Commands Index

The following are commands entered into Chimera's Command Line. Each command (but not its keywords, unless explicitly indicated) may be shortened to a unique prefix. Many commands act upon specified atoms. Past commands can be accessed using the Command History. Multiple commands can be placed in a file.

+ significantly changed or enhanced in Chimera relative to MidasPlus
U UNIX only (not on Windows)
C Chimera only (not available in MidasPlus)

acC - enable the use of accelerators (keyboard shortcuts)
addaa - add an amino acid to a peptide C-terminus
addhC - add hydrogens
alias - create an alias or list existing aliases
align - align two atoms along the line of sight
angle - measure a bond angle or torsion angle
bond - add/delete bonds
bondcolorC - color bonds independently from atoms
bonddisplayC - control how bond display depends on atom display
bondreprC - control the representation of bonds (wire or stick)
brotation - make a bond rotatable
cd - change the working directory
center - center the view on specified atoms
chain - chain specified atoms, undisplay the others
chiralityC - 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, labels, and surfaces
colordef - define a new color
conic - create a static space-filling rendering with shadows
copy+ - save or print the displayed image
defattrC - 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 Reply Log
findhbondC - identify possible hydrogen bonds
focusC - adjust the view and center of rotation to the displayed and specified atoms
freeze - stop all motion
getcrd - report untransformed coordinates
hbondsC - identify possible hydrogen bonds
help - display the manual page for a command
ksdssp - determine secondary structure from protein coordinates
label - display atom labels
labeloptC - control the information in atom labels
linewidthC - control the width of lines in the wire representation
load - restore a saved Chimera session
longbond - find and remove excessively long bonds
match - superimpose two models by a least-squares fit of specified atoms
matchmakerC - align models in sequence and then superimpose them accordingly
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
mmakerC - align models in sequence and then superimpose them accordingly
modelcolorC - set color at the model level
modeldisplayC - set display at the model level
move - translate along the X, Y, or Z axis
msmsC - (see surfcat/surfrepr)
neonU - create a static space-filling or stick rendering with shadows
objdisplay - display and undisplay VRML models
open+ - open structures or data for display or execute a command file
pdbrun - send an annotated PDB file of the current display to the system shell
push/pop - push or pop images on the picture stack
rainbow - color residues, chains, models over a range (default blue to red)
rangecolorC - color over a range according to attribute values
read - execute a command file, only updating the display at the end
representC - control the representation of atoms and bonds (wire, stick, ball-and-stick, or sphere)
reset - restore default or saved orientations
ribbackboneC - allow ribbon and all backbone atoms to be displayed simultaneously for residues within a model
ribbonC - display a secondary structure ribbon
ribbonjrU - create a static ribbon rendering
ribcolorC - set ribbon color
ribreprC - control the ribbon representation (flat, sharp, or smooth)
rlabel+ - display residue labels
rmsdC - 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 for further operations
set/unset - set options
show - display specified atoms, undisplay the others
sleep - suspend command processing for a specified length of time
source - execute a command file, updating the view continually
stereo - switch amongst stereo options and mono viewing
stop - exit from Chimera
surface+ - calculate and display molecular surface
surfcat/surfreprC - create molecular surface categories and control the surface representation
surfcolorC - set whether surface color is determined at the atom or model level
swapaa - mutate amino acid residues
swapna - mutate nucleic acid residues
system - send a command to the system shell
tcolorC - color atoms/bonds, labels, and surfaces with a texture color
textureC - define texture maps and associated colors
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
vdwdefineC - set VDW radii
vdwdensityC - set VDW surface dot density
version - show copyright information and which version of Chimera is being used
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
write - save a molecule model as a PDB file
x3dsave - save the graphical scene as an X3D file

Of the Midas commands unsupported by Chimera, some may be implemented in the future; others have been rendered obsolete or replaced by other functionality.

Command Files

Files of commands can be created manually or saved using the Command History. Comments are indicated by # at the beginning of a line. A command file can be executed: