Introduction to PyMOL
Copyright Notice
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Introduction to PyMOL
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Table of Contents
Introduction! 4
About this Booklet! 4
Getting Started! 4
The PyMOL Layout! 5
The Viewer Window! 5
The Upper Control Window! 8
Mouse Controls! 8
Features! 11
Visualization Presets! 11
Saving Images! 12
Taking Measurements: Distances, Angles, Dihedrals, and Neighbors! 13
PyMOL Sessions! 14
Sequence Viewer! 16
Representations and Selections! 17
Scenes and Shows! 19
Creating Movies! 20
Working with Multiple Objects and Selections! 21
Alignments! 22
Advanced Feature Previews! 25
Label Customization! 25
Saving Coordinates! 26
Probing Electrostatics! 26
Atom Selection Syntax! 26
Automating Tasks with Scripts! 27
Advanced Molecular Editing! 28
Next Steps! 29
Other Courses! 29
Joining the PyMOL−Users Mailing List! 29
Visiting the PyMOLWiki Community Web Site! 29
Accessing the Official Documentation Site! 29
Introduction to PyMOL
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Introduction
About this Booklet
Welcome
This is a follow-along guide for the Introduction to PyMOL classroom tutorial taught by DeLano Scientific, LLC. It
covers the basics of PyMOL for medicinal chemists and other industrial scientists, including visualization of proteinligand
interactions, creating figures, and working with session files.
This tutorial was created for PyMOL version 1.2 or greater running under Windows, Mac, or Linux.
Typographic Conventions
Words typeset in Courier font, such as extend, are commands that can be typed directly into a PyMOL command
line. Keystroke modifier keys are typeset in upper case, where CTRL, ALT, ESC, SHIFT, are “control,” “alt”, “escape,”
and “shift,” respectively. The mouse buttons are shown as upper case letters in Courier font, where LEFT,
MID, WHEEL, RIGHT, are the left mouse button, middle mouse button, wheel, and right mouse button, respectively.
The word DRAG indicates that a mouse button should be pressed and held while the mouse is moved. For example,
CTRL-MID-DRAG indicates the user should press and hold the control key, then press and hold the middle
mouse button, and drag the mouse with the control key and middle mouse button held down. Menu navigation is
shown in bold Times font as Menu→SubMenu→... For example, File→Save Image As...→PNG indicates that the
user should click on the File menu, choose the Save Image As submenu, and finally choose PNG, from the submenu.
Getting Started
Requirements
Before starting this tutorial, please ensure that you have the following.
• PyMOL version 1.2 or greater
• A 3-button wheel mouse
• Tutorial-specific data files found in the IntroductionToPyMOL subfolder of the PyMOLTutorials archive
supplied by DeLano Scientific. This archive is typically provided as a compressed “ZIP” file, which should be
extracted on to your Desktop
Also, please make sure that your keyboard Caps Lock key is turned off when using PyMOL.
Getting Ready—Starting the PyMOL Application
If you haven’t already, please launch PyMOL by double clicking on the PyMOL icon on your desktop. On Windows
PCs, PyMOL brings up two windows. The MacPyMOL version will bring up one window, which contains the same
two user interface components.
Introduction to PyMOL
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The PyMOL Layout
Try It—Loading a File and Using the Mouse
The larger, Viewer Window is where our molecules and objects will appear. Above it is the Upper Control Window
(see Figures 1 and 2).
Please load the structure file 1t46.pdb from disk. To do this, click on the Upper Control Window and choose
File→Open. Then, from the PyMOLTutorials/IntroductionToPyMOL folder on your desktop, please select the
file named 1t46.pdb. Your PyMOL should now look like Figure 2, except that the initial colors may be different.
At this time, please take a moment to familiarize yourself with the behavior of the mouse in PyMOL. Place your
mouse cursor over the protein. Now, press and hold while moving the mouse—aka dragging—with each of the
mouse buttons in turn. As Figure 3 shows, dragging with the left mouse button rotates the scene in the Display;
dragging with the middle mouse button moves the molecule in the plane of the display; and dragging with the right
mouse button zooms in and out.
Don’t worry if you get lost. Just click the Reset button in the Upper Control Window to restore the original view.
The Viewer Window
An annotated snapshot of the Viewer Window is shown in Figure 4. The
left side of the Viewer Window is called the Display Area and is where
your molecules and objects will appear when loaded. Directly beneath the
Display Area is a command line for entering PyMOL commands. Almost
everything you can do with the mouse in PyMOL can also be done by
typing commands, and this is one of two places where they can be entered.
Next, the upper right-hand side of the screen houses the Object
Menu Panel, which is used to show/hide objects and selections as well as
change many of their properties. At the bottom right of the screen are the
Mouse Controls, which we discuss later.
Figure 1: PyMOL immediately after being
launched on a Windows PC.
Figure 2. Kinase protein, PDB ID 1t46, loaded into
PyMOL on a Mac.
Figure 3: Basic mouse button functions in
PyMOL.
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Try It—Using the Viewer Window: Entering Commands and Using the Object
Menu Panel
Please click in the Display Area. Now, press the ESC key. Your command history and other information is shown
here. Press ESC to return to the normal viewing mode. This feature provides
a quick way of viewing PyMOL’s text output. If the Viewer Window
is selected as you type, what you input will appear in the lower command
line.
Type orient and hit enter. The molecule in your scene should now be
oriented, that is, displayed with the longest axis aligned with the x-axis.
Now, please type reset and hit enter. This does the same thing as clicking
on the Reset button in the Upper Control Window.
Please find the Object Menu Panel in the upper right of the Viewer Window.
An example Object Menu is shown in Figure 5. Here, you’ll see a
list of names. The objects whose names appear with light grey backgrounds
are active, and may appear in the Display Area. Click on the
name to deactivate, or disable, the object, and it will be hidden from view.
Your Object Menu should have entries for all and 1t46, and maybe something
like (sele). Please click on 1t46. This disables it. Click again to reenable
it.
Each of the five Pop-up Menus, is accessed by clicking on a
letter. A→Actions contains lots of preset actions; S→Show allows us to
control various representations; H→Hide is the opposite of Show, here
you can hide various representations; L→Label is for showing and creating
labels; and finally, C→Color is for coloring our objects. Click on each of the five letters to see what pops up.
We’ll come back to these later.
Figure 4: The Viewer Window, with annotations.
Figure 5: Example Object Menu Panel.
Kinases is a group in which there are five
kinase proteins; kinase2, a protein, is disabled,
all other kinases are enabled. Proteins
1cll and 1ggz are objects. (sele) is a
disabled selection. We will discuss groups,
objects and selections later.
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Mouse Modes
Many different tasks can be performed using the mouse inside of PyMOL, through a variety of mouse modes. Each
mouse mode just reassigns the mouse buttons to perform different tasks. PyMOL’s Viewing Mode is used primarily
used to view, rotate, translate, and change the representations of objects. Editing Mode is used to rotate bonds, replace
atoms, physically move atoms and residues, etc. The mouse mode table for each of these modes is shown, in
Figures 6a and 6b.
Try It—Setting and Using the Different Mouse Modes
In PyMOL, just click the table to cycle through the mouse modes. This table shows the current mouse mode (3Button
Viewing, 3-Button Editing) and what each keyboard and mouse action does.
Figure 6a: 3-Button Viewing Mode. Figure 6b: 3-Button Editing Mode.
