Jmol enhanced figure toolkit - a manual for authors

Introduction Why Jmol? When to use an enhanced figure How to submit an enhanced figure An introductory tutorial Tutorial 2: an inorganic crystal lattice Tutorial 3: a small metal-organic molecule Tutorial 4: a biological macromolecule molecule Toolkit options reference Some Jmol resources Acknowledgements Appendix: useful Jmol commands

Appendix: useful Jmol commands

Basic mouse controls

For a full menu of options: click the right mouse button (CTRL + click on a Mac).

To zoom in or out: SHIFT + click and hold the left mouse button (SHIFT + click on a Mac).

To rotate compounds in 3D: click and hold the left mouse button (click on a Mac).

To rotate compounds in the plane of the screen: SHIFT + click and hold the right mouse button.

To move compounds in the plane of the screen: CTRL + click and hold the right mouse button.

Synopsis of Jmol commands

The following list of commands, with a synopsis of the most useful options, is taken from the Jmol scripting documentation at http://chemapps.stolaf.edu/jmol/docs/

animation ON/OFF{default: ON}
animation direction -1/+1
animation fps [frames-per-second]
animation frame
animation mode LOOP [time-delay1] [time-delay2]
animation mode ONCE
animation mode PALINDROME [time-delay1] [time-delay2]

axes ON/OFF{default: ON}
axes (decimal)
axes DOTTED
axes (integer)
axes MOLECULAR
axes UNITCELL
axes WINDOW

backbone ON/OFF{default: ON}
backbone [backbone-radius]

background [RGB-color]
background HOVER [color-none-CPK]
background LABELS [color-none-CPK]

bondorder 0.5, 1, 1.5, 2, 2.5, 3, 4, -1, -1.5, -2.5
bondorder [connection-options]

boundbox [atom-expression]{default: all atoms}
    [line-width-or-type]{default: ON}
boundbox [atom-expression-or-coordinate] [xyz-coordinate]
    [line-width-or-type]{default: unchanged}
boundbox CORNERS [atom-expression-or-coordinate]
    [atom-expression-or-coordinate]
    [line-width-or-type]{default: unchanged}

calculate AROMATIC
calculate HBONDS
calculate STRUCTURE
calculate SURFACEDISTANCE WITHIN [atom-expression]
calculate SURFACEDISTANCE FROM [atom-expression]

cartoon ON/OFF{default: ON}
cartoon [cartoon-radius]

center [atom-expression]
center [xyz-coordinate]
center [drawn-object]
center

centerAt ABSOLUTE x y z {default: 0.0 0.0 0.0}
centerAt AVERAGE x y z {default: 0.0 0.0 0.0}
centerAt BOUNDBOX x y z {default: 0.0 0.0 0.0}

color _color_name_or_scheme
color (atom object) 
color [atom-associated-object] _color_name_or_scheme
color (bond object) 
color BONDS [color-none-CPK]
color SSBONDS [color-none-CPK]
color HBONDS [color-none-CPK]
color HBONDS TYPE
color (element) 
color [element-name] [RGB-color]
color [model-object] [RGB-color]
color (named object) 
color [drawn-object] [RGB-color]
color (scheme) 
color "colorSchemeName" RANGE [min] [max]
color measures [RGB-color]
color selectionHalos [color-none-CPK]

configuration [configuration number]

connect 

console 

data "label"
data CLEAR

define [variable-name] [atom-expression]

delay [time-delay]
delay on

depth 

dipole 

display [atom-expression]

dots ON/OFF{default: ON}
dots VANDERWAALS
dots IONIC
dots nn%
dots (decimal)
dots +(decimal)

draw [objectID] [modifying parameters] [positions] 
draw DELETE
draw LIST

echo (string)

ellipsoid or ellipsoids 
ellipsoid ON/OFF{default: ON}
ellipsoid nn%
ellipsoid [object id] ON
ellipsoid [object id] OFF
ellipsoid [object id] AXES {ax ay az} {bx by bz} {cx cy cz}
ellipsoid [object id] CENTER {x y z}
ellipsoid [object id] CENTER { atom expression }
ellipsoid [object id] CENTER $object
ellipsoid [object id] COLOR [color parameters]
ellipsoid [object id] DELETE
ellipsoid [object id] SCALE (decimal)

exit 

font [object-with-text] [font-size]
    [font-face]{default: SansSerif}
    [font-style]{default: Plain}

frame (integer >= 1)
frame (decimal) / (decimal) - (decimal)
frame 0 / 0.0
frame ALL / LAST / NEXT
frame PAUSE
frame PLAY (starting frame)
frame PLAYREV (starting frame)
frame PREVIOUS
frame RANGE (starting frame) (ending frame)
frame RESUME
frame REWIND

frank ON/OFF

geoSurface ON/OFF{default: ON}
geoSurface VANDERWAALS
geoSurface IONIC
geoSurface (integer)
geoSurface (decimal)
geoSurface +(decimal)

