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#

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#

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

# 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#