Reading the Mouse Mode Table
The mouse mode table is a reference guide to PyMOL mouse functions. Column abbreviations are: L, M, and R for
LEFT MID and RIGHT buttons. Actions are: Rota, rotate; PkAt, pick atom; Cent, center; PkTB, pick torsion bond;
MovA, move atom. Notice that the table changes when you click on it.
Click the Mouse Mode table to enable 3-Button Viewing and locate the word Selecting, colored green, as shown in
Figure 6a. The red word to the right of Selecting tells which Selecting mode the mouse is in. Clicking on the word
Selecting changes the selection mode. The first mode is Residues, which means that, when we click on any atom
with the mouse in the Display Area, the entire residue in which that atom resides is selected.Other selection modes
are Molecules, which forces PyMOL to select the entire molecule containing the chosen atom; Chains, which will
choose the chain in which the selected residue resides; Objects, which selects the entire object containing the chosen
atom; C-alphas, the alpha carbon of the residue for the chosen atom; and Segments which chooses segments,
which are special fields in a PDB file. Keep clicking to cycle through the options until you return to Residues. When
in 3-Button Editing Mode, the word Selecting is replaced with Picking and the mouse is used to pick Atoms which
represent Joints in the molecular graph.
Try It—Using Editing Mode to Move Atoms
Now, please set the mouse mode to Editing, and CTRL-Left-drag on an atom. The atom moves with the mouse
in an unphysical but compliant way, tracking with the mouse. To undo the movement, type undo and hit enter in the
PyMOL command line. PyMOL currently has a very limited undo system, so please do not rely on it. We introduce
it here to let you know that it exists, but only for undoing changes made to atom positions. Now that we’ve toured
the Viewer Window, let’s see what is offered to us in the Upper Control Window.
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The Upper Control Window
The Upper Control Window, shown in Figure 7, houses a menu bar for access to many PyMOL options and controls.
The buttons allow access to many of the most-used functions. The second of the two command lines is here.
This one is different from the other in that it will accept pasted text, and you can copy from it. The history and diagnostics
window is where PyMOL feedback will be shown. For example, if you wanted to calculate the distance between
alpha carbons number 10 and 11 you could type distance 10/CA, 11/CA and the answer would show
up in the window.
Please take a moment to find the following buttons: Reset, Ray, and Builder. As you know Reset restores the original
orientation of the molecule. Ray is a very frequently used command for making beautiful publication quality
images. We will talk about the Ray command later on. PyMOL has a built-in Builder for building smallmolecule
fragments and peptides. Please click on the Builder button to switch to builder mode (MacPyMOL doesn’t have the
builder, but you can access it by launching MacPyMOL in the PyMOLX11Hybrid mode). The Builder is discussed
in our Advanced Tutorials. Please click on Builder again to enable the default buttons.
Mouse Controls
Many different tasks are performed using the mouse in PyMOL. There is much to learn, but remember you can always
rely on the Mouse Mode table if you get lost. Producing figures that look just right often takes some skilled
mousing. So, let’s continue with the mouse.
Getting Started
A three-button mouse is required for this tutorial, although PyMOL can support other types of mice to a lesser extent.
And, please take note that when using a three-button wheel mouse, there is a difference between clicking the
wheel button and scrolling it up and down. If your mouse click turns on pink squares or small white globes, as in
Figure 8, then you can always turn these off by Left-clicking on a blank part of the Display Area. Lastly,
please make sure you Caps Lock key is not turned on.
Figure 7: Upper Control Panels. (Above) The Upper
Control Window for Windows, Linux and MacPyMOLX11Hybrid
is a separate, floating window.
(Right) The Upper Control Window for
MacPyMOL is attached to the upper part of the
single PyMOL window.
Introduction to PyMOL
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Try It—Basic Mousing: Rotations, Panning and Zooming
Using the mouse mode table for reference, take a few minutes to familiarize yourself, if you haven’t already, with
how the mouse works. Rotate the molecule with LEFT-drag. Try zooming in and out (RIGHT-drag). Try panning
with MID-drag to move the molecule about the screen. Don’t forget, you can refer to the mouse mode table if
you ever forget the mouse controls.
Trackball Mode
By default, PyMOL enables the mouse in what is called Trackball Mode. This mode allows us to make precise and
sophisticated motions with the mouse. In this mode, if you click and drag through the center of the screen to rotate
(left image of Figure 9), the scene rotates on an axis parallel to the plane of the screen. However, if you choose a
point on one of the far edges of the Display Area and drag along the edge, the molecule rotates along an axis perpendicular
to the plane of the screen (like spinning a top; right image of Figure 9).
Try It—Virtual Trackball Mode
Let’s give those motions a shot. Please, select anywhere on the protein and drag through the center of the screen.
Now, click near the far left-hand side of the screen and drag up. Notice the difference in rotations. By the way, in
PyMOL, when you rotate objects in this way, you are actually moving the display camera around the object in space.
You are not moving the object itself or changing its atomic coordinates.
Figure 9: (Left) Trackball rotations when the mouse passes through the center of the screen; (right) trackball rotations when
the mouse moves along the outer edges of the screen.
Figure 9: (Left) Trackball rotations when the mouse passes through the center of the screen; (right) trackball rotations when
the mouse moves along the outer edges of the screen.
Fig. 8: If you click in the PyMOL Display Area without dragging, you may cause pink boxes (left) or white
globes (right) to appear. For now, just left-click in a blank area to hide them.
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Axis Aligned Mode
If you don’t like trackball mode, then you may disable it through the menus by unchecking Mouse→Virtual
Trackball. When trackball mode is disabled, PyMOL uses axis-aligned mode. In this mode left-right movements
rotate the molecule across the x-axis, up-down motions will rotate the molecule across the y-axis. Combining the
motions of x- and y-axis rotations via a circular motion affords rotations about the z-axis.
Try It—Comparing Virtual Trackball and Axis Aligned Mode
Turn on trackball mode and rotate the molecule. Now, turn it off and notice the difference in rotations when you use
the same mouse motions. Try to obtain some given orientation of the molecule in each mode. In which mode is it
easier to obtain your desired orientation? Please choose whichever mode is easiest for you.
Try It—Centering
When we click—not scroll, but push down—and quickly release the middle mouse button while the cursor is over
an atom, PyMOL will place that atom at the center of the screen. This represents a convenient way to roam around
the protein focusing only on certain atoms. Please give this a try: MID-click from atom to atom in your molecule
to roam around the structure.
Clipping
Before we move on, please click Reset to restore the original view of the molecule. (And, if you are using Windows
or Linux, please click on the Viewer Window because we want to work in the Display Area some more.)
Now, using the scroll wheel on the mouse, scroll down, towards yourself. Parts of the molecule should disappear.
Scroll up, away from yourself, and those portions should now reappear. What you are doing is controlling Clipping
in PyMOL. Clipping is a way to focus in on a certain area of the protein while hiding everything else from view.
PyMOL has a near clipping plane and a far clipping plane. The space between those two clipping planes is called the
Clipping Slab. Objects within the clipping slab are visible. Everything outside of the clipping slab is hidden.
Try It—Adjusting the Clipping Planes
Try using the mouse wheel to clip out everything but one layer of amino acids. Once you’ve done that, try rotating,
panning, and zooming around the scene with the left, middle and right mouse buttons, respectively. With a little
practice you should be able to visualize and focus in on specific parts of a structure, such as a single alpha helix.
