Quick Start

Get up and running with synth-pdb in 5 minutes.

Installation

=== "PyPI (Recommended)"

```bash
pip install synth-pdb
```

=== "From Source"

```bash
git clone https://github.com/elkins/synth-pdb.git
cd synth-pdb
pip install .
```

Your First Structure

Generate a simple 10-residue alpha helix:

synth-pdb --length 10 --conformation alpha --output my_first_helix.pdb

This creates a PDB file with: - ✅ Full atomic representation (backbone + side-chains + hydrogens) - ✅ Realistic B-factors and occupancy values - ✅ Proper bond geometry and angles

Visualize It

View your structure interactively in the browser:

synth-pdb --length 10 --conformation alpha --visualize

Add Physics

Generate a more realistic structure with energy minimization:

synth-pdb --length 20 --conformation alpha --minimize --output minimized.pdb

This uses OpenMM to: - Regularize bond lengths and angles - Resolve steric clashes - Apply implicit solvent effects

Next Steps

- :material-book-open-variant:{ .lg .middle } __First Structure Tutorial__ --- Detailed walkthrough of generating your first protein structure [:octicons-arrow-right-24: Start tutorial](first-structure.md) - :material-console:{ .lg .middle } __Command-Line Reference__ --- Complete reference of all available options and flags [:octicons-arrow-right-24: View reference](../guides/cli-reference.md) - :material-image-multiple:{ .lg .middle } __Examples Gallery__ --- Browse inspiring examples and copy-paste commands [:octicons-arrow-right-24: Explore gallery](../examples/gallery.md) - :material-robot:{ .lg .middle } __AI/ML Integration__ --- Learn how to use synth-pdb for machine learning workflows [:octicons-arrow-right-24: ML guide](../guides/ml-researchers.md)

Common Use Cases

Testing Bioinformatics Tools

# Generate a test dataset
synth-pdb --mode dataset --num-samples 100 --output ./test_data

Educational Demonstrations

# Show different secondary structures
synth-pdb --structure "1-10:alpha,11-20:beta" --visualize

NMR Data Generation

# Generate structure with synthetic NMR observables
synth-pdb --length 30 --gen-nef --gen-relax --output nmr_test.pdb

Synthetic Data Factories

For high-throughput AI training, synth-pdb includes a dedicated builder for multi-modal datasets:

# Generate 500 synchronized PDB, Cryo-EM, SAXS, and NMR samples
python3 scripts/build_multimodal_dataset.py --n 500 --output-dir my_ai_dataset

This factory leverages the 900x faster vectorized walker to produce labeled training data in minutes.

Getting Help

!!! question "Need help?"

- 📖 Check the [User Guides](../guides/beginners.md)
- 💬 Ask questions on [GitHub Discussions](https://github.com/elkins/synth-pdb/discussions)
- 🐛 Report bugs on [GitHub Issues](https://github.com/elkins/synth-pdb/issues)