{"id":"5611a963-5dc0-49b8-81e6-56e1a6a10fcf","shortId":"FJ27yq","kind":"skill","title":"setup","tagline":"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, ","description":"# Setup Guide\n\nHelp users get their environment ready to run protein design tools.\n\n## Quick checklist\n\nRun through this checklist when a user encounters setup issues:\n\n| Step | Check | Fix |\n|------|-------|-----|\n| 1. Modal CLI | `modal --version` | `pip install modal` |\n| 2. Modal auth | `modal token show` | `modal setup` |\n| 3. biomodals | `ls biomodals/modal_*.py` | `git clone https://github.com/hgbrian/biomodals` |\n| 4. Test | `cd biomodals && modal run modal_boltzgen.py --help` | See troubleshooting |\n\n## Diagnosing issues\n\n### Error: \"modal: command not found\"\n\n**Cause**: Modal CLI not installed.\n\n**Fix**:\n```bash\npip install modal\n```\n\nThen restart the terminal or run `hash -r`.\n\n### Error: \"Permission denied\" or \"Unauthorized\"\n\n**Cause**: Modal not authenticated.\n\n**Fix**:\n```bash\nmodal setup\n```\n\nThis opens a browser. Click \"Authorize\" to complete authentication.\n\n### Error: \"No such file or directory: modal_boltzgen.py\"\n\n**Cause**: biomodals repository not cloned or not in correct directory.\n\n**Fix**:\n```bash\ngit clone https://github.com/hgbrian/biomodals\ncd biomodals\n```\n\n### Error: \"uvx: command not found\"\n\n**Cause**: `uvx` is an optional wrapper from the `uv` package. It's not required.\n\n**Fix**: Run modal directly (recommended):\n```bash\nmodal run modal_boltzgen.py --help\n```\n\nOr install uv if you prefer using uvx:\n```bash\npip install uv\n```\n\n## Full setup steps\n\n### Step 1: Install Modal CLI\n\n```bash\npip install modal\n```\n\nVerify: `modal --version`\n\n### Step 2: Authenticate Modal\n\n```bash\nmodal setup\n```\n\nThis opens a browser. Click \"Authorize\".\n\nVerify: `modal token show`\n\n### Step 3: Clone biomodals\n\n```bash\ngit clone https://github.com/hgbrian/biomodals\ncd biomodals\n```\n\nVerify: `ls modal_*.py` should show files like `modal_boltzgen.py`\n\n### Step 4: Test the Setup\n\n```bash\ncd biomodals\nmodal run modal_boltzgen.py --help\n```\n\nExpected: Usage instructions appear showing `--input-yaml`, `--protocol`, `--num-designs` options.\n\n## Common workflows after setup\n\nOnce setup is complete, users can:\n\n```bash\ncd biomodals\n\n# Design binders with BoltzGen (requires YAML config)\nmodal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50\n\n# Generate backbones with RFdiffusion\nmodal run modal_rfdiffusion.py --pdb target.pdb --contigs \"A1-150/0 70-100\" --num-designs 100\n\n# Validate with Chai\nmodal run modal_chai1.py --input-faa designs.fasta\n```\n\n## GPU selection\n\nSet GPU with environment variable:\n\n```bash\nGPU=A10G modal run modal_rfdiffusion.py --pdb target.pdb --contigs \"A1-100/0 50-80\" --num-designs 10\nGPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50\nGPU=A100 modal run modal_chai1.py --input-faa complex.fasta\n```\n\n| GPU | VRAM | Best For |\n|-----|------|----------|\n| T4 | 16GB | ProteinMPNN, ESM |\n| A10G | 24GB | RFdiffusion, Chai |\n| L40S | 48GB | BoltzGen, BindCraft |\n| A100 | 40-80GB | Large complexes |\n\n## Modal free tier\n\nModal offers $30/month in free credits - enough for:\n- ~500 BoltzGen designs\n- ~2000 RFdiffusion backbones\n- ~1000 Chai predictions\n\n---\n\n**Full documentation**: See [Installation 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