PyMOL allows you move the clipping slab while keeping the molecule steady with SHIFT-Scroll. Give it a
shot: when you hold down SHIFT on your keyboard and scroll the wheel on your mouse, parts of the molecule
should appear and disappear, depending on the position of the clipping slab. PyMOL allows you also to move the
molecule and keep the clipping slab steady with CTRL-Scroll. Please try this mode and compare it to the other.
If scrolling to adjust the clipping planes is too coarse, then PyMOL also allows us to SHIFT-RIGHT-drag to
more finely tune the clipping planes. SHIFT-RIGHT-dragUp/Down controls the near clipping plane; and,
SHIFT-RIGHT-dragLeft/Right controls the far clipping plane. If you drag diagonally from the upper right to
lower left corner of the Display Area, you move the clipping plane with respect to the objects. If, however, you drag
diagonally from the upper left to lower right corner, you set the width of the clipping slab.
Well, that’s it for the tour of PyMOL’s Layout and basic mouse usage. Now, let’s check out the some basic features
and common tasks that make your life easier.
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Features
Visualization Presets
Introducing Visualization Presets
PyMOL comes with an array of preset visualizations. Through a
couple clicks you can get a technical view, or a simple view, or
even a view nicely set for publishing. Each preset emphasizes
different aspects of your scene. You can access the preset visualizations
through the A→Actions→Preset menu. Figure 10
shows the result of applying the A→Actions→Preset→Ligand
Sites→Trans-parent (better). Figure 11 shows the menu of the
available presets.
Try It—Sampling the Visualization Presets
Some visualizations may be immediately useful to you for visualizing
protein-ligand complexes. Please choose the A→Action→Preset→Simple setting, which shows the protein
as a ribbon and the ligands as sticks. The ligands pop out of the scene while the polymer maintains a simple structure
allowing us to see its topology. Do you see the ligand?
Let’s now compare this to the Technical setting.
Please choose the A→Action→Preset→Technical
setting from the preset menu.
The ligand is now obscured by lots of technical
details. This is where clipping comes in handy.
While the ligand is harder to see, if you zoom
in on it, you will notice that PyMOL found and
is displaying all the hydrogen bonds that the
ligand is making with the protein. The A→Action→Preset→Ligands
preset is like the
Technical preset, but instead of finding all hydrogen
bonds, it only finds the hydrogen bonds
between the ligand and the protein. Please enable
this setting to see the difference.
The A→Action→Preset→Ligand Sites submenu
opens to show more refined options,
which render beautiful views of the ligand binding
site as a surface. Please try the various visualization presets on this protein.
Please take a few moments to try each of the presets and consider which might be best suited for your applications.
Before moving on, please choose the A→Action→Preset→Publication preset.
Figure 10: An example image made with one click
using the Transparent Ligands site preset.
Figure 11: Menu of visualization pre-sets built into PyMOL.
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Saving Images
Once your display is set up, choose File→Save Image As→PNG. PNG, or Portable Network Graphic, is a popular
lossless compressed image format for publishing. PNG files can be read by Microsoft PowerPoint, Microsoft Word,
and many other programs. To save a ray traced image press the Ray button before selecting File→Save Image
As→PNG.
Ray tracing is a technique to draw scenes
with superior detail; it smoothes edges,
adds shadows, generates better lighting
effects. Figure 12 shows the difference
between a ray traced image and a non-ray
traced images. The trade off for such
beautiful images is time: ray tracing can
take much longer, depending on the complexity
of your scene. Images for publication
are typically ray traced.
Image Resolution and Transparency
Every (raster) image has a property called resolution—usually measured in dots per inch or DPI. Images for presentation
or display on a computer are best set to 72 DPI. Images for printing or for publication are typically required to
be 300 or 400 DPI (or higher, ask your journal/publisher for their resolution requirements). Another property that
might be useful to know about is transparency. If an image has a transparent area, then whatever is underneath the
image will show through. PyMOL can save images with transparent or non-transparent (opaque) backgrounds. Fig-
ure 13 and the next paragraph illustrate the difference.
Figure 12: (Left) a non-ray traced image. (Right) the same scene, but ray traced
before saving. The difference in quality is clear.
Figure 13: Images insert easily into PowerPoint, Word and other applications. The image at left was ray traced with a transparent
background, and so the title and subtitle in PowerPoint show through. The image at the right was ray traced with an opaque white
background, and so while the text is still there in PowerPoint it is now hidden underneath the white background.
Introduction to PyMOL
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Try It—Images for PowerPoint, Projectors, and Computer Displays
Let’s make an image and import it into PowerPoint. We will also illustrate the difference between a transparent and
opaque background. Start by ray tracing your image: please press the Ray button. By default, the image has an
opaque background. Save the file containing the image to your Desktop using File→Save Image As→PNG, with
the filename pymol.png. Next, let’s save an image with a transparent background. To do this, make sure Opaque
is unchecked in the menu, Display→Background. Now press the Ray button. Save the file to your Desktop using
File→Save Image As→PNG, with the filename pymolT.png, where the T stands for transparent. Open up PowerPoint.
Where it says, “Click to Add Title,” write
“Introduction to PyMOL.” Now, click Insert→Picture
and choose the first image, pymol.png. The
image pastes nicely into PowerPoint. Notice that it
covered up your title text. That is because the
pymol.png file has an opaque background. Now,
delete that image (click on it and then hit backspace
or delete), and insert the other image, pymolT.png,
using Insert→Picture. Now, the text should show
through the background of the image. For those without
PowerPoint, Figure 13 shows the results of the
above procedure.
Lastly, you can use the clipboard to copy images into
PowerPoint if you have PyMOL for Windows or
MacPyMOL. Simply setup the scene you want, then
from the Upper Control Window menu choose Edit→Copy to copy the image to the clipboard. Now, in PowerPoint
choose Edit→Copy (or type CTRL-v) to paste the image from computer memory.
High Resolution Images (Publication and Printing)
To save a high resolution image you need to know the size of image you want (in inches) and the resolution (in dots
per inch). Then all you have to do is type one simple PyMOL command: ray W,H at the PyMOL command to save
the high-resolution file, where H is the height in pixels, W is the width in pixels. To calculate W and H you just multiply
the height or width times the DPI. For example, let’s say your publisher wants images to be 4 inches wide by 3
inches tall at 400 DPI. The height in pixels is then: 3 inches * 400 DPI = 1200 pixels; and the width in pixels is 4
inches * 400 DPI = 1600 pixels. So, the exact command to type into PyMOL would be, ray 1600, 1200.
Lastly, just do File→Save Image As→PNG to save your high resolution image.
Taking Measurements: Distances, Angles, Dihedrals,
and Neighbors
PyMOL allows you to make take measurements of distances, angles, and dihedral angles, and also to find neighbors.
The easiest way to do this is to click on Wizard→Measurement. PyMOL wizards operate by prompting the user to
take an action (usually written as a message in the upper left side of the Display Area) and then provide controls for
the user on the right side above the Mouse Mode matrix. Don’t forget, when you’re done using a Wizard, make sure
you click Done—the last button in the wizard.
Figure 14: Zoomed in on a PHE residue.
Introduction to PyMOL
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Try It—Taking Measurements
Please select S→Show→As→Lines to enable the lines visualization
for 1t46. Zoom in on a residue, as shown in Figure 14. Now, please
open the Measurement Wizard. Next, click on any two atoms; the distance
between the two should now be annotated by a dashed line and
distance measure. Let’s try measuring an angle.
