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:
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
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.
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.
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)
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.
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
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.
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.
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.
