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 C-terminus
addcharge - assign Amber partial charges and atom types
addh - add hydrogens
alias - create an alias or list the existing aliases
align - align two atoms or sets of atoms along the line of sight
angle - measure a bond angle or torsion angle
aniso - show thermal ellipsoids
aromatic - show ring aromaticity
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
chirality - report the R/S configuration of a chiral center
clip - move clipping planes
close - close a model
cofr - report or change the center of rotation
color - color atoms/bonds, ribbons, labels, and molecular surfaces
colordef - define a new color
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 an image (Chimera graphics or POV-Ray)
coulombic - color molecular 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 for sets of atoms
delete - delete atoms and bonds
display - display and undisplay atoms
distance - measure the distance between two atoms
echo - send text to the status line and Reply Log
export - save the graphical scene (X3D, VRML, POV-Ray, RenderMan formats) or the surfaces only (OBJ format)
fillring - show rings as filled
findclash - identify clashes and/or contacts
findhbond - identify possible hydrogen bonds
fly - smoothly traverse a series of saved positions
focus - adjust the view and center of rotation
freeze - stop all motion
getcrd - report untransformed coordinates
hbonds - identify possible 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
ksdssp - determine secondary structure from protein coordinates
label - display atom labels
labelopt - control the information in atom labels
lighting - adjust lighting and shininess
linewidth - control the width of wire bonds
longbond - show/hide pseudobonds representing missing segments
mask - extract volume data bounded by surfaces
match - superimpose two models by a least-squares fit 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
measure - perform various calculations on structures, surfaces, maps
meshmol - create a "molecule" from surface mesh for stick display
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 - create a trajectory that morphs between two or more 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 - name and save 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
pdbrun - send an annotated PDB file to the system shell
perframe - specify an alias to be executed at each display frame
preset - apply a predefined combination of display settings
rainbow - color residues, chains, or models over a range
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
ribbackbone - allow display of both ribbon and backbone atoms
ribbon - display 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)
rlabel - display residue labels
rmsd - evaluate the RMSD between specified sets of atoms
rock - rotate models back and forth (oscillate)
roll - rotate models
rotation - make a bond rotatable
runscript - run Python script with command-line arguments
save - save the current Chimera session
savepos - save the current orientations
scale - scale the view
scolor - color surfaces a single color or by volume data or geometry
section - move the clipping planes in parallel
segment - act on segmentation models
select - activate models for motion or select atoms
set/unset - set background color and 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 - edit a surface model
split - make the chains of a molecule model separate submodels
start - start Chimera tools by name
stereo - switch amongst stereo options and mono viewing
stop - exit from Chimera
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 the clipping planes in opposite directions
tile - arrange models in a plane
topography - plot values in a volume data plane as heights in a surface
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
volume - visualize volume data (3D numerical data such as electron density)
vop - edit volume data to create a new volume data set
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

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 an explicit multiple-frame wait (not the implicit single-frame wait mentioned above) to prevent subsequent commands from executing until it is finished. Usually wait without arguments will serve this purpose.
• 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.