Difference between revisions of "Smooth"

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(NOTES)
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= NOTES =
 
= NOTES =
 
* This type of averaging is often used to suppress high-frequency vibrations in a molecular dynamics trajectory.
 
* 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.
+
* 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 =
 
= See Also =
 
*[[load_traj]]
 
*[[load_traj]]

Revision as of 18:05, 4 July 2011

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

See Also