To change the type of measurement, click on the top button in the
measurement wizard, which, in Figure 15, displays Distances. A menu
will pop up, giving you the other options. If you choose Distances,
you need to select two atoms. If you want to measure Angles, you
need to select three atoms. Dihedrals require four
atoms. Polar, Heavy and all Neighbors need just one. Please take a few moments now to make
various measurements. By default, each measurement creates a new object. You can change this
by merging the new object with the previous one, or by overwriting the previous object. Control
of this feature is through the third menu option in the measurement wizard (in Figure 15, Delete
Last Object).
A common use of the measurement wizard is to create a dashed line between two atoms. To do
this, make your measurement and then, on the Pop-up Menu for the measurement object, hide the
label with H→Hide→Labels (see Figure 16). Mistakes in the Measurement Wizard can be remedied
by choosing Delete Last Object, or by deleting the last measurement object choosing A→Action→Delete, in
the row of the measurement object you wish to delete.
PyMOL Sessions
PyMOL allows you to save your work as a PyMOL Session. Sessions store all of your objects, selections, views,
scenes, representations, etc. This is a good way to save your work for later or share it with others. To create a
PyMOL Session, just click File→Save Session
As and then supply a file name. PyMOL sessions
end in .pse. If you’re in a PyMOL session
and want to overwrite a saved .pse file, choose
File→Save Session. When saving a PyMOL
Session, please do not quit the program until
your receive a confirmation that PyMOL has
successfully written your session file. If you
quit without waiting, then your work may not
be saved.
To open a PyMOL session, simply double-click
on the session file icon. If you are already inside
PyMOL, click File→Open and then
browse to your session file.
Figure 15: Measurement Modes Pop-up Menu.
Click on Distances to show this menu.
Figure 16: The
hide menu.
Figure 17: The example Kinase Session loaded into PyMOL.
Introduction to PyMOL
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If you work in a pharmaceutical or biotech company, there may be computational chemists, crystallographers, or
even automated systems that will prepare PyMOL sessions for you. Such prepared sessions are generally accessed
via file servers, database systems, or your intranet. If such a system doesn’t yet exist, consider asking your structural
biologist and computational chemist colleagues about making PyMOL session files available to you.
Try It—Loading and Perusing a Prepared PyMOL Session
Please load the PyMOL session in the PyMOLTutorials/IntroductionToPyMOL folder on your desktop, called
KinaseSes- sion.pse. Figure 17 is a screenshot of MacPyMOL opened to the KinaseSession.
In the Display Area you can see the structure of Phosphoinositide−Dependent Kinase 1 (PDK1) complexed with the
inhibitor Staurosporine. The structure you are viewing is Protein Data Bank (PDB) structure 1OKY. If you click on
the (+) button next to 1OKY, you see that all four active objects in the Viewer Window start with the prefix 1OKY,
and are contained in a group called 1OKY. Groups
allow you to collect objects under one common name
for better organization. Open groups are prefixed with
minus sign (-) and closed groups are prefixed with a
plus sign (+). Try turning the 1OKY objects on and off
individually. The displays of the protein, the inhibitor,
the solvent, and hydrogen bonds can each be enabled
and disabled independently by clicking on the object
names. Also note that you can click and drag downward
over the object names to toggle display of multiple objects
at once.
Disable all of the objects except 1OKY.prt, and then
enable object 1Z5M.prt, which is a crystal structure of
PDK1 with a different ligand. From this view, you can
observe that, while the chemical structures are the
same, the two structures differ in the precise orientations
of various side chains. If you enable 1OKY.inh, 1OKY.hbd, 1Z5M.inh, and 1Z5M.hbd, you can see how the
two ligands interact differently with PDK1.
Note that there are four atom selections listed at the top of the Upper Control Window: (inhibs), (prots), (solvs), and
(sites). Clicking on its name will activate or deactivate a selection. These selections are useful for changing the way
various groups of atoms are represented across all complexes in the session. For example, the (sites) atom selection
can be used to selectively display a transparent molecular surface on each protein’s active site. To do this, first disable
all but one of the protein objects, for example, 1T46.prt (V−Kit). Then select S→Show→Surface, next to the
(sites) selection. A molecular surface will appear on the 1T46.prt object. If you enable the other 1T46 objects, you
can middle click to center and scroll to move the clipping plane to visualize Gleevec inside its binding pocket (see
Figure 18). To remove the surfaces, simply H→Hide→Surface for the (sites) selection. Likewise, you can use the
(inhibs) selection to change how the inhibitors are displayed. For example, try showing spheres for the (inhibs) selection
in order to obtain a space−filling view of the inhibitors. Although the input PDB files used to create this session
did not contain bond valence information, PyMOL will generally attempt to guess bond valences for unknown
residues. To display those bond valences, select Display→Show Valences from the Upper Control Window. FigFigure
18: Gleevec in its binding pocket. The pocket is rendered
as a surface, Gleevec is rendered in sticks, and the rest in lines.
Introduction to PyMOL
15
ure 19 (left) shows bond valences turned on, and the binding pocket as a surface turned off (right). You can always
use a session file such as this as a starting point for your own customized figures. If you get lost or make a mistake,
you can start over by quitting PyMOL and reopening the original session. Please spend some more time with this
session file until you feel quite comfortable with it.
Using Sessions for Backup—Important!
Because PyMOL lacks a general undo command, you must get in the habit of saving sessions periodically (e.g.
every five minutes) when using PyMOL for extended tasks. It is also generally a good idea to save multiple versions
of the session as you make progress, just in case something goes wrong and you need to backtrack. An alternative
approach to saving PyMOL commands, used by advanced PyMOL users, is scripting. PyMOL scripts can automate
tasks and take advantage of the underlying Python interpreter for expanded functionality. PyMOL Scripting is covered
in depth in an Advanced Tutorial.
Sequence Viewer
Using the Sequence Viewer
PyMOL’s sequence viewer, shown in Figure 20, is turned off by default. Please find the S below the mouse mode
table and click it. You can also turn on the sequence viewer by going to Display→Sequence from the Upper Control
Window. You should now have the amino acid sequence of your protein in the familiar one-letter codes. The sequence
viewer can be used to select residues. Using the left mouse button, please select and drag out a rectangle of
residues in the sequence viewer. The residues selected will be indicated by small purple boxes in the Viewer Window.
Now, try right-clicking on the selected residues in the Sequence Viewer. Notice that a context sensitive pop-up
menu appears. This menu gives you access to a variety of options for this selection.
Figure 19: Bond valences are now shown on Gleevec (left). A custom representation of the kinase binding pocket, filled
with ADP shown as a surface (right).
Introduction to PyMOL
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Representations and Selections
Representations in PyMOL
Representations in PyMOL are controlled through the pop-up menus. Again, S→Show,
allows us to turn on various representations; H→Hide, the opposite of Show, turns off various
representations; L→Label, creates, shows, and hides labels; and finally, C→Color, colors objects
and selections. The Show menu is displayed in Figure 21.
Try It—Working with Molecular Representations
At this time, please restart PyMOL and load the 1t46 structure from disk. Please hide everything in
your PyMOL window by clicking H→Hide→Everything in the all object row. Now, let’s show the
protein as lines. To do so for 1t46, select S→Show→Lines. Now show S→Show→Cartoon. Our
molecule will be shown as lines and cartoons because PyMOL’s show command acts additively.
