Commands

The following are commands entered into Chimera's Command Line (Midas Emulator). Each command (but not its keywords, unless explicitly indicated) may be shortened to a unique prefix. Many commands act upon specified atoms.

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

ac^C - enable the use of accelerators (keyboard shortcuts)
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
brotation - make a bond rotatable
cd - change working directory
center - center specified atoms in the graphics window
chain - create a simplified chain display of protein, DNA, or RNA
clip - move clipping planes
close - delete open models
cofr - report or change the center of rotation
color⁺ - color atoms, labels, and surfaces
colordef - define a new color
conic^U - create a static space-filling rendering with shadows
copy⁺ - save or print the displayed image
display - display and undisplay atoms
distance - measure the distance between two atoms
echo - send text to the reply buffer
focus^C - adjust the view and center of rotation to the displayed and specified atoms
freeze - halt any ongoing motion
getcrd - report the untransformed coordinates of an atom
help - display the manual page for a command
ksdssp - determine secondary structure from protein coordinates
label - label and unlabel atoms
labelopt^C - change what information is shown in labels
linewidth^C - change the thickness of lines in wireframe displays
load - restore a saved Chimera session
longbond - find and remove excessively long bonds
match - superimpose models by a least-squares fit to specified atoms
matrixcopy - apply the transformation matrix of one model to another
modelcolor^C - set color at the model level
modeldisplay^C - set display at the model level
move - translate a model along the x, y, or z axis
msms^C - (see surfcat/surfrepr)
neon^U - create a static space-filling or stick rendering with shadows
objdisplay - display and undisplay VRML models
open⁺ - open a model or execute a Python file
pdbrun^U - send an annotated PDB file of the current display to the system shell
push/pop - save (retrieve) model orientations to (from) an image stack
rainbow - rainbow-color biopolymer chains, starting with red and ending with blue
read - read and execute commands from a file, updating the display after the entire file is read
represent^C - change molecular representations among wire, stick, ball-and-stick, and sphere
reset - restore default or saved orientations
ribbon^C - display a secondary structure ribbon
ribbonjr^U - create a static ribbon rendering
ribcolor^C - set ribbon color
ribrepr^C - change among different secondary structure ribbon representations
rock - rock a model back and forth about the x, y, or z axis
roll - rotate a model about the x, y, or z axis
rotation - make a bond rotatable
save - save a Chimera session
savepos - save orientations
scale - scale the view
section - move both clipping planes in the same direction
select⁺ - activate models for motion or select atoms for further operations
set/unset - set autocoloring of new models or independent centers of rotation
show - display specified atoms and undisplay the others
sleep - pause command execution for a specified number of seconds
source - read and execute commands from a file, updating the display after each
stop - exit from Chimera
surface⁺ - create and display a molecular surface
surfcat/surfrepr^C - create molecular surface categories and control the surface representation
surfcolor^C - 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
tcolor^C - color atoms, labels, and surfaces with a texture color
texture^C - define texture maps and associated colors
thickness - move the clipping planes in opposite directions
turn - rotate a model about the x, y, or z axis
vdw - display a van der Waals (VDW) dot surface
vdwdefine^C - change VDW radii
vdwdensity^C - change the VDW surface dot density
version - report which version of Chimera is being used
wait - pause command execution a specified number of frames or until ongoing motions are complete
window - adjust the view to contain the displayed and specified atoms
write - save a molecule model as a PDB 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.