Load traj: Difference between revisions
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===NOTES=== | ===NOTES=== | ||
You must first load a corresponding topology file before attempting to load a trajectory file. | *You must first load a corresponding topology file before attempting to load a trajectory file. | ||
*PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the [http://amber.scripps.edu/tutorials/basic/tutorial5/index.html ptraj] program first to do this. | |||
PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the | *The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file. | ||
The average option is not a running average. To perform this type of average, use the | |||
===SEE ALSO=== | ===SEE ALSO=== | ||
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[[Category:Commands|load_traj]] | [[Category:Commands|load_traj]] | ||
[[Category:Performance]] | |||
Revision as of 15:23, 23 September 2008
DESCRIPTION
load_traj reads trajectory files (currently just AMBER files). The file extension is used to determine the format. AMBER files must end in ".trj"
In newer builds of PyMOL (namely, version 1.0 or newer), several additional formats are accepted. CHARMM trajectories (".dcd") are also valid files and only require a structure to be loaded first while the trajectory file gets loaded as sequential states into the associated object. However, it should be noted that, unless the defer_builds_mode is set (to 3), loading a large trajectory may take up a lot of RAM.
USAGE
load_traj filename [,object [,state [,format [,interval [,average ]
[,start [,stop [,max [,selection [,image [,shift
]]]]]]]]]
PYMOL API
cmd.load_traj(filename,object='',state=0,format='',interval=1,
average=1,start=1,stop=-1,max=-1,selection='all',image=1,
shift="[0.0,0.0,0.0]")
NOTES
- You must first load a corresponding topology file before attempting to load a trajectory file.
- PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the ptraj program first to do this.
- The average option is not a running average. To perform this type of average, use the smooth command after loading the trajectory file.