ChimeraX Visualization Tutorial

ChimeraX is a free molecular visualization software used for making high-quality images
of biochemical structures. Note that ChimeraX is similar but separate from the program
Chimera, and this tutorial covers ChimeraX alone.

Learning objectives
In this tutorial, you will learn the basics of ChimeraX and how to create images like the
ones presented above. There will be links to different sections throughout. All bold or
colored words are section links. This tutorial will cover:
1. Installation: How to install and run ChimeraX for PC, Mac, or Linux
2. User Interface (UI): Explanation of the basic UI
3. Creating a Visualization: Complete walkthrough of creating a visualization,
including opening a PDB file, basic commands, visual techniques, and saving an
image
Installation
ChimeraX is a free and open-source visualization software, meaning it is easy to install
and does not require a license file to use for academic purposes. ChimeraX is run
through the University of California San Francisco (UCSF), and can be accessed
through the UCSF ChimeraX website or by following this link:

Download UCSF ChimeraX

The link above should take you to this site:

The red boxes are the links to download the installers. Click on the link for your
operating system. After completing the installation, you can run ChimeraX on your
computer. This installation also installs Chimera, so be sure you run the correct program
when you start it up.
User Interface
Shown below is an in-use window in ChimeraX on Windows 10. Each section is
organized by color. While most of the program is the same between operating systems,
there are slight differences in the placement of menus.

Each of the following are links to their section. In addition, any bold menu titles or
colored section titles link to their respective sections.

Main Interface

Command Line

Graphical Menus

Other Menus

Model Panel

Log
Main Interface

This area of the screen shows the models of the protein or DNA. The current view is
what the final image would appear as if a snapshot were taken. The model can be
moved around using the following controls:

● Left mouse (click and drag): Rotates the model. Clicking towards the center
allows complete rotation, clicking towards the edge of the interface rotates it
along the z-axis.

● Middle mouse (scroll): Zooms in and out.

● Middle mouse (click and drag): Moves the model around translationally (i.e.,
without rotating).

● Right mouse: Variable. See the Right Mouse tab of the Graphical Menus
section for more information.

Command Line

This area allows commands to be input rather than completed by clicking buttons on the
menus. Since using the command line allows settings of a command to be input as well
as the command itself, you can specify what you want much more using the command
line than using the menus.

If you are confused about the arguments of a command, type help followed by the
command in question. This will bring up a page about the command and how to run it.

For additional information to help with the command line, see the Log and Model Panel
sections.
Graphical Menus

These menus contain functions which primarily change how the model is displayed and
visualized. While there are many functions here, only the most common ones are
discussed here. On Macs, each of these commands are still here, but they are not
organized in the same way.

Home

These options are the most common functions used, and many of them are also in later
menus. The only ones here present only on the home tab are Open, Recent, Save,
Snapshot, and Spin Movie.

● Open – opens a molecule file or ChimeraX session file

● Recent – opens the most recent file used in ChimeraX
● Save – saves a ChimeraX session file, image, or molecule file
● Snapshot – takes a screenshot of the interface
● Spin Movie – records a video of the current model being rotated 360 degrees

For the Snapshot and Spin Movie options, this will always save to the desktop folder of
your computer and will always be named “Image#.png” or “Movie#.mov”. To dictate file
name, location, or type, use the save command in the Command Line.

To save an image to a custom location, type:

save C:\directory\filename.png

Indicating the path and file name. This command can also be used to save session files,
molecule files (like .pdb files), or most other types of image files. For more information,
type help save. Alternatively, this can also be done using the save function. A similar
thing can be done with movies but using the movie command instead of the save
command. Alternatively, the Save button on the home menu allows a similar process.
Molecule Display

These options change the appearance of a selection. By default, proteins are loaded as
atoms displayed as spheres, colored by chain.

● Atoms – show or hide atoms. Appearance is determined by the style selected

● Cartoons – show or hide cartoons to show the backbone of a protein
● Surfaces – show or hide the surface of the model
● Styles – the appearance of atoms (if shown) or nucleotides (if present)
○ Stick – bonds are shown as a stick with no sphere for the atom
○ Sphere – each atom is displayed as a large sphere
○ Ball Stick – atoms are small spheres, and bonds are sticks
● Coloring – the color of the model. For more options, see the Actions tab of the
Other Menus section
○ Heteroatom – color by element, with blue nitrogens, red oxygens, etc.
○ Chain – colors each chain a different color
○ Rainbow – colors every residue a different color of the rainbow

Graphics

These settings affect the appearance and view of a model and background. By default,
a black background is given with simple lighting, no shadows, and no silhouettes.

