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

Currently, ChimeraX is mostly controlled by typed commands. The help for a specific command can be shown with the help command (for example, help style).

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. (See more tutorials with click-to-execute links.)

Example Atomic-Structure Commands

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

open 2bbv
light full
style /b stick Mouse drag to move. 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. Press up-arrow key. 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 style solvent sphere
style ~solvent stick
sym #1
2bbv mmCIF Assemblies
1complete icosahedral assembly60 copies of chains A-F,N
2icosahedral asymmetric unit1 copy of chains A-F,N
3icosahedral pentamer5 copies of chains A-F,N
4icosahedral 23 hexamer6 copies of chains A-F,N
PAUicosahedral asymmetric unit, std point frame1 copy of chains A-F,N
XAUcrystal asymmetric unit, crystal frame5 copies of chains A-F,N
Show the solvent-excluded surface of each chain. Enlarge waters to spheres (from balls) and change other atoms from sphere to stick. 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 f 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:

open 1080 from emdb
light full
volume #1 level 0.9 Click icon 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
vop 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.

set bg black; set silhouettes false
open 1a0m from eds
open 1a0m
hide ribbon
show atoms
vol #1 level 1.0 style mesh
vop zone #1 near #2 range 2
vol #3 level .5 style mesh transp 0.6
Open x-ray map for PDB 1a0m from Uppsala Electron Density Server. Show atomic model and x-ray map as mesh. Show map zone within 2 Å of atoms.

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.