This is a read-only mirror of pymolwiki.org
Difference between revisions of "Load Traj"
Jump to navigation
Jump to search
m (13 revisions) |
(description, examples) |
||
| Line 1: | Line 1: | ||
| − | '''load_traj''' | + | '''load_traj''' loads a trajectory as "states" into an already loaded molecular object. |
| − | + | Since version 1.0, PyMOL uses the [http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ 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 == | ||
| − | |||
<source lang="python"> | <source lang="python"> | ||
load_traj filename [,object [,state [,format [,interval [,average ] | load_traj filename [,object [,state [,format [,interval [,average ] | ||
[,start [,stop [,max [,selection [,image [,shift | [,start [,stop [,max [,selection [,image [,shift | ||
| + | [, plugin ] | ||
]]]]]]]]] | ]]]]]]]]] | ||
</source> | </source> | ||
| − | === | + | == 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 == | ||
| + | |||
| + | <syntaxhighlight lang="python"> | ||
| + | # 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 | ||
| + | </syntaxhighlight> | ||
| − | === | + | == 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://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. | *The average option is not a running average. To perform this type of average, use the [[smooth]] command after loading the trajectory file. | ||
| Line 33: | Line 52: | ||
catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd | catdcd -o all.pdb -otype pdb -s autopsf.psf -stype psf out.dcd | ||
| − | == | + | == See Also == |
[[Load]], [[defer_builds_mode]] | [[Load]], [[defer_builds_mode]] | ||
Revision as of 17:47, 8 February 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