Commands Index

Commands are entered into Chimera's Command Line. Past commands can be accessed from the Command History, and commands can be placed in an executable command file. Chimera commands are listed below and in the Quick Reference (PDF).

All commands can be truncated to unique strings, but their keywords cannot be truncated except as noted in the documentation. Entering the contents of the Command Line (pressing return) executes the contents and updates the display. To hide intermediate stages of processing, multiple commands can be combined into one line with semicolon separators. Certain text conventions are used to describe usage.

2dlabels - create labels with text, symbols, and arrows in 2D
ac - use accelerators (keyboard shortcuts)
addaa - add an amino acid to a peptide N- or C-terminus
addcharge - assign Amber partial charges and atom types
addh - add hydrogens
adjust - change bond angle or bond length
alias - create an alias or list the existing aliases
align - align two atoms or sets of atoms along the line of sight
angle - measure angles formed by atoms or by axes and planes
aniso - show thermal ellipsoids
apbs - interface to electrostatics calculations with APBS (Adaptive Poisson-Boltzmann Solver)
aromatic - show ring aromaticity
background - set background color, gradient, or image
bond - add/delete bonds
bondcolor - color bonds independently from atoms
bonddisplay - control how bond display depends on atom display
bondrepr - control bond style (wire or stick)
bondzone - make zoning tools use points along bonds
cd - change the working directory
center - center the view on specified atoms
chain - chain specified atoms, undisplay the others
changechains - reassign chain identifiers
chirality - report the R/S configuration of a chiral center
clip - move global clipping planes
close - close a model
cofr - report or change the center of rotation
color - color atoms/bonds, ribbons, labels, and surfaces
colordef - define a new color
colorkey - create a color key
combine - combine molecule models into a single model or create another copy of a molecule model
conic - create a shadowed space-filling image
coordset - play through frames of a trajectory
copy - save image files
coulombic - color surfaces by Coulombic electrostatic potential
crystalcontacts - identify clashes between PDB symmetry copies
defattr - assign attribute values to atoms, residues, or models
define - calculate axes, planes, centroids for sets of atoms
delete - delete atoms and bonds
display - display and undisplay atoms
distance - measure distances between atoms, axes, planes, and/or centroids
echo - send text to the status line and Reply Log
export - save the graphical scene
fillring - show rings as filled
findclash - identify clashes and contacts
findhbond - identify hydrogen bonds
fitmap - fit atoms or map into map
fly - smoothly traverse a series of saved positions
focus - adjust the view and center of rotation
freeze - stop all motion
getcrd - report coordinates
hbonds - identify hydrogen bonds
help - display the manual page for a command
hkcage - create a hexagon/pentagon mesh that covers an icosahedron
intersurf - generate and display interface surfaces
invert - swap substituents of an atom
ksdssp - determine secondary structure from protein coordinates
label - display atom labels
labelopt - control the information in atom labels
leap - use a Leap Motion Controller with Chimera
lighting - adjust lighting and shininess
linewidth - control the width of wire bonds
list - report attribute information
listen - report Chimera status
longbond - show/hide pseudobonds representing missing segments
mask - extract volume data bounded by surfaces
match - perform least-squares fitting of specified atoms
matchmaker - align models in sequence, then in 3D
matrixcopy - apply the transformation matrix of one model to another
matrixget - write the current transformation matrices to a file
matrixset - read and apply transformation matrices from a file
mclip - control per-model clipping
mcopy - copy settings from one molecule model to another
mda - MultiDomain Assembler: perform several steps toward homology-modeling a multidomain protein
measure - perform various calculations on structures, surfaces, maps
meshmol - create a “molecule” to show surface mesh as sticks
minimize - energy-minimize structures
mmaker - align models in sequence, then in 3D
modelcolor - set color at the model level
modeldisplay - set display at the model level
molmap - create a density map from atomic coordinates
morph - morph (interpolate) between different structures
move - translate models
movie - capture image frames and assemble them into a movie file
msc - color Multiscale Models surfaces to match atoms
msms - (see surfcat/surfrepr)
namesel - save and name the current selection
neon - create a shadowed stick/tube image (not available on Windows systems)
nucleotides - create special nucleotide representations
objdisplay - display and undisplay VRML models
open - read local files or fetch by ID
pause - pause script execution until the user presses a key
pdb2pqr - interface to structure cleanup and charge/radius assignment with PDB2PQR
pdbrun - send an annotated PDB file to the system shell
perframe - specify commands to be executed at each display frame
pipes - create pipes-and-planks representations of proteins
play - script various complex motions
preset - apply a predefined combination of display settings
rainbow - color residues, chains, or models over a range
ramachandran - show peptide φ,ψ distribution (Ramachandran plot)
rangecolor - color over a range according to attribute values
read - execute a command file, updating the display at the end
represent - control atom/bond display style (wire, stick, ball-and-stick, or sphere)
reset - restore default or saved orientations
resrenumber - reassign residue numbers
ribbackbone - allow display of both ribbon and backbone atoms
ribbon - display ribbon
ribclass - set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
ribcolor - color ribbons
ribinsidecolor - set a separate color for the insides of protein helix ribbons
ribrepr - control ribbon style (flat, edged, or rounded)
ribscale - control ribbon secondary-structure-specific dimensions (Chimera default or licorice)
ribspline - control ribbon path method (B-spline or cardinal spline)
rlabel - display residue labels
rmfalias - create command-line specifiers for sets of nodes in RMF Viewer
rmsd - evaluate the RMSD between specified sets of atoms
rna - build rough but potentially large-scale models of RNA and DNA
rock - rotate models back and forth (oscillate)
roll - rotate models
rotation - rotate bonds
runscript - run Python script with command-line arguments
save - save the current Chimera session
savepos - save model positions
scale - scale the view
scene - save and restore scenes (positions plus styles, colors, labels, etc.)
scolor - color surfaces a single color or by volume data or geometry
section - move global clipping planes in parallel
segment - act on segmentation models
select - select atoms or activate models for motion
sequence - show Sequence for specified chains
set/unset - set visual effects, make models rotate about individual centers
setattr - set an attribute to a specified value
shape - create a surface of a specified geometric shape
show - display specified atoms, undisplay the others
sleep - pause script execution for a specified length of time
solvate - add solvent using AmberTools
sop - adjust capping, edit surface models
split - partition a molecule model into separate submodels
start - start Chimera tools by name
stereo - switch amongst stereo options and mono viewing
stop - exit from Chimera
struts - add pseudobonds to a molecule to strengthen it for 3D printing
surface - calculate and display molecular surfaces
surfcat/surfrepr - create molecular surface categories and control surface style
surfcolor - set molecular surface color source
surftransparency - adjust surface transparency
swapaa - mutate amino acids or swap rotamers
swapna - mutate nucleic acid residues
sym - generate symmetry-related copies of a structure
system - send a command to the system shell
tcolor - color atoms/bonds, labels, and surfaces with a texture color
texture - define texture maps and associated colors
thickness - move global clipping planes in opposite directions
tile - arrange models in a plane
topography - plot values in a volume data plane as heights in a surface
transparency - make atoms/bonds, ribbons, and surfaces transparent
turn - rotate models
vdw - display van der Waals (VDW) dot surface
vdwdefine - set VDW radii
vdwdensity - set VDW surface dot density
version - show copyright information and Chimera version
viewdock - start ViewDock and load docking results
vina - requires installing Autodock Vina locally (Apr 2020)
volume - display volume data (3D numerical data such as electron density)
vop - edit volume data
vseries - display an ordered sequence of volume data sets; can also be used to process and save the data
wait - suspend command processing a specified number of frames or until motion has stopped
window - adjust the view to contain the displayed and specified atoms
windoworigin - set graphics window location
windowsize - adjust the dimensions of the graphics window
write - save atomic coordinates (pdb, mol2)
writesel - write a list of the currently selected (or unselected) items
zonesel - select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces

