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.

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 arbitrary text labels and place them in 2D
ac - use accelerators (keyboard shortcuts)
addaa - add an amino acid to a peptide C-terminus
addcharge - assign partial charges to atoms
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
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
brotation - make a bond rotatable
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 surfaces
colordef - define a new color
conic - create a shadowed space-filling image
copy - save an image (Chimera graphics or POV-Ray)
crystalcontacts - identify clashes between PDB symmetry copies
defattr - assign attribute values to atoms, residues, or models
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)
findclash - identify clashes and/or contacts
findhbond - identify possible hydrogen bonds
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
linewidth - control the width of wire bonds
load - restore a saved Chimera session
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
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
move - translate along the X, Y, or Z axis
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)
objdisplay - display and undisplay VRML models
open - read local files or fetch by ID
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
push/pop - push or pop images on the picture stack
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 - set ribbon color
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 - rock back and forth about the X, Y, or Z axis
roll - rotate about the X, Y, or Z axis
rotation - make a bond rotatable
save - save the current Chimera session
savepos - save the current orientations
scale - scale the view
section - move the clipping planes in parallel
select - activate models for motion or select atoms
set/unset - set options
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 command processing
solvate - add solvent using AmberTools
source - execute a command file, updating the display continually
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 surface color source
surftransparency - adjust molecular surface transparency
swapaa - mutate amino acids or swap rotamers
swapna - mutate nucleic acid residues
sym - generate copies of a structure at symmetric positions that update automatically
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
topography - plot values in a volume data plane as heights in a surface
thickness - move the clipping planes in opposite directions
turn - rotate about the X, Y, or Z axis
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
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
x3dsave - save the graphical scene as an X3D file

Chimera Command Files

Chimera command files are simply text files containing the same commands that could be entered at the Command Line. Examples:

rescol.com for coloring amino acid residues
setup.com from the ViewDock tutorial
movie content examples

Command files can be created manually or by saving the Command History. A midasrc file is a command file that is executed automatically when the Command Line is started (see the Midas preferences). Placing aliases and color definitions in a midasrc file is a convenient way to apply them each time Chimera is used.

Rules and tips:

Lines that begin with a pound sign (#) are interpreted as comments.
The locations of files opened by a command file can be specified relative to the command file's location, or with absolute pathnames. If the files are in the same directory as the command file, for example, only their names need to be given.
Multiple commands can be combined on a single line with semicolons (;) to suppress the display of intermediate states. In this way, multiple graphical changes such as in style and color can be made to appear simultaneously instead of one by one.
Certain commands are especially useful for scripting continuous motion, and wait enforces their ordered rather than simultaneous execution.

Ways to execute a command file:

with the command source, which updates the display after each line as needed
by simply opening the file (equivalent to using source). 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 Midas preferences

In addition, Chimera demos are largely constructed from commands.

UCSF Computer Graphics Laboratory / June 2008