill in any chat where you want it available.

Store

Installed

Skills

Add skills

Import one or more skills from a public GitHub folder or a local .skill or .zip archive, or SKILL.md file.

From GitHub URLFrom .skill, .zip, or SKILL.md

GitHub repo or folder

https://github.com/ai4protein/VenusFactory2/tree/main/src/agent/skills/structure_file_prep

Points to a single skill folder, or any folder that contains multiple skills. Public repos only.

CancelContinue

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/ai4protein/VenusFactory2.git /tmp/VenusFactory2
mkdir -p .claude/skills
cp -r /tmp/VenusFactory2/src/agent/skills/structure_file_prep .claude/skills/structure_file_prep

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

Use it in TypingMind

Enable Structure File Prep 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 Structure File Prep 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 Structure File Prep 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.

Structure & Sequence File Prep

Project Tools (VenusFactory2)

Tool	Purpose
read_fasta	Parse multi-FASTA → headers/sequences
extract_uids_from_fasta	Pull UIDs from headers
uid_file_to_chunks	Chunk UID lists for batch jobs
pdb_chain_sequences	Per-chain sequences from PDB
get_seq_from_pdb_chain_a	Chain A sequence shortcut
pdb_dir_to_fasta	Directory of PDBs → FASTA
check_pdb_apo	Ligand-free / apo heuristic
maxit_structure_convert	`pdb2cif` / `cif2pdb` / `cif2mmcif` (needs MAXIT)
extract_uniprot_id_from_rcsb_metadata	UniProt from RCSB metadata JSON
unzip_archive / ungzip_file	Unpack downloads

Workflows

PDB → design/mutation ready

check_pdb_apo (if apo backbone required)
pdb_chain_sequences → choose designed chains
Optional maxit_structure_convert for format mismatches

RCSB metadata → UniProt → AlphaFold

download_rcsb_entry_metadata_by_pdb_id
extract_uniprot_id_from_rcsb_metadata
Hand off to alphafold_database / protein_structure_pipeline

Common mistakes

Hardcoding chain lengths without pdb_chain_sequences
Calling MAXIT strategies other than pdb2cif/cif2pdb/cif2mmcif
Feeding directories to tools that expect a single file path

Frequently asked questions

What does the Structure File Prep AI skill do?

Why use Structure File Prep on TypingMind?

Because you install it once and use it with any model. Structure File Prep 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 Structure File Prep in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/ai4protein/VenusFactory2/tree/main/src/agent/skills/structure_file_prep. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Structure File Prep?

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 Structure File Prep?

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

Is the Structure File Prep AI skill free?

Yes. It is published on GitHub by ai4protein under the Apache-2.0 license. 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

Structure & Sequence File Prep

Project Tools (VenusFactory2)

Workflows

PDB → design/mutation ready

RCSB metadata → UniProt → AlphaFold

Common mistakes

Frequently asked questions

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