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“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.

See Also

command/smooth.txt · Last modified: 2013/08/19 21:01 (external edit)