setup

name	setup
description	First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.
license	MIT
category	utilities
tags	["setup","onboarding","installation"]
source	https://github.com/adaptyvbio/protein-design-skills

Setup Guide

Quick Checklist

Step	Check	Fix
1. Modal CLI	modal --version	pip install modal
2. Modal auth	modal token show	modal setup
3. biomodals	ls biomodals/modal_*.py	git clone https://github.com/hgbrian/biomodals
4. Test	cd biomodals && modal run modal_boltzgen.py --help	See troubleshooting

Full Setup Steps

Step 1: Install Modal CLI

pip install modal

Step 2: Authenticate Modal

modal setup
# Opens browser → click "Authorize"

Verify: modal token show

Step 3: Clone biomodals

git clone https://github.com/hgbrian/biomodals
cd biomodals

Step 4: Test

modal run modal_boltzgen.py --help

Common Errors

Error	Cause	Fix
modal: command not found	Not installed	pip install modal
Permission denied	Not authenticated	modal setup
No such file: modal_boltzgen.py	Wrong directory	cd biomodals
uvx: command not found	Optional wrapper	Use modal run directly

GPU Selection

GPU=T4 modal run modal_proteinmpnn.py ...  # 16GB, ProteinMPNN/ESM
GPU=A10G modal run modal_chai1.py ...      # 24GB, Chai/Boltz
GPU=L40S modal run modal_boltzgen.py ...   # 48GB, BoltzGen/BindCraft
GPU=A100 modal run modal_bindcraft.py ...  # 40-80GB, BindCraft/large complexes

Modal Free Tier

$30/month in free credits — enough for:

• ~500 BoltzGen designs
• ~200 BindCraft designs
• ~1000 Chai predictions