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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