Setup
Claude Code skills for protein design
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What its author says it does
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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.
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SKILL.md
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Setup Guide
Help users get their environment ready to run protein design tools.
Quick checklist
Run through this checklist when a user encounters setup issues:
| 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 |
Diagnosing issues
Error: "modal: command not found"
Cause: Modal CLI not installed.
Fix:
pip install modal
Then restart the terminal or run hash -r.
Error: "Permission denied" or "Unauthorized"
Cause: Modal not authenticated.
Fix:
modal setup
This opens a browser. Click "Authorize" to complete authentication.
Error: "No such file or directory: modal_boltzgen.py"
Cause: biomodals repository not cloned or not in correct directory.
Fix:
git clone https://github.com/hgbrian/biomodals
cd biomodals
Error: "uvx: command not found"
Cause: uvx is an optional wrapper from the uv package. It's not required.
Fix: Run modal directly (recommended):
modal run modal_boltzgen.py --help
Or install uv if you prefer using uvx:
pip install uv
Full setup steps
Step 1: Install Modal CLI
pip install modal
Verify: modal --version
Step 2: Authenticate Modal
modal setup
This opens a browser. Click "Authorize".
Verify: modal token show
Step 3: Clone biomodals
git clone https://github.com/hgbrian/biomodals
cd biomodals
Verify: ls modal_*.py should show files like modal_boltzgen.py
Step 4: Test the Setup
cd biomodals
modal run modal_boltzgen.py --help
Expected: Usage instructions appear showing --input-yaml, --protocol, --num-designs options.
Common workflows after setup
Once setup is complete, users can:
cd biomodals
# Design binders with BoltzGen (requires YAML config)
modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50
# Generate backbones with RFdiffusion (official repo, not biomodals)
python run_inference.py inference.input_pdb=target.pdb contigmap.contigs=[A1-150/0 70-100] inference.num_designs=100
# Validate with Chai
modal run modal_chai1.py --input-faa designs.fasta
GPU selection
Set GPU with environment variable:
GPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50
GPU=A100 modal run modal_chai1.py --input-faa complex.fasta
| GPU | VRAM | Best For |
|---|---|---|
| T4 | 16GB | ProteinMPNN, ESM |
| A10G | 24GB | RFdiffusion, Chai |
| L40S | 48GB | BoltzGen, BindCraft |
| A100 | 40-80GB | Large complexes |
Modal free tier
Modal offers $30/month in free credits - enough for:
- ~500 BoltzGen designs
- ~2000 RFdiffusion backbones
- ~1000 Chai predictions
Full documentation: See Getting started