Commands: Difference between revisions

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Commands are functions in pymol that are used for viewing, manipulating, and storing molecules.
Commands are functions in pymol that are used for viewing, manipulating, and storing molecules.
The PyMOLWiki has a complete list of commands in PyMOL.  Just check out the [[:Category:Commands|Commands' category]] page.


You can get a list of some common commands by typing "help commands" into the pymol command line. Typing this in to version 1.1r1 returns the following:
You can get a list of some common commands by typing "help commands" into the pymol command line. Typing this in to version 1.1r1 returns the following:


*INPUT/OUTPUT
<code>
**[[load]]
    INPUT/OUTPUT load     save     delete   quit
**[[save]]
    VIEW         turn     move     clip     rock
**[[delete]]
                  show     hide     enable   disable
**[[quit]]
                  reset     refresh   rebuild  
 
                  zoom     origin   orient  
*VIEW
                  view     get_view set_view
**[[turn]]
    MOVIES       mplay     mstop     mset     mdo
**[[move]]
                  mpng     mmatrix   frame
**[[clip]]
                  rewind   middle   ending
**[[rock]]
                  forward   backward
**[[show]]
    IMAGING       png       mpng
**[[hide]]
    RAY TRACING   ray      
**[[enable]]
    MAPS         isomesh   isodot
**[[disable]]
    DISPLAY       cls       viewport splash  
**[[reset]]
    SELECTIONS   select   mask  
**[[refresh]]
    SETTINGS     set       button
**[[rebuild]]
    ATOMS         alter     alter_state  
**[[zoom]]
    EDITING       create   replace   remove   h_fill   remove_picked
**[[origin]]
                  edit     bond     unbond   h_add   fuse      
**[[orient]]
                  undo     redo     protect   cycle_valence attach
**[[view]]
    FITTING       fit       rms       rms_cur   pair_fit
**[[get_view]]
                  intra_fit intra_rms intra_rms_cur  
**[[set_view]]
    COLORS       color     set_color
 
    HELP         help     commands
*MOVIES
    DISTANCES     dist       
**[[mplay]]
    STEREO       stereo
**[[mstop]]
    SYMMETRY     symexp
**[[mset]]
    SCRIPTS       @         run
**[[mdo]]
    LANGUAGE     alias     extend
**[[mpng]]
</code>
**[[mmatrix]]
**[[frame]]
**[[rewind]]
**[[middle]]
**[[ending]]
**[[forward]]
**[[backward]]
 
*IMAGING
**[[png]]
**[[mpng]]
 
*RAY TRACING
**[[ray]]
 
*MAPS
**[[isomesh]]
**[[isodot]]
 
*DISPLAY
**[[cls]]
**[[viewport]]
**[[splash]]
 
*SELECTIONS
**[[select]]
**[[mask]]
 
*SETTINGS
**[[set]]
**[[button]]
 
*ATOMS
**[[alter]]
**[[alter_state]]
 
*EDITING
**[[create]]
**[[replace]]
**[[remove]]
**[[h_fill]]
**[[remove_picked]]
**[[edit]]
**[[bond]]
**[[unbond]]
**[[h_add]]
**[[fuse]]
**[[undo]]
**[[redo]]
**[[protect]]
**[[cycle_valence]]
**[[attach]]
 
*FITTING
**[[fit]]
**[[rms]]
**[[rms_cur]]
**[[pair_fit]]
**[[intra_fit]]
**[[intra_rms]]
**[[intra_rms_cur]]
 
*COLORS
**[[color]]
**[[set_color]]
 
*HELP
**[[help]]
**[[commands]]
 
*DISTANCES
**[[dist]]      
 
*STEREO
**[[stereo]]
 
*SYMMETRY
**[[symexp]]
 
*SCRIPTS
**[[@]]
**[[run]]
 
*LANGUAGE
**[[alias]]
**[[extend]]


[[Category:Commands]]
[[Category:Commands]]

Revision as of 06:44, 27 April 2009

Commands are functions in pymol that are used for viewing, manipulating, and storing molecules.

You can get a list of some common commands by typing "help commands" into the pymol command line. Typing this in to version 1.1r1 returns the following: 

   INPUT/OUTPUT  load      save      delete    quit
   VIEW          turn      move      clip      rock
                 show      hide      enable    disable
                 reset     refresh   rebuild   
                 zoom      origin    orient   
                 view      get_view  set_view
   MOVIES        mplay     mstop     mset      mdo
                 mpng      mmatrix   frame
                 rewind    middle    ending
                 forward   backward
   IMAGING       png       mpng
   RAY TRACING   ray       
   MAPS          isomesh   isodot
   DISPLAY       cls       viewport  splash    
   SELECTIONS    select    mask   
   SETTINGS      set       button
   ATOMS         alter     alter_state 
   EDITING       create    replace   remove    h_fill   remove_picked
                 edit      bond      unbond    h_add    fuse       
                 undo      redo      protect   cycle_valence  attach
   FITTING       fit       rms       rms_cur   pair_fit  
                 intra_fit intra_rms intra_rms_cur   
   COLORS        color     set_color
   HELP          help      commands
   DISTANCES     dist      
   STEREO        stereo
   SYMMETRY      symexp
   SCRIPTS       @         run
   LANGUAGE      alias     extend

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