From PyMOLWiki
Revision as of 14:43, 28 August 2015 by OsvaldoMartin (talk | contribs) (See Also)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

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.

See Also

Load_Traj, protect.