UCSF ChimeraX User Guide

Add Charges
Add Hydrogens
AlphaFold – get protein structures predicted by AlphaFold artificial intelligence
AlphaFold Error Plot – plot AlphaFold estimated residue-residue distance errors
Altloc Explorer
Angles/Torsions
Axes/Planes/Centroids
Basic Actions
Blast Protein
Build Structure – build atomic structures, adjust bonds and torsions, join models, invert chiral centers
Cage Builder
Change Chain IDs
Check Waters
Clashes
Color Actions
Color Key
Color Zone
Command Line Interface
Contacts
Crystal Contacts
DICOM Browser
DICOM Metadata
Distances
Dock Prep
Download DICOM
ESMFold – get protein structures predicted by ESMFold artificial intelligence
ESMFold Error Plot – plot ESMFold estimated residue-residue distance errors
File History
Find Cavities
Fit in Map
Fit to Segments
Foldseek (Similar Structures)
H-Bonds
Help Viewer (ChimeraX Browser)
Hide Dust
Log
Map Coordinates – set map placement and scale
Map Eraser
Map Filter
Map Statistics – report min, max, mean, standard deviation, root-mean-square deviation from zero
Marker Placement
Matchmaker – superimpose proteins or nucleic acids, guided by sequence alignment
Measure and Color Blobs
Measure Volume and Area
Meeting – connect separate instances of ChimeraX for shared virtual reality or collaborative modeling
Model Loops – interface to building missing segments or refining existing parts of a protein structure with Modeller
Model Panel
Modeller Comparative – interface to comparative modeling with Modeller
Registration
Render/Select by Attribute – show attribute values with colors, atomic radii, or worms, or select items based on those values
Renumber Residues
Rotamers – view and evaluate amino acid rotamers; “mutate” residues
Scale Bar
Segment Map
Segmentations – manually segment medical image or other map data plane by plane, or with a spherical cursor in the 3D view or in virtual reality
Selection Inspector – view/modify attributes of the current selection
Send to Quest – send ChimeraX scene to Quest standalone VR headset
Sequence Viewer – view sequences and sequence alignments, optionally structure-associated
Side View – intuitive zooming and clipping
Surface Color
Surface Zone
Task Manager
Toolbar – icons for performing actions with a single click: [...]
Unit Cell
Volume Viewer – view maps (density, microscopy, 3D imaging, etc.)

Usage Conventions
- Target Specification
- Color Specification
2dlabels – add text, symbols, and straight arrows to the display for presentation images and movies
addcharge – assign atomic partial charges and Amber/GAFF atom types
addh – add hydrogens
alias – define a command alias (shortcut or composite action)
align – superimpose sets of atoms
alphafold – get protein structures predicted by AlphaFold artificial intelligence
altlocs – list and manage atomic alternate locations
angle – set or report bond angles
blastprotein – search for similar protein sequences
bond – add or delete covalent bonds
build – build and modify atomic structures
bumps – identify and mark isosurface protrusions
buttonpanel – define a simple custom interface of buttons to execute commands
camera – set mono or stereo viewing and related parameters
cartoon or ribbon – create cartoons or worms, adjust parameters and styles
cd – change the working directory
changechains – change chain IDs
clashes, contacts – identify interatomic clashes or contacts
clip – control clipping planes
close – close models or session
cofr – report or adjust center of rotation
color, rainbow – color atoms/bonds, cartoons, surfaces
combine – combine or copy atomic models
coordset – play through frames of a trajectory
coulombic – calculate Coulombic electrostatic potential (ESP), color surfaces
crossfade – interpolate between image frames
crosslinks – analyze crosslinks or other pseudobonds by length, etc.
crystalcontacts – identify close contacts between symmetry-related copies
define – define axis, centroid, or plane for a set of atoms
delete – delete atoms, bonds, pseudobonds
device – enable virtual reality or modes for other devices (webcam, Space Navigator^®, etc.)
distance – monitor atom-atom distances
dockprep – prepare atomic structures for other calculations
dssp – define secondary structure of proteins using atomic coordinates
esmfold – get protein structures predicted by ESMFold (Evolutionary Scale Modeling) artificial intelligence
exit or quit – exit from ChimeraX
fitmap – fit atoms or map into map
foldseek – search for similar protein structures
fly – smoothly traverse a series of named views
functionkey – assign commands to function keys
getcrd – report atomic coordinates
graphics – set background color, triangulation fineness, frame rate, outline appearance, etc.