Now show Ribbon. The ribbon traces the backbone of the protein; lines display backbone and side
chains. The Hide menu works like the Show menu: when you turn off a representation, other representations
are left unchanged. For example, please hide the Lines representation by choosing
H→Hide→Lines. Just the ribbons and cartoons should be showing now.
Please color your molecule marine, by choosing C→Color→Blues→Marine. PyMOL allows us to
use myriad colors, and even allows us to define our own. Now, try S→Show→As→Cartoon. See
the difference? The Show As command turns off all other representations before drawing the one
you chose.
Figure 20: Example of using the sequence viewer in PyMOL. Left-click drag to select residues; right
click to open up menus for those residues. The purple dots represent those residues selected from the
sequence viewer. The menus appeared after a left-click on the selected residues in the sequence.
Figure 21: The
Show Menu.
Introduction to PyMOL
17
Please note that the Surface and Mesh representations can take a long time to generate for large molecules. Try
S→Show→As→Surface to see your protein as a surface.
The Show and Hide commands operate on the entire molecule. But, many times when working with molecular
structures, we wish to show some portion of the structure in one representation (eg. the ligand as sticks) and then
show another portion in another representation (eg. the binding pocket as a surface). Well, we can do that in PyMOL
using Selections.
Understanding Selections
Selections in PyMOL are just sets of atoms that you define, and do not have any properties of their own other than a
name. Selection names appear in the viewer window surrounded by parentheses, as in (sele), to distinguish them
from objects. Objects are proteins, molecules, and other entities in PyMOL’s memory, whereas selections are just
listings of atoms in those objects. You can turn selection indicators on and off by clicking their names in the Viewer
Window just as you do for objects, except that only one selection can be turned on, or enabled, at a time. Atoms in
enabled selections are shown in the Display Area with purple boxes over their atom centers. To deselect atoms when
in viewing mode, just left click away from any atoms in the Display Area, click the selection name, or click Deselect
in the Upper Control Window.
Try It—Creating Selections
In PyMOL there are three different ways to select residues. First, you can simply click on them in the Display Area
when in Viewing Mode. Please make sure your mouse is in Viewing Mode, and then try clicking on an atom. Click
after click, the atoms you choose will be added to a special selection
called (sele). Selected atoms are shown with little indicator
boxes, the purple boxes, around them, as in Figure 22. Second,
you can enable the Sequence Viewer and click on residues there.
Please try that too: enable the Sequence Viewer in the Display
Menu, and click on residues in the sequence. Also, try right clicking
on residues in the Sequence Viewer. Last, you can use the
command line, which provides a more powerful and precise way
to choose atoms and residues. Because of the complexity of typed
selections, we will present that material in the Advanced Selections
portion of the Appendix, and our Intermediate Tutorial.
Try It—Renaming Selections
PyMOL allows us to rename selections. Let’s try it. First, please show 1t46 as lines. Please use your mouse to select
a few residues. Make sure there are some pink boxes showing on the screen. Then, for the active selection (sele),
please click on A→Action→Rename Selection. When prompted, type the name myFirstNamedSelection and return.
You don’t need to supply the parentheses. PyMOL will add them for you since it knows this is a selection.
Try It—Using Selections
We use selections as much as we use objects. Once you’ve created a selection, you can use the menus next to its
name to change its representation. Please note that A→Action→Delete Selection doesn’t delete the atoms, it just
clears the selection name from memory. However, if you choose A→Action→Remove Atoms, for any object or
selection, that indeed will remove the selected atoms from PyMOL’s memory.
Figure 22: The three selected atoms are shown with
purple boxes around their atoms.
Introduction to PyMOL
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Let’s try a few actions with selections. First, let’s select all the waters and delete them. To do this, turn on the Sequence
Viewer and then scroll to the end of the sequence. Select all the O residues by left clicking and dragging with
the mouse. Remember mouse selections are additive so, to select all the waters you can, slide the rest into the
Viewer using the grey slider box under the sequence, and then select those, too. Once you’ve selected all of the waters,
please remove them by selecting A→Action→Remove Atoms, for the selection (sele). Please also delete the
selection we made earlier called myFirstSelection. (Hint: an easier way
to remove waters is to select A→Action→Remove Waters.)
Let’s show the ligand as spheres, select it, and then color it ‘wheat.’
Start by selecting S→Show→Organic→Spheres for 1t46. Now, please
find the ligand in your structure. Using the mouse select it and rename
the selection to “myLigand”. Once that is done, please select
S→Show→As→Spheres, and then C→Color→Tints→Wheat, for
this selection.
Lastly, if you rapidly right-click on an active selection, PyMOL brings
up a context sensitive pop-up menu. Because you’ve selected an active
selection, PyMOL knows what to operate on, so it’s menu is tailored for
that selection (see Figure 23, left). If you right clicked on an atom that is
not in an active selection, PyMOL brings up a different menu, allowing
you to operate on the atom, its residue, chain, molecule, etc (see Figure 23, right).
Here’s a hint: look at the menus shown in Figure 23. Menu options that have a grey border to the right or left, such
as actions, colors, and show, will open up a sub-menu. Those menu items with a solid blue border, such as zoom,
orient, center, do not—clicking on them will perform the given action.
Scenes and Shows
Using Scenes, PyMOL allows you to very quickly make simple animated sequences, called Shows. A Scene in
PyMOL is simply a memory-snapshot, in which PyMOL saves current colors, visualizations, representations and the
position of the camera. A Show is simply an interactive ‘movie’ created as you advance (or reverse) through your
predefined scenes. In a show, PyMOL animates smooth transitions from scene to scene, in order to provide a continuous
sense of 3-dimensional context for the viewer. To see how a PyMOL Show works, please open the
ExampleShow.psw file, which can be found in the PyMOLTutorials/Introduction/sessions folder on your desktop,
and use the Page Down (PgDn) and Page Up (PgUp) keys to step through the presentation. Pressing the space bar
also advances though scenes. Note that you can manipulate the view using the mouse anytime you want without
corrupting the preset scenes. Let’s take a look at making scenes and shows.
Try It—Creating and Viewing Scenes
Let’s setup two scenes and make a movie that visits each one. Please start by reloading the kinase session file and
expand the 1OKY group by clicking on the plus (+) next to 1OKY. Now, let’s store this scene: please select Scene→Append.
Next, let’s create our second scene, which will be a close-up of the ligand while in the Publication
preset. Please apply the Publication preset for the 1OKY group by selecting A→Action→Preset→Publication for
1OKY. Next, please orient the scene with respect to the ligand; for the object 1OKY.inh only, please select A→Action→Orient.
Now, store this scene with Scene→Append.
Figure 23: Comparing the menu for right
clicking on an active selection (left image) or
atoms that are not in a selection (right image).
Introduction to PyMOL
19
As this demonstrates, to create a scene we start by positioning molecules, coloring them, setting their representations
and getting the screen to look exactly as desired. Then, to store the scene and assign it a name, we click Scene→Append
in the Upper Control Window. PyMOL automatically assigns a name to the Scene, which we need to
refer to it (eg. “001”). And, now that two or more scenes have been defined, we can switch between them with
Scene→Previous/Next.
Please use Scene→Previous now to return to the first scene. If you prefer, you can also use the Page Down (PgDn)
and Page Up (PgUp) keys to advance forward or retreat backward through the sequence of scenes. Also note
that pressing CTRL−PgDn will insert a new scene after the current one, and CTRL−PgUp will insert a new scene
before the current one.
