Commands Index

The following commands can be entered into Chimera's Command Line. Certain conventions are followed in their usage descriptions. Past commands can be accessed from the Command History, and commands can be placed in an executable command file.

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

2dlabelsC - create arbitrary text labels and place them in 2D
acC - enable the use of accelerators (keyboard shortcuts)
addaa - add an amino acid to a peptide C-terminus
addchargeC - assign partial charges to atoms
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, ribbons, 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
findclashC - identify clashes and/or contacts
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
intersurfC - generate and display interface surfaces
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 - show/hide pseudobonds representing missing segments
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
minimizeC - energy-minimize structures
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
movieC - capture image frames and assemble them into a movie file
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
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
setattrC - set an attribute to a specified value
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
startC - start Chimera tools by name
stereo - switch amongst stereo options and mono viewing
stop - exit from Chimera
surface+ - calculate and display molecular surfaces
surfcat/surfreprC - create molecular surface categories and control the surface representation
surfcolorC - set whether surface color is determined at the atom or model level
surftransparencyC - adjust molecular surface transparency
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
viewdockC - start ViewDock and load docking results
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 all or part of a molecule model as a PDB file
writeselC - write a parsable text file containing specifications of the currently selected (or unselected) items
x3dsaveC - 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.

Chimera Command Files

Chimera command files are simply text files containing the same commands that could be entered at the Command Line (see an example command file). Command files can be created manually and/or by saving the Command History. Rules and tips:

Ways to execute a command file: In addition, Chimera demos are largely constructed from commands.

UCSF Computer Graphics Laboratory / September 2006