# How to wrap trajectories

## Goal

Re-image atoms into the central periodic box so that molecules appear whole rather than split across box boundaries.

## Minimal example

```python
from moleculekit.molecule import Molecule

mol = Molecule("topology.psf")
mol.read("trajectory.xtc")

# Wrap and center the box on the protein
mol.wrap("protein")
```

## Parameters that matter

| Parameter | Type | Default | What it does |
|---|---|---|---|
| `wrapsel` | `str` | `"all"` | Atom selection that defines the center of the wrapping box |
| `fileBonds` | `bool` | `True` | Use bonds from the loaded topology file |
| `guessBonds` | `bool` | `False` | Fall back to distance-based bond guessing if `fileBonds` yields too few bonds |

## Common variations

```python
# Wrap around a ligand instead of the whole protein
mol.wrap("resname LIG")
```

```python
# Topology file has complete bonds — skip guessing for speed
mol.wrap("protein", guessBonds=False)
```

## Gotchas

- Wrapping requires a valid `mol.box` array (one column per frame). If `mol.box` is all zeros, `wrap` logs a warning and returns without modifying coordinates — the original `mol` is unchanged.
- Non-orthorhombic (triclinic) boxes use `mol.boxangles` in addition to `mol.box`; make sure both are read from the trajectory.
- `wrap` operates on all frames in place.
- Molecules that are already centered in the box will be re-wrapped (the operation is applied regardless).

## See also

- [How to read a trajectory](read-a-trajectory.md)
- [How to align structures](align-structures.md)