Chimera Command Files

Chimera command files (scripts) are simply text files containing the same commands that could be entered at the Command Line. Only plain text is accepted, not rich text format or Microsoft Word format. Example files:

• rescol.com for coloring amino acid residues
• setup.com from the ViewDock tutorial
• convergent.com from the Similar Binding Sites image tutorial
• movie content examples

• Lines that begin with a pound sign (#) are interpreted as comments.
• Multiple commands separated by semicolons (;) can be combined into a single line. The last semicolon in a line can precede either a command or a pound sign and in-line comment.
• During execution, a single-frame display update (implicit wait 1) will be added at the end of each line that:
  • contains one or more commands that could change the display
    – and –
  • does not already end with an explicit wait of any length
  (Exception: display updates are not added when a command file is executed with read.) Multiple commands can be combined into a single line as described above to suppress the display of intermediate states. This allows multiple graphical changes to appear simultaneously instead of one by one.
• Several of the movie-related commands execute over multiple frames to generate gradual changes such as continuous motion. A multiple-frame command should be followed by a multiple-frame wait (not the implicit single-frame wait mentioned above) to prevent subsequent commands from executing until it is finished.
• Even when multiple actions occur within a single image update frame, their order is important, and one command may need to precede or follow another to give the desired result. In general, the order of execution is the order in which the commands are given. For example, if a script plays a molecular dynamics trajectory and at each frame shows a molecular surface and colors it by electrostatic potential, the coloring should come after the surface calculation.
• The locations of files opened by a command file can be specified relative to the command file's location, or with absolute pathnames. For example, if the files are in the same directory as the command file, only their names need to be given.
• Structure files can be opened with open noprefs to circumvent any New Molecules preferences; this prevents inconsistent behavior of command files and demos potentially caused by the different preferences settings of different users.

• by simply opening the file, which updates the display after each line as needed. The file type is specified with a suffix (.cmd or .com, part of the filename) or prefix (cmd: or com:, not part of the filename).
• with the command read
• automatically at Command Line startup, as specified in the Command Line preferences

A midasrc file is a command file that is executed automatically when the Command Line is started (see the Command Line preferences). Placing aliases and color definitions in a midasrc file is a convenient way to apply them each time Chimera is used.

Chimera demos are largely constructed from commands.

Chimera commands do not provide a way to loop through multiple residues or models, but this can be done by combining Chimera commands with Python code or a shell script. The Chimera Programmer's Guide includes a primer on looping.