Modifying, Annotating and Saving Scenes in a Session
The last scene displayed can be updated by selecting Scene→Update from the Upper Control Window. You can also
add textual annotation to the current scene via a typed command such as scene auto, update, Some annotation
information. This will display "Some annotation information" on the screen the next time the
scene is recalled. When you save a PyMOL Session, all of the scenes you have defined will be saved as well. You
can then share the session file with a collaborator, and he or she will be able to open up the session file into PyMOL
and view the sequence of scenes you defined.
Creating Shows and Interconverting with Sessions
A Show File is simply a PyMOL Session file that contains one or more scenes and is saved with a .psw file name
extension instead of the normal .pse. When a .psw file is opened, PyMOL automatically enters full−screen mode and
displays the first scene in the sequence. To convert a Session to a Show, change the .pse file name extension to .psw.
To convert a PyMOL Show back to a Session, change the .psw back to .pse. If you are using Microsoft Windows and
cannot see the file name extension, then it may be hidden per the Windows default. To change this, click on
Tools→Folder Options from the menu of the enclosing Microsoft Windows folder. Ensure that View→Hide extensions
for known file types option is not checked.
Creating Movies
Introduction
Movies tell stories better than static images, but complex movies can be difficult and time-consuming to create.
Here, we cover the absolute basics. DeLano Scientific will soon offer additional tutorials focused on intermediate
and advanced moviemaking.
Please find the Movie menu in the Upper Control Window. Take a moment to scan through all the options and sub-
menus.
Movie→Append will add a given number of seconds to a movie, but will not program any content for the new time.
Movie→Program will program a given movie task for a new time of a given duration. PyMOL comes with some
pre-programmed animations. Just select Movie→Program and then choose from Camera Loop, Scene Loop, State
Loop or State Sweep. Camera loops are animations in which the camera pans around a given scenein a rocking,
rolling or combined motion. This is a nice way to visualize a pocket or a simple structure. Other camera loops are xrock,
x-roll, y-rock and y-roll. A roll is a complete 360 degree rotation about a given axis. A rock is a back-and-forth
Introduction to PyMOL
20
rocking motion. If your movie gets too long, or is not what you want, just select Movie→Reset from the Upper
Control Window.
Try It—Make a Movie using Scenes and Movie Presets
Let’s use the Movie→Program submenus to make a movie. We already set up our two scenes in the last section
(Scenes and Shows). Now we will have PyMOL cycle through those two scenes in a Scene Loop movie. A scene
loop essentially stitches together all your scenes with a predefined pause at each scene transition. Let’s make our
movie now by selecting, Movie→Program→Scene Loop→Nutate→2 Seconds Each. To watch the movie, press
the Play button in the movie controls (lower right of the Viewer Window).
Before moving on, please clear any movies you have made by selecting Movie→Reset from the Upper Control
Window. Also, please disable all objects except for the first two proteins, 1OKY.prt and 1Z5M.prt.
Working with Multiple Objects and Selections
Try It—Viewing Many Structures with Grid Mode
PyMOL has a feature called grid mode which subdivides the Display Area into as many equal sized rectangles as
you have visible objects. Please enable grid mode by selecting Display→Grid→By Object in the Upper Control
Window. PyMOL now displays each protein in its own grid slot. Figure 24, shows what grid mode looks like when
enabled with six proteins. Rotate the scene with the left mouse button in the Viewer Window; notice how each of the
molecules rotates in its own window. At this point, to illustrate the next feature, please quit PyMOL.
Loading Many Structures
Provided that your computer has enough memory and processing power, PyMOL can be used to simultaneously
visualize dozens of structures or more. Structures can be loaded from the File menu one at a time, or if you multipleselect,
many at a time. Alternatively, one can use a script to load multiple files using the load command (or the
fetch command, which loads structures directly from the PDB given appropriate PDB identifiers). Last, if you’re
launching PyMOL from the command line, you can provide file names there—and even use wildcards. For example,
you may type pymol myPDBs/*.pdb to load all the PDB files in the directory named myPDBs.
Try It—Loading Many Files
Please load the six kinase files in the PyMOLtutorials/IntroductionToPy-MOL/kinases directory. To do this,
launch PyMOL, select File→Open, and multiple-select the files.
Figure 24: Grid mode turned off (left) and on (right), where each protein receives its own grid
slot.
Introduction to PyMOL
21
Alignments
Sequence Based
PyMOL can perform sequence-driven structure alignment through
the A→Action→Align menu, shown in Figure 25. You can align
all proteins to a currently selected one (A→Action→Align→All
to this), or align proteins one by one (A→Action→Align→To
Molecule). Finer control over the alignment process can be exercised
by creating selections that represent the two regions to be
aligned. In this case, one selection (e.g. sel01) should be created in
the target molecule and a second independent selection (e.g. sel02)
should be created in the molecule to be aligned. Then for selection
sel02, you click on the A→Action→Align→To Selection→sel01
to perform a superposition based on only those two regions.
Alignments performed using the A→Action menu are based on a
protein sequence alignment followed by an interactive structure
superposition, and only the CA atom positions are considered.
Greatest control over alignment can be exercised by typing an
align command in the command line. For example, the kinase
structure 1uwh actually contains two copies of the enzyme, chains
A and B, whereas 1t46 only contains one copy. The default alignment
of 1t46 and 1uwh matches only the 1uwh B chain. To force
alignment of 1t46 against the "A" chain of 1uwh, type the following
command: align 1t46////CA, 1uwh//A//CA. This
command uses selection macros, which are discussed in the
Advanced Features at the end of this tutorial. PyMOL comes
with a more robust alignment command called super. Use
super if align doesn’t do so well.
Try It—Quickly Align Multiple Structures to One Target
Let’s align all of the kinase proteins in our session to 1Z5M. For 1Z5M, choose A→Action→Align→All to this. All
enabled proteins should now be aligned to 1Z5M. To see the alignment more clearly, please select
S→Show→As→Ribbon.
Specific Atom Pairs
Sometimes we don’t want a global alignment of two proteins, but rather, an alignment based on specific atom pairs.
If you already know which atoms in protein A should be matched with which atoms in protein B, then you can use a
fitting procedure instead of an alignment procedure. The difference is that fitting is an easy problem to solve, and
PyMOL can fit perfectly. In fact, there’s a wizard to help us with fitting.
Figure 25: To perform a structure alignment, choose
A→Action→Align, as shown in this screenshot.
Introduction to PyMOL
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Try It—Pair Fitting
Please disable all proteins except 1Z5M and 1UWH. Because we just aligned all proteins to 1Z5M, corresponding
atoms from 1UWH should be nearby their mates in 1Z5M. Next, zoom in and make the clipping slab thin so just a
few residues are visible, as in Figure 26 (left). Now, open the Pair Fitting Wizard by selecting Wizard→Pair Fitting.
At this point PyMOL will be prompting you to select a “mobile atom.” Please select an atom from one structure.
PyMOL now asks you to select a “target atom,” so select an atom from the other structure. PyMOL should have
connected the two atoms with a dashed line. Please continue pairing atoms until you have four pairs. Once you are
done selecting atoms, please choose the Fit 4 Pairs. PyMOL will fit those four pairs, by moving the mobile structure.
Next, click Delete Last Pair to remove the last pair. Now, refit the 3 pairs; notice that PyMOL updates the
RMSD of the fit in the Display Area. Clicking Clear will remove your atom pairings. Done will dismiss the Pair
Fitting Wizard. At this time, please click Done.
