Chimera Keyboard Shortcuts (Accelerators)

Keyboard shortcuts are disabled by default, but can be enabled:

The following keyboard shortcuts are included with Chimera (and more can be defined):
Visualization Framework
Opening, Saving, Closing
Move Viewpoint or Models
Background Color and Effects
Selecting Objects
Model Display and Clipping
Commands, Mouse, Messages
Zones and Selections
Comparing Domain Orientation
Multimers and Symmetry
Volume Data
Opening, Saving, Closing
Surface Display
Measure Area, Volume, Length, ...
Segmenting and Filtering
Fit or Build Models
Opening, Saving, Closing
opOpen file
osOpen session
ffFetch file from web
lsOpen last session
olOpen last file
okOpen 2nd to last file
ojOpen 3nd to last file
o2Open last 2 files
o3Open last 3 files
loShow names of files last opened
(via dialog or accelerator only)
siSave image
SsSave session
ssSave session as
CaClose all models
CsClose session
QtQuit Chimera
Move Viewpoint or Models
vaView all models
soStandard orientation
x9Turn 90 degrees about x axis
y9Turn 90 degrees about y axis
z9Turn 90 degrees about z axis
svShow Side View dialog
crSet center of rotation (pivot)
a0 Activate model 0 (toggle)
a1Activate model 1 (toggle)
a2Activate model 2 (toggle)
a3Activate model 3 (toggle)
aaActivate all models
aoActivate only selected models
arInactivate active models and activate inactive models
atActivate all models and remember which were inactive; used again, inactivates remembered models
OpOriginal model positions (reset default)
wtWrite relative transformation matrices
na nd
nf nz
SpaceNavigatorTM (3D mouse) settings
Background Color and Effects
bkSet background to black
wbSet background to white
dcToggle depth cueing
shToggle shadows
seToggle silhouettes
3dToggle sequential stereo camera mode
Model Display and Clipping
mpShow Model Panel dialog
klShow Per-Model Clipping dialog
caToggle clipping mouse mode for selected model
ccToggle per-model clipping of selected and displayed models
cvToggle per-model clipping of current set of volume data
orToggle between orthographic and perspective projection
Selecting Objects
saSelect all
csClear selection
isInvert selection (selected models)
iSInvert selection (all models)
Molecule Display
daDisplay atoms
haHide atoms
DaDelete atoms and bonds
wrWire representation
stStick representation
spSphere representation
bsBall & stick representation
bbBackbone only
ctShow chain trace only
sxShow side chains only
rrRound ribbon
reEdged ribbon
rfFlat ribbon
hrHide ribbon
rhHide ribbon
sfShow surface
sFSurface selected atoms
hsHide surface
Commands, Mouse, Messages
clShow Command Line
ocType one command
hcHide Command Line
afDisable accelerators
adShow Keyboard Shortcuts dialog
rlReply Log
rtReport graphics frame rate
psPython shell (IDLE)
pfPreferences dialog
mmMouse preferences (mouse button assignments)
slShow/Hide status line
ugUser's Guide
Molecule Coloring
c2Color ribbons by secondary structure
ceColor atoms by element
raShow Render by Attribute dialog
rcRainbow chains
Molecule Zones and Selections
scSelect connected atoms/bonds
c3Find 3-Å contacts between selected and unselected atoms
c5Find 5-Å contacts between selected and unselected atoms
riSelect residue interval
rnSelect next residue
rpSelect previous residue
zdShow zone dialog
znSelect zone using zone dialog settings
Comparing Domain Orientation
ab Superimpose two structures using selected backbone atoms with matching residue/chain IDs
ai Show transformation between two structures using selected backbone atoms with matching residue/chain IDs
Multimeric Molecules and Symmetry
buShow molecule biological unit using Multiscale Models
mBSet molecule PDB BIOMT matrices for selected multiscale chains (details...)
ucShow Unit Cell dialog
xcExtend multiscale selection to sequence copies
Opening, Saving, Closing Volume Data
ovOpen volume
vsShow volume
fvShow full volume
vhHide volume
vRRemove volume
vvShow Volume Viewer dialog
wgWrite GRASP surface file
xsExport scene
Surface Display
cmShow Surface Color dialog
coColor selected surfaces
cpShow Surface Capping dialog
DsDelete selected surfaces
fsShow selected surfaces in filled style
msShow selected surfaces using mesh style
ScSplit selected surfaces into connected pieces (see also sop split)
szResize selected surfaces with mouse (one drag with button 3)
tsToggle surface selectability
t0Make selected surfaces 0% transparent
t5Make selected surfaces 50% transparent
Volume Appearance
obToggle volume outline box display
pxToggle solid style pixel display
Segmenting and Filtering Volume Data
ddDelete selected segmentation regions
ebErase volume data inside subregion selection box
esErase volume data inside sphere
eoErase volume data outside sphere
ezCopy volume with zeros inside zone
FTShow Fourier transform
ggGroup selected segmentation regions
ImInvert map values
LTShow volume Laplacian
rhHide selected segmentation regions
rsShown only the selected segmentation regions
smSplit map by color zone
u8Interpret MRC signed 8-bit map as unsigned
uuUngroup selected segmentation regions
vmMask volume inside selected surfaces
wvMake writable copy of volume data
zbZero volume boundary
zB2Zero volume boundary for step size 2
zB4Zero volume boundary for step size 4
zvCopy volume with zeros outside zone
Measure Area, Volume, Length ...
maMeasure area of selected surfaces
mdMeasure mean, standard dev, rms of volume data
mvMeasure volume of selected surfaces
mwReport molecular weight of selected atoms
pLShow total length of selected bonds for each model
plShow total length of selected bonds
sdMeasure distance from selected atoms/markers to surface, assign atom attribute distance
Placing Models in Volume Data
frRotate model to maximize density at selected atoms
ftMove model to maximize density at selected atoms
oaFind selected atoms outside contour surface
bvExtend periodic map to cover selected atoms
vpShow Volume Tracer dialog
dpDisplay path tracer markers
hpHide path tracer markers
mzPlace marker at (0,0,0) in local coordinates of selected models, in global coordinates if no models selected
mcPlace marker at center of rotation
mCPlace marker at center of selected atoms
mEPlace a marker at center of area of each selected surface piece
mkPlace marker under mouse
mPPlace one marker at center of area of multiple surface pieces
mSPlace markers on selected atoms


