Load traj: Difference between revisions
No edit summary |
No edit summary |
||
| Line 2: | Line 2: | ||
'''load_traj''' reads trajectory files (currently just AMBER files). The file extension is used to determine the format. AMBER files must end in ".trj" | '''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 ( | 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=== | ===USAGE=== | ||
| Line 26: | Line 26: | ||
===SEE ALSO=== | ===SEE ALSO=== | ||
[[Load]] | [[Load]], [[defer_builds_mode]] | ||
[[Category:Commands|load_traj]] | [[Category:Commands|load_traj]] | ||
Revision as of 16:47, 10 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.