Pair Fitting from the Command Line—The pair_fit Command
Clicking atoms pairs can be tedious, so PyMOL has another way to pair fit. Now, please type pair_fit 1uwh//
A/563-582/CA, 1z5m///193-212/CA into one of PyMOL’s command lines. This command superimposes
the alpha carbons in chain A of 1UWH for residues 563-582 to the alpha carbons of 1Z5M for residues 193-212.
Please note: to fit atoms you must identify exactly the same number of atoms in one object to fit to the other. Also, no
spaces are allowed inside selection macros.
Figure 26: (Left) Thin-slab view of two proteins ready to be fitted. (Right) The red lines shown paired atoms from the two structures.
The goal is to optimally pair and align those atoms to maximize structural overlap.
Introduction to PyMOL
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Editing Molecular Objects
PyMOL allows you to create and replace bonds, atoms, residues, and commonly used chemical groups. After modification,
you can clean the structure using an open-source implementation of the Merck Molecular Force Field
(MMFF).
Removing Unwanted Atoms
PyMOL provides a quick way of removing waters or hydrogens, by simply clicking
A→Actions→Remove Waters or Remove Hydrogens, shown in Figure 27. You can
also remove a specific atom, residue, chain, segment, or covalent molecule from a
molecular object by right-clicking on an unselected atom in the graphics area to display
the atom's default pop-up menu, following the desired level in the hierarchy, and then
choosing remove atoms. Selections can also be used to remove groups of atoms. To do
this, create a selection consisting of those atoms that you wish to remove, and then
choose A→Actions→Remove Atoms for that selection. Finally, you can type the remove
command to specifically eliminate a specified set of atoms. For example, to remove
chains B and Y in PDB structure 1uwh, one could enter the following command:
remove /1uwh//B+Y. Please try removing all waters from these proteins.
Changing Bond Valences
One of the problem with PDB files is that they do not contain bond valences for ligands.
As a consequence, it is not possible to display correct chemistry for ligands. PyMOL
may not always recognize the correct hydrogen-bonding interactions between proteins
and ligands until the valences have been properly specified.
Try It—Changing Bond Valences
To edit bond valences on a Windows PC, please click on the Builder button in Upper Control Window. Next,
CTRL−Right-click to pick the bond whose valence you wish to change. You should see a white band appear
about the bond as in Figure 28. Please cycle through the available bond valences by clicking on the Cycle button in
the Builder area of the Upper Control Window, or by pressing CTRL−W on your keyboard. Once you have set the
correct valence for that bond, you can CTRL−right−click to select the next bond to fix, continuing until all valences
have been fixed. Note that PyMOL adds missing hydrogens to the atoms involved in the bond. If hydrogens
are not desired, use A→Actions→Remove Hydrogens for the object, after correcting all of the bond valences.
Figure 28: Cycling valences. First, select the bond with CTRL-right-click. Then type cycle_valence at the command line
or click Cycle in the Builder. Notice the automatic addition of hydrogens. If they are not desired, you can remove them after
setting the valence.
Figure 28: Cycling valences. First, select the bond with CTRL-right-click. Then type cycle_valence at the command line
or click Cycle in the Builder. Notice the automatic addition of hydrogens. If they are not desired, you can remove them after
setting the valence.
Figure 28: Cycling valences. First, select the bond with CTRL-right-click. Then type cycle_valence at the command line
or click Cycle in the Builder. Notice the automatic addition of hydrogens. If they are not desired, you can remove them after
setting the valence.
Figure 27: How to easily
remove waters or hydro-
gens.
Introduction to PyMOL
24
Advanced Feature Previews
Label Customization
Introduction
In addition to labeling atoms based on identifiers and properties, PyMOL supports custom labels with arbitrary text.
Here, we will touch on a few useful ideas. To get the most out of this, you should be comfortable with typing commands
in the command line and also making named selection (either with the mouse or from the command line).
Setting the Label
You can label a selection by clicking L→Label and then choose the appropriate label type desired. To make a custom
label, however, you need to type commands into the PyMOL command line. Basic labeling is accomplished by
typing in the command line label selectionName, labelText and return, where selectionName is
any valid PyMOL selection or selection name, and labelText is the string or keyword you want to use as the label.
PyMOL will also accept interpreted strings as well (see the intermediate Tutorial or PyMOLWiki for more details).
An example label command is label name CA, resn, which labels each alpha carbon with the three
letter code of the amino acid it which it resides. Other keywords of interest are: resi, and b. Resi is the residue
number and b is the b-factor.
Now that we know how to make more advanced labels, let’s learn how to customize them using PyMOLs options
for labels. This requires using the set command at the command line.
Label Color
You can set label_color in PyMOL to any valid PyMOL color, for example by typing: set label_color,
blue. Colors can be valid PyMOL color names, found in the color menus for each object or selection. Label Size
You can change the size of the label with set label_size, nSize, where nSize is a number representing
the size of the label. If nSize is positive then the label is rendered at a size of n points (72 points/inch). However if
nSize is less than 0, it is converted to the absolute value and the label is rendered in that many Angstroms. For
example, to render a 14 point font, set label_size, 14; to set labels to be 2 Angstroms (big), set label_size,
-2.
Label Font and Extended Unicode Characters
PyMOL supports Unicode fonts to display characters such as α, β and Å. To use Unicode characters you need to
know the correct character code for your symbol; please visit http://unicode.org/charts/symbols.html for the list of
codes. Once you know the proper code, for this example it is \316\261, you can issue the label command: label
5/CA, "\316\261-Helix" will print “α-Helix” on the 5th atom’s alpha carbon. PyMOL allows us to
change the font that our labels are rendered in. For that, use set label_font_id, nLabel, where nLabel is
an integer in the rage 5-15. To use Unicode fonts, first set the PyMOL option label_font_id to 15 or 16.
Label Position
In Editing Mode, you can CTRL-Left-drag labels around your scene. Use CTRL-Right-drag to move the
label toward or away from the camera. This is a useful feature as many time a surface or structural feature
will hide a label.
Introduction to PyMOL
25
Saving Coordinates
PyMOL has a limited ability to write out coordinates for input into other programs. The interchange file formats
supported are: PDB (Protein Data Bank), MOL (MDL MOL-file), and MMD (Macromodel). PyMOL can also save
molecules in an internal PKL (Pickle) file format, which is able to preserve all of the molecular information, including
bond valences and atomic properties, something none of the other file formats do well. To save a molecule, first
make sure that the atoms you wish to save are contained in either a distinct object or are pointed to by a named selection.
Then choose File→Save Molecule..., pick the name of the object or selection in the next window, and enter
the filename. Add the correct file name extension is appended to the file name (e.g. ".pdb"), and then click Save.
Probing Electrostatics
Quantitative electrostatics calculations are typically difficult and time-consuming to perform. They require the specialist
skills of a computational chemist to carefully consider missing protein segments and side chain atoms, histidine
ionization, and the presence of specific counter-ions from bulk solvent. Furthermore, calculations involving
ligands usually require high-level quantum calculations to obtain reasonable atomic partial charges for novel scaffolds.
Assuming that such issues have been addressed, PyMOL can call upon the Adaptive Poisson-Boltzmann
Solver (APBS) under a Unix environment to perform quantitative electrostatic calculations. The program can also
read pre-calculated potentials from the Grasp, Delphi, or Zap electrostatics solvers.