ab and ai - superimpose and compare backbone segments that have the same sequences, numbering, and chain identifiers.

Atoms from exactly two models must be selected, and atoms other than CA (proteins) and P (nucleic acids) are ignored. Only atoms with the same name, residue type, residue number, and chain identifier are paired; ab performs a least-squares fit and applies the resulting transformation, whereas ai does not apply the transformation but shows it with two rectangular slabs colored to match the structures. Both ab and ai report the RMSD, number of atom pairs, and angle of rotation in the status line and Reply Log.

One application is to measure changes in relative domain orientation in different conformations of a multidomain protein. For example, the thioredoxin reductase structures 1f6m and 1tde differ by a rotation of one domain relative to the other. They are different conformations of essentially the same protein and are numbered in the same way (chains other than A can be deleted). After selection of one domain (approximately residues 1-117, 245-320) in both structures, ab could be used to superimpose that domain. The selection could then be inverted to encompass the other domain (approximately residues 118-244) in both structures and ai used to compute the transformation, in this case a rotation of ~67°. This conformational change is described in Lennon et al., Science 289:1190 (2000). The two accelerators do not have to be used together; the first domain could be superimposed manually or with MatchMaker before ai is used to compare the orientations of the second domain. See also: measure rotation

bv - Extend periodic map to cover selected atoms.

Creates a new map that covers the currently selected atoms plus 5 Å padding on all sides. The map is derived from the current set of data (active map) in Volume Viewer. If the atoms plus padding extend beyond the bounds of the active map, then it is assumed that the active map is periodic along all three axes (such as a unit cell crystallographic density map). The new map is displayed using the thresholds and colors of the original map and the original map is undisplayed. See also: vop cover

Im - Invert map values.

If the map value type is signed (e.g. 32-bit float or signed 16-bit integer), each value is multiplied by -1. For unsigned 8-bit maps, the values are multiplied by -1 and 255 is added so that the values remain unsigned. For other unsigned maps, the values are multiplied by -1 and the maximum map value is added so that the map remains unsigned. The accelerator acts on the current set of data in Volume Viewer. A copy of the map is made unless the map is itself a copy (for example, made using wv, zb, or Volume Eraser). The original file is not modified. Use the volume dialog menu (File... Save map as...) to save the inverted map.

sd - Measure distance from selected atoms/markers to surface.

The distance from each selected atom or path tracer marker to each displayed surface is printed in the Reply Log. Example:

Distance from #0:18.water@O to surface MSMS main surface of 1a0m.pdb
 d = 2.09, surface point (3.14, -1.28, 7.85), side 1
Whether a surface is displayed is evaluated at the levels of surface model and surface piece (but not at the per-atom level of a molecular surface).

The coordinates of the nearest surface point and the side of the surface that the point lies on (+1 = outside, –1 = inside) are given. The closest surface point may lie within a triangle, on a triangle edge, or at a triangle vertex of the triangulated surface. If multiple surface points are equidistant, only one is reported. The calculation has been implemented in C++ for better performance. Each selected atom's distance to the surface last measured is assigned as the atom attribute named distance. To remove any ambiguity in interpreting the attribute values, it is best to perform the measurements with only a single surface present.

u8 - Interpret MRC signed 8-bit map as unsigned.

The MRC volume file format does not support unsigned 8-bit map values. Some EM tomography programs use it to hold unsigned 8-bit values (0-255) with the data type in the file header incorrectly indicating that the values are signed 8-bit (-128 to 127). Use the u8 accelerator to reinterpret the data values as unsigned 8-bit. The original file is not modified. The accelerator acts on the current set of data in Volume Viewer. It only works on MRC format maps.

UCSF Computer Graphics Laboratory / September 2014