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Revision as of 03:47, 7 March 2016
load_traj loads a trajectory as "states" into an already loaded molecular object.
Since version 1.0, PyMOL uses the Molfile Plugin backend, which supports a variety of trajectory file formats. Older versions only supported the ascii AMBER format (".trj" file extension).
Loading a large trajectory may take up a lot of RAM, unless the defer_builds_mode is set to 3.
Usage
load_traj filename [,object [,state [,format [,interval [,average ]
[,start [,stop [,max [,selection [,image [,shift
[, plugin ]
]]]]]]]]]
Arguments
- filename = str: trajectory file path
- object = str: name of the molecular object where the trajectory should be appended as states {default: guess from filename}
- state = int: object state where to start appending states. To discard the currently loaded coordinates, use state=1. To append new states, use state=0 {default: 0}
- format = str: specify file type instead of guessing from file extension (only affects AMBER .trj format, use "plugin" argument for Molfile Plugin types) {default: }
Examples
# topology from PDB file, trajectory from DCD file
load sampletrajectory.pdb
load_traj sampletrajectory.dcd
# gromacs trajectory, using "mytraj" as object name
load sampletrajectory.gro, mytraj
load_traj sampletrajectory.xtc, mytraj
# playing through states, memory optimized (but eventually slower)
set defer_builds_mode, 3
mplay
Notes
- 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
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10266.html
in one line convert dcd and psf to pdb :
catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd