# Quickstart: `pdb2reaction all`

## Goal

Run the end-to-end workflow once from two full PDB structures.

## Prerequisites

- pdb2reaction installed (see [Installation](installation.md))
- Two PDB files (reactant R and product P) with **hydrogen atoms** already added
- The same atoms in the same order across all input PDB files

## Minimal command

```bash
pdb2reaction all -i 1.R.pdb 3.P.pdb -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' \
 --out-dir ./result_all
```

If you want post-processing in the same run:

```bash
pdb2reaction all -i 1.R.pdb 3.P.pdb -c 'SAM,GPP,MG' -l 'SAM:1,GPP:-3' \
 --tsopt --thermo --dft --out-dir ./result_all
```

## Expected output

A successful run produces a directory like:

```text
result_all/
├── summary.log                    # Human-readable summary
├── summary.json                   # Machine-readable results
├── path_opt/
│   ├── mep.pdb                    # Merged MEP trajectory
│   ├── energy_diagram_uma_all.png # Energy profile
│   ├── summary.json               # Path-opt results
│   └── post_seg_01/               # Post-processing (if --tsopt)
│       ├── ts/final_geometry.pdb
│       ├── irc/finished_irc.pdb
│       └── freq/
└── seg_01/                        # IRC-optimized R/TS/P structures
    ├── reactant.pdb
    ├── ts.pdb
    └── product.pdb
```

**What to check:**

1. `summary.log` — look for `status: success` and the barrier height (kcal/mol)
2. `seg_01/*.pdb` — open in PyMOL to verify the R/TS/P structures make chemical sense
3. `energy_diagram_*.png` — the energy profile should show a clear barrier

**Sample terminal output (successful run):**

```
[all] Elapsed for Whole Pipeline: 00:05:06.123
```

If `--tsopt` is enabled, you should also see:

```
[Imaginary modes] n=1  ([-425.9])
```

One imaginary mode with |frequency| > 100 cm⁻¹ indicates a valid TS.

## Tips

- `pdb2reaction all --help` shows core options; `pdb2reaction all --help-advanced` shows the full list.

## Next step

- Single-structure staged scan route: [Quickstart: `pdb2reaction scan`](quickstart-scan.md)
- TS optimization and validation: [Quickstart: `pdb2reaction tsopt`](quickstart-tsopt-freq.md)
- Full option reference: [all](all.md)
