Load Traj - Revision history

Cchem: 1 revision

2018-03-05T03:14:56Z

1 revision

Hongbo zhu: /* Notes */ fix broken link to ptraj: it is now cpptraj!

2018-02-22T15:50:21Z

Notes: fix broken link to ptraj: it is now cpptraj!

Cchem: 1 revision

2016-04-04T00:22:29Z

1 revision

Speleo3: desmond example

2016-03-31T12:41:26Z

desmond example

Bell: 1 revision

2016-03-07T03:47:39Z

1 revision

Speleo3: description, examples

2016-02-08T17:47:25Z

description, examples

Pyadmin: 13 revisions

2014-03-28T01:52:57Z

13 revisions

Esguerra: /* NOTES */

2012-06-26T16:02:43Z

NOTES

Esguerra: /* NOTES */

2012-06-26T16:02:24Z

NOTES

Esguerra at 16:02, 26 June 2012

2012-06-26T16:02:03Z

@@ Line 42: / Line 42: @@
 == 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.
 *For quickly viewing Trajectories as a movie, use the [[mset]] command to map each state to a movie frame.

@@ Line 31: / Line 31: @@
 load      sampletrajectory.gro, mytraj
 load_traj sampletrajectory.xtc, mytraj
 # playing through states, memory optimized (but eventually slower)

@@ Line 1: / Line 1: @@
-'''load_traj''' reads trajectory files (currently just AMBER files).  The file extension is used to determine the format.  AMBER files must end in ".trj"
+'''load_traj''' loads a trajectory as "states" into an already loaded molecular object.
-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.
+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).
 <source lang="python">
 load_traj filename [,object [,state [,format [,interval [,average ]
                     [,start [,stop [,max [,selection [,image [,shift
                     ]]]]]]]]]
 </source>
-===PYMOL API===
+== Arguments ==
-<source lang="python">
-cmd.load_traj(filename,object='',state=0,format='',interval=1,
+* '''filename''' = str: trajectory file path
-           average=1,start=1,stop=-1,max=-1,selection='all',image=1,
+* '''object''' = str: name of the molecular object where the trajectory should be appended as states {default: guess from filename}
-           shift="[0.0,0.0,0.0]")
+* '''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}
-</source>
+* '''format''' = str: specify file type instead of guessing from file extension (only affects AMBER .trj format, use "plugin" argument for Molfile Plugin types) {default: }
-===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.
 *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
-===SEE ALSO===
+== See Also ==
 [[Load]], [[defer_builds_mode]]

@@ Line 23: / Line 23: @@
 *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
+useful notes from the email list:
 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg04272.html
 <br/>

@@ Line 25: / Line 25: @@
 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

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