Smooth performs a window average of coordinate states.
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
To see smooth in context see this example
- 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.