● Background – The color of the background of the Main Interface

● Lighting & Effects – Features which change the appearance of the model
○ Simple – default texture and subtle lighting
○ Soft – matte texture and little lighting
 ○ Full – three-dimensional rendering with lots of lighting
○ Shadows – toggle whether the model projects a shadow
○ Silhouettes – toggle a black outline around the model
● Camera – this changes the view of the model
○ Side View – this provides a second view of the protein from 90 degrees to
the right to better orient the molecule in space
○ View Selected – Fills the view with the selected part of the model
○ View all – Fills the view with all visible models
○ Orient – returns the model to its default orientation and camera angle

Right Mouse

Each of the settings on this tab redefines the function of the right mouse button.

● Movement – Manual movement of the camera and model

○ Select – Selects a single atom. Right clicking and dragging allows for
selecting multiple atoms. Clear selections by right clicking in space
○ Rotate – Rotates the model, same as left mouse button
○ Translate – Moves the model without rotating, same as middle mouse
button
○ Zoom – Allows zooming in and out by right clicking and dragging up (zoom
in) or dragging down (zoom out)
● Annotation – Sets and edits annotations
○ Distance – Measures and labels the distance between two atoms. Right
click each atom measured once to measure
○ Label – Labels a selected residue with its three-letter code followed by its
number
○ Move Label – Moves previously created labels
Other Menus

These menus have various functions, from graphical changes to structural predictions.
Again, not every function is covered, just the most common ones.

File

These options are primarily for opening and saving files. The open and save functions
act the exact same as the open and save commands from the Home menu of the
Graphical Menus section.

Select

This allows for selection of certain parts of the visible model. By visible model, this
means a model which is currently loaded into the session, whether it is seen in the Main
Interface or not. For more information, see the Model Panel section.
 ● Chains – Select individual chains from the model
● Chemistry – Select all of a particular element or functional group
● Residues – select a particular residue type, both amino acids and nucleic acids
● Structure – Select the backbone, side chains, ligands, or secondary structures
● Clear – Clears the current selection
● Invert – Deselects all selections and selects everything not selected
● All – Selects everything visible

Actions

This menu contains display options very similar to the Molecule Display menu of the
Graphical Menus section but provides a few more options.

● Atoms/Bonds – Show or hide atoms or bonds, and change the style shown
● Cartoon – Show or hide cartoons of the backbone and change the appearances
of alpha helices and beta sheets
● Surface – Show or hide the surface of the model, change how the surface is
displayed, and change transparency
● Color – Change the color of a selection. For more color options, select “All
Options”
● Label – Set labels and edit label settings
Tools

This menu contains options for editing and analyzing the structure of a model.

● General – Gives options for tabs you can open. By default the Log, Model Panel,
and Command Line Interface are active
● Sequence – Allows for a BLAST search of the sequence
● Structure Analysis – Allows detection of clashes, distances, and h-bonds. Also
allows superimposing two proteins using the Matchmaker feature
Model Panel

This section gives a summary of the models in use in the session. There are five major
components of this section, each highlighted with a box in the image above.

Name

This component gives the name of every model in use. When using crystals from the
Protein Data Bank, this is given as the pbd code, but if a pdb file is loaded, this will
name the model by its file name.

ID

Every model is given a number used to identify it. When referring to a model in the
command line, refer to it by its ID. So, for example, to center the protein 6uea in the
view, you would type view #4.

Color

This allows changes to the color of a whole model. Click on the box and select a color to
change the color of the model. To color a specific part of a model or only a selection,
refer to the Actions menu in the Other Menus section.

Shown

This makes models visible or invisible in the session. While a model is invisible, settings
changed will not affect that model.
Selected

This selects and deselects entire models. Models selected completely will have a check
in the box. Models that have a part of them selected but not the entire model have a
square in this box.

Log

This section provides a history of all commands and actions taken, whether written in
the Command Line or performed through one of the menus. Regardless of how an
action is performed, it is written in the log exactly how the action would be performed
using the command line, so to repeat an action, the action can be copied and pasted
from the log. All blue words are commands and clicking on them opens the help menu
for that command. The log does not save when ChimeraX is closed.

