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Difference between revisions of "Load Traj"
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===DESCRIPTION=== | ===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" | |
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| − | + | 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. | |
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===USAGE=== | ===USAGE=== | ||
| − | + | <source lang="python"> | |
| − | + | load_traj filename [,object [,state [,format [,interval [,average ] | |
| − | + | [,start [,stop [,max [,selection [,image [,shift | |
| − | + | ]]]]]]]]] | |
| − | + | </source> | |
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===PYMOL API=== | ===PYMOL API=== | ||
| − | + | <source lang="python"> | |
| − | + | 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]") | |
| − | + | </source> | |
===NOTES=== | ===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. | |
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===SEE ALSO=== | ===SEE ALSO=== | ||
| − | + | [[Load]] | |
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[[Category:Commands|load_traj]] | [[Category:Commands|load_traj]] | ||
Revision as of 13:46, 28 April 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.
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.