PyMOL Wiki - User contributions [en]

Load Traj

2010-10-13T22:36:00Z

Yoyoq: /* NOTES */

'''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===
<source lang="python">
load_traj filename [,object [,state [,format [,interval [,average ]
[,start [,stop [,max [,selection [,image [,shift
]]]]]]]]]
</source>

===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===
*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.
*The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file.
*For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.

useful notes from the email list
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg04272.html

in one line convert dcd and psf to pdb :

catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd

===SEE ALSO===
[[Load]], [[defer_builds_mode]]

[[Category:Commands|Load Traj]]
[[Category:Performance|Load Traj]]
[[Category:States|Load Traj]]

Load Traj

2010-10-13T22:35:32Z

Yoyoq: /* NOTES */

'''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===
<source lang="python">
load_traj filename [,object [,state [,format [,interval [,average ]
[,start [,stop [,max [,selection [,image [,shift
]]]]]]]]]
</source>

===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===
*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.
*The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file.
*For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.

useful notes from the email list
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg04272.html

dcd and psf to pdb
catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd

===SEE ALSO===
[[Load]], [[defer_builds_mode]]

[[Category:Commands|Load Traj]]
[[Category:Performance|Load Traj]]
[[Category:States|Load Traj]]