“smooth” performs a window average of coordinate states.

smooth [ selection [, passes [, window [, first [, last [, ends]]]]]]

ends = 0 or 1: controls whether or not the end states are also smoothed using a weighted asymmetric window

This type of averaging is often used to suppress high-frequency vibrations in a molecular dynamics trajectory.

This function is not memory efficient. For reasons of flexibility, it uses two additional copies of every atomic coordinate for the calculation. If you are memory-constrained in visualizing MD trajectories, then you may want to use an external tool such as ptraj to perform smoothing before loading coordinates into PyMOL.

load_traj | cmd.smooth | commands