Smooth: Difference between revisions
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(Created page with '= Overview = Smooth performs a window average of coordinate states. = Usage = <source lang="python"> smooth [ selection [, passes [, window [, first [, last [, ends]]]]]] ...') |
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[[Smooth]] performs a window average of coordinate states. | [[Smooth]] performs a window average of coordinate states. | ||
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* ends = 0 or 1: controls whether or not the end states are also smoothed using a weighted asymmetric window | * 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 [http://www.pymolwiki.org/index.php/Protect#Example example] | |||
= 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, | * 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]], [[protect]]. | ||
[[Category:Commands]] | [[Category:Commands|Smooth]] | ||
[[Category:Performance]] | [[Category:Performance|Smooth]] | ||
Latest revision as of 14:43, 28 August 2015
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
To see smooth in context see this example
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.