Additionally, the log displays information about each chain and model when the model is
loaded in. This allows for easy selection and recognition of each chain.
Visualization Tutorial
Biomolecules exist as 3-dimensional entities (not just 2D from textbooks!) and are
comprised of building blocks and make up complex subunits. Scientists can use
different techniques to create a model of these 3D structures for use in bioinformatics. A
common format of these structures is the Protein Data Bank (PDB) format. This format
contains a list of atoms that are found in protein residues and assigns an x, y, z
coordinate for each. In these next steps, we will apply some of the tools above to
create a visualization of the PDB structure 5VMS, a Potassium Channel-Calmodulin
Complex (KCNQ1):

KCNQ1 is a pore-forming subunit of a cardiac potassium channel, and it binds

specifically to calmodulin, which, when mutations occur, can cause congenital long QT
syndrome, a propensity for irregular heartbeats. (ChimeraX, 2018)

1. Load in the model: In the Command Line, type open 5vms. This fetches the crystal
structure from rcsb.org. Alternatively, the pdb file can be downloaded from the Protein
Data Bank and opened using the Open option on the Home menu.
2. Create copies of the protein: Type in the command line sym #1 assembly 1 copies
true. The command sym is used to create symmetrical copies. #1 assembly 1 specify
the protein (if another protein is loaded before this, it should be #ID assembly 1).
Copies true (can be written copies t) means these symmetrical copies are loaded as
complete models, not just graphical clones.
After the copies are shown, close the original one by typing in the command line close
#1. This closes the original protein, leaving more space in the Model Panel.
3. Focusing on the channel. To turn the view so it is looking straight down the
channel, use the Orient command in the Graphics menu or type view orient. We want
to have a look at the other side of the channel and zoom in slightly, so type zoom 1.1;
turn x 180. This is two commands at once (this is done with a semicolon) that zooms in
slightly while rotating 180 degrees around the x-axis.

4
. Display the surface of the channel. Type in the command line surf /a to only show
the molecular surface of chain A. Using the command line here is more efficient, but the
same thing can be accomplished by selecting all the copies of chain a (Select -> Chains
-> Potassium Voltage-Gated Channel -> All) and then selecting the “show surfaces”
button in the Molecule Display menu.
To prevent clipping from the cartoons of chain A, we can hide them by typing hide /a
cartoons or, if chain A is still selected, by clicking the “hide cartoon” button in the
Molecule Display menu. At this moment there is no visual difference, though.
5. Hide bonds. To clean the image up more, we can hide the residues and bonds with
the calcium ions in green. Type in hide /b. Technically this hides the whole of chain B,
but the hide command by default only hides atoms and bonds. This can also be done by
selecting chain B (Select -> Chains -> Calmodulin -> All) and clicking the “hide atoms”
button in the Molecule Display menu.

We still want to show the calcium ions, though, since they are an important part of the
protein. This can easily be done by typing show Ca (capitalization is important!) into the
command line. There are a couple of bonds that are still present after this, so
additionally type hide pbonds.
6. Improving display. To make the cartoons appear nicer, we can change how helices
are portrayed. Type car style modeH tube to change the cartoon style (car style),
specifically helices (modeH) to tubes. This can also be done by clicking Actions ->
Cartoons -> Tube Helices.

We can then improve the lighting by typing lighting gentle. This is like soft lighting with
shadows from the Graphics menu.
Set the background color to white by typing set bg white or by clicking the white
background button in the Graphics menu. White backgrounds are important for
publication images since they both provide better contrast while also saving ink for print
publications.

Enable silhouettes by typing set sil t or by clicking the silhouettes button in the
Graphics menu. We can then increase silhouette depth and contrast by typing set
silhouettedepth 0.02.
To emphasize the calcium ions more, we can type size ions atom 1.6. This increases
the size of any ions shown.
7. Improving colors. While the view and texture are good, we want to make the colors
more appealing. Starting with the calcium ions, we can change their color by typing
color mod ions hue +45. Since colors are subjective, you can change them to whatever
color you want by selecting the ions (Select -> Structure -> Ions) and coloring them
your own way (Actions -> Color).

We can now change the color of the rest of the structure. Again, this is subjective, and
you do not need to follow this exactly. For this case, though, type rainbow palette PuBu-
5. The command rainbow colors a structure by a variety of colors instead of just one.
Palette PuBu-5 sets the options of colors on a scale of white to dark blue. Type help
palette and click on the “palette” link in the menu to see a complete list of palettes. By
default, the rainbow command colors by residue, so, in this case, the residues closest to
the N-termini are white and the residues closest to the C-termini are blue. Other options
are available and typing rainbow polymers palette PuBu-5 also looks good, as it colors
the calmodulin and the channel different colors.

8. Saving the image. Click the save button on the Home menu to save. Be sure to
change the file type to an image file like .png or .jpg, the default is a session file .cxs. If
you must leave in the middle of a session, save a session file and it will save your
progress in ChimeraX.