Commands

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 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:

• 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