rfdiffusion

Files (4)

• SKILL.md
• binder-walkthrough.md · examples/
• hotspot-selection.md · references/
• parameters.md · references/

SKILL.md (first lines)

# RFdiffusion Backbone Generation

## Prerequisites

| Requirement | Minimum | Recommended |
|-------------|---------|-------------|
| Python | 3.9+ | 3.10 |
| CUDA | 11.7+ | 12.0+ |
| GPU VRAM | 16GB | 24GB (A10G) |
| RAM | 16GB | 32GB |

## How to run

> **First time?** See [Installation Guide](../../docs/installation.md) to set up Modal and biomodals.

### Option 1: Modal (recommended)
```bash
# Clone biomodals
git clone https://github.com/hgbrian/biomodals && cd biomodals

# Basic binder design
modal run modal_rfdiffusion.py \
  --pdb target.pdb \
  --contigs "A1-150/0 70-100" \
  --hotspot "A45,A67,A89" \
  --num-designs 100

# With custom GPU/timeout
GPU=A100 TIMEOUT=60 modal run modal_rfdiffusion.py \
  --pdb target.pdb \
  --contigs "A1-150/0 70-100" \
  --num-designs 100
```

**GPU**: A10G (24GB) | **Timeout**: 30min default

### Option 2: Local installation
```bash
# Clone and install
git clone https://github.com/RosettaCommons/RFdiffusion.git
cd RFdiffusion && pip install -e .

# Download weights
wget http://files.ipd.uw.edu/pub/RFdiffusion/models/Complex_base_ckpt.pt

# Run inference
python run_inference.py \
  inference.input_pdb=target.pdb \
  contigmap.contigs=[A1-150/0 70-100] \
  ppi.hotspot_res=[A45,A67,A89] \
  inference.num_designs=100
```

## Config Schema (Hydra)

### Contigmap Syntax
```bash
# De novo single chain (50-100 residues)
contigmap.contigs=[50-100]

# Binder + target (A = target chain, fixed with /0)
contigmap.contigs=[A1-150/0 70-100]

# Motif scaffolding (preserve residues, /0 = fixed)
contigmap.contigs=[20-40/0 A10-30/0 20-40]

# Multi-chain binder
contigmap.contigs=[A1-100/0 B1-100/0 60-80]

# Variable length ranges
contigmap.contigs=[A1-150/0 50-100]  # Binder 50-100 AA
```

### Hotspot Specification
```bash
# Residues for interface (chain + resnum, no spaces)
ppi.hotspot_res=[A45,A67,A89]
```

## Common mistakes

### Contig Syntax
✅ **Correct**:
```bash
contigmap.contigs=[A1-150/0 70-100]  # Target fixed (/0), binder variable
```

❌ **Wrong**:
```bash
contigmap.contigs=[A1-150 70-100]    # Missing /0 - target will move!
contigmap.contigs="A1-150/0 70-100"  # Quotes break parsing
contigmap.contigs=[A1-150/0, 70-100] # Comma breaks parsing
```

### Hotspot Residues
✅ **Correct**:
```bash
ppi.hotspot_res=[A45,A67,A89]        # Chain letter + residue number
```

❌ **Wrong**:
```bash
ppi.hotspot_res=[45,67,89]           # Missing chain letter
ppi.hotspot_res=[A45, A67, A89]      # Spaces break parsing
ppi.hotspot_res="A45,A67,A89"        # Quotes break parsing
```

### Complete Parameter Reference

#### Core Parameters
| Parameter | Default | Range | Description |
|-----------|---------|-------|-------------|
| `inference.num_designs` | 10 | 1-10000 | Number of designs to generate |
| `inference.input_pdb` | - | path | Target structure file |
| `inference.output_prefix` | output | string | Output filename prefix |
| `diffuser.T` | 50 | 20-200 | Diffusion timesteps |
| `denoiser.noise_scale_ca` | 1.0 | 0.0-2.0 | CA atom noise (0.5-0.8 = conservative) |
| `denoiser.noise_scale_frame` | 1.0 | 0.0-2.0 | Frame noise |
| `inference.ckpt_override_path` | - | path | Model checkpoint |

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