Smooth

Overview

Smooth performs a window average of coordinate states.

Usage

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

# for example, smooth and object with 30 passes and
# a window size of 100.
smooth myObj, 30, 100

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

NOTES

• 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, hen you may want to use an external tool such as ptraj to perform smoothing before loading coordinates into PyMOL.

See Also

• load_traj
• To see this in action, see protect.