Align Trajectory

Trajectories obtained from molecular dynamics, scans or other simulations usually contain overall translations and rotations of the molecule, which hide the internal motions of interest. The Align Trajectory tool removes these motions by superposing every frame of a trajectory onto a reference frame, using a least-squares fit (Kabsch algorithm). Only the atoms of the chosen subset are used to compute the fit, but the whole system is moved.

To open the tool:

• Open the Main Menu.

• Go to Analysis.

• Select Align Trajectory.

The options of the Align Trajectory window (Figure 1, below) are:

• System / Coordinates: the system and the coordinate object (trajectory) that will be aligned.

• By: the atoms used to compute the superposition: Protein (all heavy atoms of protein residues), Backbone (N, CA, C, O), Backbone subset (N, CA, C), C-alpha only, or Current Selection (the atoms selected in the 3D view).

• Reference: the index of the reference frame. Frames are counted from 0, so the default value (0) uses the first frame.

• Ignore Hydrogens: hydrogen atoms are left out of the fit, which only uses heavy atoms.

Click Align to run. The frames of the selected object are replaced by the aligned frames and the view returns to the first frame. Since the original coordinates are overwritten, save or export the trajectory first if you need to keep them.

Aligning the trajectory is recommended before visual inspection and before structural analyses such as the RMSD Tool or RMSF Analysis. For periodic systems, run Reimaging (Wrapping) first, so that molecules split across the box boundaries do not distort the fit.