In lieu of rigorous calculations, a simple, local (but technically incomplete), quasi-Coulombic calculation can often
help answer the qualitative question, "Is this region of the protein surface likely to be positive, negative, or neutral
relative to the rest of the protein?" PyMOL provides such answers for proteins by performing an automated calculation
that amounts to smoothing out the local charge density from nearby atoms (within 10 β ngstroms), without taking
into account solvent screening effects. To perform this calculation, select Actions→generate→vacuum electrostatics→protein
contact potential. After a minute or two, PyMOL will create a new object with the protein shown
as an electrostatic surface colored blue in the positive regions and red the negative regions. You can then CTRL
−click−and−drag along the slider to change the color levels.
Atom Selection Syntax
PyMOL has a powerful atom selection language that is covered in-depth in the PyMOL Users Manual. Here we provide
some simple example selections that you can hopefully adapt for your needs:
1. To select a numbered residue in a specific object (e.g. 1t46):
! select my_resid, 1t46///640/
2. To select all residues with a given identifier in any object:
! select my_resids, 606/
3. To select specific residues and ranges of residues by identifier:
! select my_range, 601−610/
Introduction to PyMOL
26
! select my_resids, 1t46///602+606+621−631/
4. To select specific residues by residue type:
! select my_negative, 1t46///GLU+ASP/
5. To select specific atoms by name:
! select my_main_chain_atoms, 1t46////N+CA+C
6. To select one or more chains:
! select my_chain, A+B//
! select my_chains, 1uwh//A+B//
7. To select atoms in multiple objects
! select my_object, 1uwh////CA or 1t46////CA
Automating Tasks with Scripts
Scripts are text files that contain a sequence of PyMOL commands, and they can be used to perform repetitive tasks
automatically. For example, if you wish to prepare a series of standardized figures, but would like to use a different
crystal structure for each figure, then it would make sense to use a script to perform some or all of the figure preparation
tasks automatically.
To run a script, select File→Run, or type "@" followed by the file name path into a command line. The following
example PyMOL command script contains six commands that color and represent the target and ligand in a standard
way. To use a different input structure with this script, you would just update the first command in the file with a
new PDB filename.
Code 1: Example script to automate figure generation.
# load a PDB file
load kinases/1t46.pdb
# show the ligands as space−filling spheres
# and show the protein as a cartoon
hide everything
show spheres, organic
show cartoon, polymer
# color the protein carbons cyan
# and the ligand carbons yellow
color cyan, polymer and elem c
color yellow, organic and elem c
In addition to command scripts, PyMOL can also be controlled using the Python programming language, which also
makes it possible to create custom applications that integrate PyMOL for molecular visualization.
Introduction to PyMOL
27
Advanced Molecular Editing
Rotating Bond Torsions
Bond torsions can be rotated by CTRL−Right-Drag near the mobile end of the bond. Once a bond has been
picked with the mouse using CTRL-Right-click you can also rotate the atoms on either end of the bond by
CTRL−Left−Drag. If you make a mistake, CTRL−Z will undo recent conformational changes.
Figure 29: Rotating torsion bonds. Right side of the bond is
selected (left image); and molecule is modified by rotating the
torsion bond with CTRL-LeftDrag (right image). Notice
that the white cuff is on the right half of the bond. This indicates
that the right side of the bond will be rotated. The left
side is unchanged. Compare this to Figure 30.
Figure 29: Rotating torsion bonds. Right side of the bond is
selected (left image); and molecule is modified by rotating the
torsion bond with CTRL-LeftDrag (right image). Notice
that the white cuff is on the right half of the bond. This indicates
that the right side of the bond will be rotated. The left
side is unchanged. Compare this to Figure 30.
Figure 30: Similar to Figure 30, but left side of the bond is
selected (left image), and the white cuff indicates this fact, as
it is located on the left half of the bond. (Right image) Molecule
shown after slight rotation. The right side of the molecule
is unchanged.
Figure 30: Similar to Figure 30, but left side of the bond is
selected (left image), and the white cuff indicates this fact, as
it is located on the left half of the bond. (Right image) Molecule
shown after slight rotation. The right side of the molecule
is unchanged.
Creating or Removing Bonds
Bonds can be formed by picking two atoms sequentially and then Build→Create Bond in the Upper Control Window
or by pressing CTRL−T. Once a bond has been created, the valence can be changed as described in Figure 28.
To delete a bond, pick it by by CTRL-right-clicking on it. The picked bond can then be deleted by pressing
CTRL−D or by hitting the Delete key.
Creating One Object Out of Another
Atoms in a selection can be copied into a new object by choosing the A→Action→Create Object for the selection.
A new object name will appear in the names list, and you can then rename this object using A→Actions→Rename
Object. Certain properties of atoms in a newly created object can be manipulated independently from those in the
source object(s), while those properties of a selection cannot. For example, independent objects can have different
transparencies, while a selection must have the transparency of its parent object.
Mutating Protein Residues
PyMOL can suggest alternate rotamers (conformations) for existing side chains and
even mutate individual side chains of proteins. Such actions are performed using the
Mutagenesis Wizard. To launch the Mutagenesis Wizard, select Wizard→Mutagenesis
in the Upper Control Window. Then click on the side chain you wish to alter.
Initially, PyMOL will load the set of common rotamers for the existing side
chain, in the order of most frequent occurrence. You can use the left and right arrow
keys or the movie controls, below the mouse mode table, to step through the side
chain rotamer conformations. To choose a different residue type for mutation, click
on the first pop−up menu (initially set to No Mutation, as shown in Figure 31).
Once you have chosen the mutation and set the desired rotamer, click the Apply
button in the Viewer Window. When you are finished making mutations, click Done.
Figure 31: Mutagenesis Wizard
menu. Click on No Mutation to
display the residue list of possible
mutant residues.
Introduction to PyMOL
28
Next Steps
Other Courses
Congratulations on finishing the Introduction to PyMOL tutorial. We hope you enjoyed the lesson and are motivated
to use PyMOL for your molecular visualization, movie-making, scripting, and editing tasks. This isn’t the end,
though: DeLano Scientific will soon have other courses available covering Intermediate Topics, Scripting/
Programming, Moviemaking, and Molecular Editing and Cleanup. Please contact us for more information on those
courses via support@delsci.com.
Joining the PyMOL−Users Mailing List
As of Summer 2009, well over 1,000 PyMOL users subscribe to the pymol−users mailing list, which is where the
community exchanges tips on how to use the software effectively and how to solve any problems that come up. To
join the mailing list, please click on the Mailing List link that appears at the top of the PyMOL Home Page,
(http://www.pymol.org). Or, to quickly search the mailing list archives for posts on a specific topic, click the
Mailing List Archive link.
Visiting the PyMOLWiki Community Web Site
The community also runs a "Wiki" dynamic content site that aggregates information from the mailing list and provides
other kinds of PyMOL−related documentation (http://www.pymolwiki.org). PyMOLWiki users can
create their own pymol−related pages, on this site or elaborate upon useful information that is already posted. The
site boasts over 1,000 users, over 3,000,000 page views, is typically accessed between 3,000–4,000 times a day, and
has many useful scripts, plugins and tutorials free for download.
Accessing the Official Documentation Site
PyMOL subscribers access DeLano Scientific’s Official Documentation site (http://delsci.info) using the
subscription credentials shown from their most recent PyMOL receipt. This site contains the latest chapters from an
updated PyMOL Manual, an assortment of narrated ScreenCasts, and plenty of reference information to help users
on their way becoming PyMOL experts.
Introduction to PyMOL
29