PyMOL Wiki - User contributions [en]

User:Zachcp

2010-05-26T02:19:12Z

Zachcp:

A video I made using pymol for the molecular graphics: [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap]

Another video made for the Think Free Project. All of the molecular images are made in Pymol. [http://www.youtube.com/watch?v=eQWw6x3fLF0 Think Free]

Another video about the practice of structural biology. Many of the images are from Pymol. [http://www.youtube.com/watch?v=LVZJsBNLjV0 The Structural Biology Rap]

Copy

2010-02-24T23:57:13Z

Zachcp: /* User Comments/Examples */

'''copy''' creates a new object that is an identical copy of an existing object

===USAGE===
<source lang="python">
copy target, source
copy target = source # (DEPRECATED)
</source>

===PYMOL API===
<source lang="python">
cmd.copy(string target,string source)
</source>

===SEE ALSO===
[[Create|create]]

===User Comments/Examples===
[[Category:Commands|Copy]]

<source lang="python">
## will copy the object "trna" into six new objects with a number suffic
s = range(6)
for x in s:
cmd.copy("trna%s" %x, "trna")
</source>

User:Zachcp

2010-01-13T19:35:32Z

Zachcp:

User:Zachcp

2009-11-18T15:00:52Z

Zachcp: Created page with 'A video I made using pymol for the molecular graphics: [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap]'

A video I made using pymol for the molecular graphics: [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap]

Mset

2009-07-05T21:13:47Z

Zachcp: /* EXAMPLES */

===DESCRIPTION===
'''mset''' sets up a relationship between molecular states and movie frames. This makes it possible to control which states are shown in which frame.

===USAGE===
mset specification [ ,frame ]

===PYMOL API===
<source lang="python">
cmd.mset( string specification [, int frame] )
</source>

===EXAMPLES===
<source lang="python">
mset 1 // simplest case, one state -> one frame
mset 1 x10 // ten frames, all corresponding to state 1
mset 1 x30 1 -15 15 x30 15 -1
// more realistic example:
// the first thirty frames are state 1
// the next 15 frames pass through states 1-15
// the next 30 frames are of state 15
// the next 15 frames iterate back to state 1
</source>

<source lang="python">
cmd.mset("1 -%d" % cmd.count_states())
// this will create a one-to-one mapping of states to movie frames. useful for making movies from trajectory files.
</source>

===SEE ALSO===
[[Cmd mdo]], [[Cmd mplay]], [[Cmd mclear]]

[[Category:Commands|Mset]]
[[Category:States|Mset]]

Load Traj

2009-07-05T21:12:04Z

Zachcp: /* NOTES */

===DESCRIPTION===
'''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===
<source lang="python">
load_traj filename [,object [,state [,format [,interval [,average ]
[,start [,stop [,max [,selection [,image [,shift
]]]]]]]]]
</source>

===PYMOL API===
<source lang="python">
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]")
</source>

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

===SEE ALSO===
[[Load]], [[defer_builds_mode]]

[[Category:Commands|Load Traj]]
[[Category:Performance|Load Traj]]
[[Category:States|Load Traj]]

Select

2009-06-29T14:28:37Z

Zachcp: /* EXAMPLES */

===DESCRIPTION===
'''select''' creates a named selection from an atom selection. Selections are one of the most powerful aspects of PyMOL and learning to use selections well is paramount to quickly achieving your goals in PyMOL.

===USAGE===
select (selection)
select name, (selection)
select name = (selection) # (DEPRECATED)

===PYMOL API===
<source lang="python">
cmd.select(string name, string selection)
</source>

===EXAMPLES===
select near , (ll expand 8)
select near , (ll expand 8)
select bb, (name ca,n,c,o )
<source lang="python">
cmd.select("%s_%s"%(prefix,stretch), "none")
</source>

===NOTES===
Type '''help selections''' for more information about selections.

===SEE ALSO===
*[[Selection Algebra]]
*[[Property Selectors]]

[[Category:Commands|Select]]
[[Category:Selecting|Select]]