hbonds – identify hydrogen bonds
help – show command help in the ChimeraX browser
hkcage – create a cage of hexagons and pentagons to represent an icosahedral virus capsid
info – report model and other information to the user or to other programs
interfaces – draw chain-chain network diagram based on interface surface areas
key – draw a color key
kvfinder – identify cavities or pockets in an atomic structure
label – label atoms, residues, models, bonds, pseudobonds
lighting – report or adjust lights and shadows
log – clear, save to file, and other actions related to the Log
marker – create, change, delete markers and links
matchmaker or mmaker – superimpose proteins or nucleic acids, guided by sequence alignment
material – report or adjust material properties for light reflection and shadowing
mcopy – copy settings from one atomic model to another
measure – measure surface area, enclosed volume, center, path length, map statistics, etc.
meeting – connect separate instances of ChimeraX for shared virtual reality or collaborative modeling
mlp – calculate molecular lipophilicity potential (MLP) for proteins, color surfaces
modelcif pae – plot residue-residue scores for theoretical structures from the ModelArchive database
modeller – comparative modeling, loop modeling, and model evaluation with Modeller
molmap – create a density map from atomic coordinates
morph – morph (interpolate) between atomic structures; create a morph trajectory
mousemode – report or adjust mouse button assignments
move – translate
movie – record image frames and assemble them into a movie file
mseries – display an ordered series of models
mutationscores – analyze data from deep mutational scanning
name – assign a name to a selection or longer target specification for subsequent easy use
nucleotides – show special representations of nucleic acids
open – read data from local file, URL, or database fetch
palette list – list predefined palettes for coloring sequentially or by map value
pbond – add a pseudobond between two atoms
perframe – specify operations to execute at every (or every N^th) display frame
preset – apply a predefined combination of display settings
pwd – report the working directory
registration status – report ChimeraX registration status or days of use
remotecontrol – allow sending commands to ChimeraX using REST or XML-RPC
rename – change model name and/or ID number
renumber – renumber residues
resfit – show density fit of successive amino acid residues along a chain
rmsd – measure RMSD between sets of atoms without fitting
rna – build rough but potentially large-scale models of RNA
rock – rock back and forth
roll – rotate continuously
runscript – run Python or ChimeraX command scripts with command-line arguments
save – save image, session, map, coordinates, sequences, or other data to a file
scalebar – draw a scale bar
segger – act on segmentations created with Segment Map
segmentation – show an existing segmentation as surfaces or with coloring
segmentations – functions associated with the Segmentations tool
select – select items (models or their parts) for subsequent operations
sequence – show the sequence of a structure chain, manage sequence associations and headers, align sequences
set – set background color, subdivision level
setattr – general attribute-setting
shape – create a surface of a specified geometric shape
show, hide – show/hide atoms, bonds, cartoons, models
similarstructures – analyze large sets of similar protein structures
size – set atom radii and stick thickness
smoothlines – smooth paths in line models
snapshot – save snapshot image, set default location for snapshot and spin-movie toolbar icons
split – partition an atomic model into submodels
stop – halt ongoing motions
struts – add pseudobonds to a molecule to strengthen it for 3D printing
style – set display style of atoms, bonds, and pseudobonds
surface – create and show/hide molecular surfaces
swapaa – “mutate” amino acid residues
swapna – “mutate” nucleic acid residues
sym – build multimers using assembly information
taskman – list and kill background jobs
tile – spread models out into a plane
toolshed – install/update ChimeraX bundles from the Toolshed (web repository)
topography – plot values in a volume data plane as heights in a surface
torsion – set or report torsion angles (rotate bonds)
transparency – adjust transparency of atoms/bonds, cartoons, surfaces
tug – pull a set of atoms to target locations using OpenMM dynamics
turn – rotate
ui – set tool-interface preferences, show/hide graphical interfaces, assign functions to buttons, show orthogonal slice views of volume data
undo, redo – undo and redo a limited set of actions/commands
unitcell – build crystallographic unit cells
usage – show a brief description of command syntax and options
version – report ChimeraX version
view – focus the view on specified items, save/restore named views, set camera and model positions with matrices
volume – display or process volume data (density maps, etc.)
vr – virtual reality mode and related options
vseries – display, analyze, or process an ordered sequence of maps
wait – update the display and enforce ordered execution of commands in scripts
windowsize – set pixel width and height of the graphics window
wobble – perform a figure-eight rotation
zone – show atoms, labels, density within a zone around a residue
zoom – change the apparent size of the view