ChimeraX Quick Start Guide

UCSF ChimeraX is the next-generation visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco, following Chimera. See also: ChimeraX tutorials

Many ChimeraX actions require typing commands. The help for a specific command can be shown with the help command (for example, help style). Other ways to interact with the program include:

clicking toolbar icons, optionally after making a selection
graphical tools
context menus shown by right-click (Ctrl-click on Mac, Alt-click on Windows trackpad)

Command-Execution Links

Clicking command links in the examples below will execute them in ChimeraX if this page is shown in the ChimeraX internal browser, such as with Help... Quick Start Guide in the ChimeraX menu.

Example Atomic-Structure Commands

Example structure: Protein DataBank 2BBV, black beetle virus capsid

open 2bbv color bychain	style /b stick	Mouse drag to move. color /n teal	hide /c

File is fetched from the PDB in mmCIF format and cached locally. Lighting with shadows.	Change chain b to stick style.	Rotate by dragging, translate by dragging with middle mouse button or with option* key pressed (Mac) (more...).*	Hide chain c atoms.

ribbon /c	Mouse click with ctrl key pressed to select an atom, or command select /N:4@C5'	Press up-arrow key, or command select up	color sel gold select clear

Display backbone ribbon.	Selection has green outline, shift-ctrl-click to add to selection, ctrl-click background to clear selection.	Up-arrow and down-arrow keys expand and unexpand selection.	Use “sel” to refer to the selected atoms in any command. Clear the selection.

surface #1
color /n fromatoms

style solvent sphere
color solvent red

sym #1

2bbv mmCIF Assemblies
1	complete icosahedral assembly	60 copies of chains A-F,N
2	icosahedral asymmetric unit	1 copy of chains A-F,N
3	icosahedral pentamer	5 copies of chains A-F,N
4	icosahedral 23 hexamer	6 copies of chains A-F,N
PAU	icosahedral asymmetric unit, std point frame	1 copy of chains A-F,N
XAU	crystal asymmetric unit, crystal frame	5 copies of chains A-F,N

Show the solvent-excluded surface of each chain, and color chain N to match atoms.

Enlarge waters to spheres (from balls), color them red.

List mmCIF assemblies in the Log. Do not click the links in the Log to generate an assembly since it will be done with the next command instead. (If done by mistake, however, it can be reversed with command close #2; show #1 model)

sym #1 assembly 3 newmodel false copies false	view	set bg white set silhouettes true save ~/Desktop/2bbv.png	Click the video camera icon to record a spin movie.

Show assembly “3” according to the information in the Log* from the previous command.*	Bring all models into view.	Set background color to white, show thin black outlines. Save PNG image file to Desktop.	Movie saved on Desktop as movie.mp4.

measure buriedarea /a with /b measure sasa #1 & ~solvent	interfaces #1 & protein	close set bg black set silhouettes false
Buried area between /a and /b = 1900.4 area /a = 15385, area /b = 14989, area both = 26573 Solvent accessible area for #1 & ~solvent = 34093	6 buried areas: C A 1675, C B 1671, A B 1663, C F 739, A D 714, B E 699
Compute solvent accessible buried surface area between chains A and B. Also compute total solvent accessible area excluding waters.	Display contact graph between all chains.	Close all 3D data. Go back to black background, no outlines.

Example Density-Map Commands

Example data:

EMD-1080, an 11.5-Å single-particle reconstruction of GroEL, and an atomic structure, 1GRL
EMD-1273, a tomogram of an immunological synapse
crystallographic density (from the Electron Density Server) and atomic structure of Protein DataBank 1A0M, an α-conotoxin

open 1080 from emdb light full	volume #1 level 0.9	Click icon (in Right Mouse tab of toolbar) to control the contour level with the mouse, then drag with right mouse button.	vol #1 enclose 1e6 step 1 color tan

Open EM Databank map 1080. Lighting with shadows.	Hover mouse over map reports contour level 1.675 in status line. Then change level.	With Mac one-button mouse drag while pressing command* key.*	Set level to enclose 1,000,000 cubic Å, show full resolution and set color.

set bg gray set silhouettes true	open 1grl light default	Click icon to move selection with the mouse. Ctrl-click atom to select. Then right-mouse drag to move molecule into map.	fit #2 in #1 volume #1 transparency 0.5

Gray background and thin black edges.	Open atomic model to fit in map. Simpler lighting, without shadows.	Can also use rotate selection mouse mode.	Locally optimize fit of atomic model in map. Make map 50% transparent.

molmap #2 10 vol #3 style mesh	vol subtract #1 #3 minrms t vol #4 color pink transparency 0 hide atoms; show ribbon

Create simulated map for atomic model at 10 Å resolution and show as mesh.	Subtract simulated map from experimental map.

close set bg black set silhouettes false open 1a0m from eds	open 1a0m hide ribbon show atoms vol #1 level 1.0 style mesh	vol zone #1 near #2 range 2 vol #1 level 0.5 transp 0.6

Open x-ray map for PDB 1a0m from Uppsala Electron Density Server.	Show atomic model and adjust contour level of x-ray map.	Show map zone within 2 Å of atoms.

close open emdb:1273	volume #1 region all showOutline true

Open tomogram of a T-cell (200 Mbytes), single-plane grayscale displayed because of large map size.	Show all planes of tomogram, grayscale rendering.