Load traj
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.
- 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