Loading Trajectories¶

Basic Usage¶

/traj load topology.pdb trajectory.xtc

This loads the topology (atom definitions) and trajectory (coordinates over time) into the viewer.

Supported Formats¶

Format	Extension	Description
XTC	`.xtc`	GROMACS compressed trajectory
TRR	`.trr`	GROMACS full-precision trajectory
DCD	`.dcd`	CHARMM/NAMD trajectory
PDB	`.pdb`	Multi-model PDB
CIF	`.cif`	Multi-model mmCIF

Loading Options¶

From Files¶

/traj load topology.pdb trajectory.xtc

Load All Trajectories in a Directory¶

/traj loadall /path/to/md_runs/

From Atlas¶

If using the Atlas integration, trajectories stored remotely can be loaded:

/atlas fetch TRAJ_ID

After Loading¶

Once a trajectory is loaded, the frame slider and playback controls become available:

/traj info          # Show frame count, time range
/traj frame 50      # Jump to frame 50
/traj play          # Start playback
/traj stop          # Pause playback

Multi-Structure Trajectories¶

Each trajectory is associated with its structure via the session system. When you activate a different structure, its trajectory state (current frame, playback speed) is preserved.