Difference between revisions of "Load traj"

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m (Speleo3 moved page Load Traj to Load traj: lowercase)
 
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load      sampletrajectory.gro, mytraj
 
load      sampletrajectory.gro, mytraj
 
load_traj sampletrajectory.xtc, mytraj
 
load_traj sampletrajectory.xtc, mytraj
 +
 +
# desmond trajectory
 +
load      sample-out.cms, mytraj
 +
load_traj sample_trj/clickme.dtr, mytraj
  
 
# playing through states, memory optimized (but eventually slower)
 
# playing through states, memory optimized (but eventually slower)
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== Notes ==
 
== Notes ==
*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.
+
*PyMOL does not know how to wrap the truncated octahedron used by Amber You will need to use the [http://ambermd.org/tutorials/analysis/tutorial0/index.htm cpptraj] 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.
 
*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.
 
*For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.

Latest revision as of 06:17, 25 February 2019

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

# desmond trajectory
load      sample-out.cms, mytraj
load_traj sample_trj/clickme.dtr, 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 cpptraj 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

See Also

Load, defer_builds_mode