PyMOL User Interface
Upper Control Window
Rotate
Zoom
Translate 	
and Clip
Z Axis
X and Y Axes
PyMOL Viewing Window
Object Control Menu
The Upper Control Window is where the main drop
down menus are located. These menus control files,
settings, and tools. Other points of interest in this
window are the Ray button in the top right and the
command line entry point along the bottom.
The Object Control
Menu is used to control
atoms/molecules (called
objects), and sets of
atoms/molecules (called
selections). This menu and
its many pop-up menus
allow a lot of control
over how objects are
represented in the PyMOL
Viewing Window.
A=Action S=Show H=Hide
L=Label C=Color
PyMOL’s mouse controls for moving the
camera in the PyMOL Viewing Window
utilizes a virtual track ball. Holding the
left mouse button while the pointer
is inside the molecule will cause the
camera to rotate along the X and Y axes.
If however the pointer is outside the
molecule, the camera will rotate along
the Z axis.
Mouse Controls
In the PyMOL Viewing Window molecules can be viewed
and directly interacted with. In this window, the camera
and molecules can be moved and rotated, sets of atoms
can be selected directly by clicking on the molecule or by
clicking in the Sequence Viewer located at the top, scenes
can be changed and updated via the scene buttons in
the lower left hand corner, movies can be controlled with
the movie bar controller in the bottom right, and model
representation of individual atoms can be changed by
right-clicking on the molecule to call up pop-up menus.
Common Operations in PyMOL
Loading Molecules
Upper Control Window:
File > Open >
Plugin > PDB Loader Service
Command Line:
load “file name”
fetch “pdb_code”
Mouse Controls
Left button:
Hold: rotate
Click: select (residues by default)
Right button:
Hold: zoom
Click: pop-up menu
Center button:
Hold: translate
Click: center on atom
Scroll: adjust clipping plane
Selections
Selections in PyMOL are sets of atoms and are differentiated from objects by
the use of ( ) in the Object Control Menu. The default selection is (sele) which
is automatically created upon selecting any atom or residue. To start a second
selection, rename (sele) and deselect it, then start a new selection.
Creating selections:
Left mouse button
Clicking on the molecule will select/deselect resides by default
Sequence Viewer
Display-> Sequence
Left click and drag on sequence to select/deselect large portions of the 	 	
molecule
Renaming a selection:
> rename selection > delete and retype new name
Representations
PyMOL has many options when it comes
to representing molecules many of which
can be controlled from the Object Control
Menu via the single letter pop-up menus
and can be applied to both
objects and selections.
Example commands:
> as > cartoon
shows a cartoon representation only
> sticks
adds sticks to the current representation
> waters
hides waters from the current 	 	
representation
> preset > ball and stick
classic ball and stick representation
> residue
labels residues with three letter code and 	
number
> blues > marine
colors the representation marine
Display and Settings
Many display options and other effect settings
can be controlled from the Display and Setting
drop down menus located in the Upper Control
Window.
Example Commands:
Display > Sequence
starts up the Sequence Viewer
Display > Background > White
sets the background color white
Setting > Transparency > Surface > 50%
sets transparency of all surfaces to 50%
Setting > Rendering > Shadows > None
turns off shadows during ray tracing
Setting > Edit All...
brings up a new window with all settings
Scene Control
Scenes are snapshots of the PyMOL viewing area
that include all of the representation information
as well as the camera position. Changing and
updating scenes is very easy from the PyMOL
Viewing Window if you turn on the Scene
Buttons.
Example Commands:
Scene > Append
stores a new scene
Scene > Buttons
toggles the interactive scene buttons in the 	
PyMOL Viewing Window
Measurement Wizard
PyMOL has a built-in measurement tool, for
distances, angles, dihedrals, and neighbors.
Wizard > Measurement
starts the measurement wizard
(distance by default)
Click to toggle measurements >
		 pick atoms as directed
Programmed Movies
PyMOL is a very powerful moviemaker with many
sophisticated options, however there are also
several pre-programmed movie options available
for the beginner to use.
Example Commands:
Movie > Program > Camera Loop > 		
		 Y-roll-> 4 sec
creates a movie that rotates 360˚around 	 	
the Y-axis in 4 seconds
Movie > Program > Scene Loop > 		
	 Nutate > 4 sec
creates a movie that loops through stored 	 	
scenes and oscillates them for 4 seconds
Saving and Exporting Files
It is important to save your work and very easy to
export your figures and movies.
Example Commands:
File > Save Session As...
saves the entire contents of your PyMOL 	 	
session
Click , then
File > Save Image As > PNG...
exports a ray traced image
Movie > Ray Trace Frames, then
File > Save Movie As > MPEG/QuickTime
exports the current movie and ray traces every 	
frame
Further Help
PyMOL has a diverse and active community, and
much of PyMOL’s functionality can be learned
from community-sponsored resources and
professional support.
visit www.pymol.org/support