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scene makes it possible to save and restore multiple scenes scene within a single session. A scene consists of the view, all object activity information, all atom-wise visibility, color, representations, and the global frame index.


scene [ key [, action [, message [, view [, color [, active [, rep
    [, frame [, animate [, new_key ]]]]]]]]]]


  • key = string, new, auto, or *: use new for an automatically numbered new scene, use auto for the current scene (if one exists), and use * for all scenes (clear and recall actions only).
  • action = store, recall, insert_after, insert_before, next, previous, update, rename, clear or append: (default = recall). If rename, then a new_key argument must be explicitly defined.
  • message = string: a text message to display with the scene.
  • view = 1 or 0: controls whether the view is stored {default: 1}
  • color = 1 or 0: controls whether colors are stored {default: 1}
  • active = 1 or 0: controls whether activity (objects enabled/disabled) is stored {default: 1}
  • rep = 1 or 0: controls whether the representations are stored {default: 1}
  • frame = 1 or 0: controls whether the frame is stored {default: 1}
  • animate = float: animation duration in seconds {default: scene_animation_duration}
  • new_key = string: the new name for the scene

Using Scene

The Scene command has quite a few actions/options that can be enabled by using the mouse and the keyboard through the usual Scene command or hot-keys. Also, you can shift the scenes around using the new Scene_buttons and just dragging the scene names.

Storing scenes

# store this scene in the next spot, giving it the default name.
scene auto, store

has the hot-key equivalent of CTRL-PageDown (FN+CTRL+DownArrow on the Mac). Try turning on Scene_Buttons and then doing CTRL-PageDown; see the scene buttons popping up?

Scenes as Movies

If you desire to make a movie that only has camera changes or representation changes, then scenes are your friend. Simply setup each view and then when ready you can do Scene->Store from the PyMOL menus (or scene auto, store on the command line or the third method Ctrl+PgDn (Fn+Ctrl+DownArrow on the Mac)). Do this for each view you setup. Once done, you can scroll through your scenes by pushing PgUp/PgDn. PyMOL automatically interpolates when you use the PgUp/PgDn buttons, so you get the desired smooth transitions. Mix this with AxPyMOL and you have movies in PowerPoint with very little work.

Auto-play through Scenes

With this simple trick you can auto-play through scenes. This is similar to "Movie > Program > Scene Loop" but uses only a single frame.

cmd.set('movie_fps', 1.0 / 5.0)
cmd.mdo(1, 'scene auto, next')


Simple Examples.

scene F1, store
scene F2, store, This view shows you the critical hydrogen bond.
scene F1
scene F2

scene *

This example shows how to use scenes in a movie!


# This script demonstrates one way of creating a movie from scenes.
# It assumes that we have three scenes, each running for 10 seconds
# (300 frames apiece) including 2-second transitions.

# 1) Load or create content for three scenes (this could just as easily
#    come from a session file).

load $TUT/1hpv.pdb
turn x,180
as cartoon
scene 001, store

show sticks, organic
orient organic
scene 002, store

hide cartoon
show lines, byres organic expand 5
turn x,45
turn y,45
scene 003, store

# 2) Specify a 30-second movie -- state 1, 900 frames at 30 frames per second.

mset 1 x900

# 3) Program scene matrices as movie views at appopriate frames
#    and also add y-axis rocking between scenes.

scene 001, animate=0
mview store, 1
mview store, 240

turn y,-30
mview store, 70
turn y,60
mview store, 170

scene 002, animate=0
mview store, 300
mview store, 540

turn y,-30
mview store, 370
turn y,60
mview store, 470

scene 003, animate=0
mview store, 600
mview store, 840

turn y,-30
mview store, 670
turn y,60
mview store, 770

# 4) Now interpolate the movie camera.

mview interpolate
mview smooth
mview smooth

# 5) Activate scene content at the appropriate movie frames.
mdo 1: scene 001, view=0, quiet=1
mdo 240: scene 002, view=0, quiet=1
mdo 540: scene 003, view=0, quiet=1
mdo 840: scene 001, view=0, quiet=1

# 6) Force frame 1 content to load.


# 6) And play the movie.



cmd.scene(str key='auto', str action='recall', str-or-list message=None, bool view=1, bool color=1,
    bool active=1, bool rep=1, bool frame=1, float animate=-1, str new_key=None)


  • To scroll through your frames, as in a presentation, just use the PG-UP and PG-DN keys. Very handy.
  • Scenes F1 through F12 are automatically bound to function keys provided that "set_key" hasn't been used to redefine the behaviour of the respective key.
  • If you have a script that modifies the representation of the molecules and stores them, quickly, then the stored frames may not be up to date. I suggest calling "refresh" between the commands.

See Also

View, Set_View, Get_View, Movie_from_scenes


Add support for save/restore of a certain global and object-and-state specific settings, such as: state, surface_color, ribbon_color, stick_color, transparency, sphere_transparency, etc. This would probably best be done by defining a class of "scene" settings which are treated in this manner. The current workaround is to create separate objects which are enabled/disabled differentially.