Difference between revisions of "Smooth"
Jump to navigation
Jump to search
(→Usage) |
|||
| Line 12: | Line 12: | ||
* 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. | ||
Revision as of 15:42, 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.