getProperty animationInfo
getProperty appletInfo
getProperty atomInfo (atom expression)
getProperty atomList (atom expression)
getProperty auxiliaryInfo
getProperty bondInfo (atom expression)
getProperty boundBoxInfo
getProperty centerInfo
getProperty chainInfo (atom expression)
getProperty dataInfo type
getProperty extractModel (atom expression)
getProperty fileContents
getProperty fileContents filepath
getProperty fileHeader
getProperty fileName
getProperty image
getProperty jmolStatus statusNameList
getProperty jmolViewer
getProperty measurementInfo
getProperty messageQueue
getProperty modelInfo
getProperty moleculeInfo (atom expression)
getProperty orientationInfo
getProperty polymerInfo (atom expression)
getProperty shapeInfo
getProperty stateInfo (atom expression)
getProperty transformInfo

halos ON/OFF{default: ON}
halos [radius-in-angstroms]
halos nn%

hbonds ON/OFF{default: ON}
hbonds [width-in-angstroms]
hbonds CALCULATE

help query

hide [atom-expression]

history ON/OFF{default: ON}

hover (integer)

initialize 

invertSelected 
invertSelected POINT point_definition
invertSelected PLANE plane_express
invertSelected HKL {h k l}

isosurface 
isosurface DELETE
isosurface LIST

javascript "javascript commands"

label ON/OFF/string
label TOGGLE (atom expression)

lcaoCartoon ON/OFF{default: ON}
lcaoCartoon CREATE "[type]"
lcaoCartoon CREATE "[type]" MOLECULAR
lcaoCartoon COLOR [RGB-color]
lcaoCartoon COLOR [RGB-color] [RGB-color]
lcaoCartoon DELETE
lcaoCartoon LIST
lcaoCartoon ROTATE [x|y|z] (decimal) "[type]"
lcaoCartoon SCALE (decimal)
lcaoCartoon SELECT (atom expression)
lcaoCartoon SELECT "[type]"
lcaoCartoon TRANSLUCENT or OPAQUE

load
load "filename"
load [param-ignored] "filename"
load APPEND "filename"
load FILES "filename1" "filename2"
load "filename" (integer)
load "filename" {i j k}
load "filename" {ijk i'j'k' 1}
load "filename" {ijk i'j'k' 0}
load "filename" {ijk i'j'k' [0 or 1]} range xxx
load "" {i j k}
load "filename" {i j k} spacegroup "name"
load "filename" {i j k} spacegroup "ignoreOperators"
load "filename" {i j k} spacegroup "x,y,z;x+1/2,y,z"
load "filename" {i j k} unitcell {a b c alpha
    beta gamma}

loop [time-delay]
loop on

measure or monitor 
measure ON/OFF{default: ON}
measure "n:labelFormat"
measure (integer) (integer) "labelFormat"
measure (integer) (integer) (integer) "labelFormat"
measure (integer) (integer) (integer)
    (integer) "labelFormat"
measure (two to four atom expressions, each in
    parentheses) labelFormat
measure ALL (two to four atom expressions, each
    in parentheses) "labelFormat"
measure ALLCONNECTED (two to four atom expressions,
    each in parentheses) "labelFormat"
measure DELETE
measure DELETE (integer)
measure DELETE (two to four atom expressions, each
    in parentheses)
measure RANGE (decimal) (decimal)
    ALL|ALLCONNECTED|DELETE

meshribbon ON/OFF{default: ON}
meshribbon [mesh-ribbon-radius]

message (string)

mo ON/OFF{default: ON}
mo (integer)
mo COLOR [RGB-color]
mo COLOR [RGB-color] [RGB-color]
mo CUTOFF (decimal)
mo DELETE
mo HOMO [+/-n]
mo LUMO [+/-n]
mo NEXT
mo NOPLANE
mo PLANE plane_expression
mo PREVIOUS [RGB-color]
mo RESOLUTION (decimal)
mo TITLEFORMAT "format"

model 

move [x-rotation] [y-rotation] [z-rotation]
    [zoom-factor] [x-translation] [y-translation]
    [z-translation] [slab-cutoff] [seconds-total]
    [move-frames-per-second]{default: 30}
    [maximum-acceleration]{default: 5}

moveto timeSeconds FRONT|BACK|LEFT|RIGHT|TOP|BOTTOM
moveto timeSeconds {x y z} degrees zoomPercent transX
    transY {x y z} rotationRadius navigationCenter
    navTransX navTransY navDepth
moveto timeSeconds {x y z} degrees 0 transX transY
    (atom expression) 0 zoomAdjustment
    navigationCenter navTransX navTransY navDepth
moveto timeSeconds {x y z} degrees (atom expression)
    0 zoomAdjustment navigationCenter navTransX
    navTransY navDepth

navigate timeSeconds CENTER {x y z}
navigate timeSeconds CENTER (atom expression)
navigate timeSeconds CENTER $object
navigate timeSeconds DEPTH percent
navigate timeSeconds PATH $object
navigate timeSeconds PATH (any combination of
    coordinates, atom expressions, and objects)
navigate timeSeconds ROTATE X degrees
navigate timeSeconds ROTATE Y degrees
navigate timeSeconds ROTATE Z degrees
navigate timeSeconds TRACE (atom expression)
navigate timeSeconds TRANSLATE xxx yyy
navigate timeSeconds TRANSLATE X xxx
navigate timeSeconds TRANSLATE Y yyy
navigate timeSeconds TRANSLATE {x y z}
navigate timeSeconds TRANSLATE (atom expression)
navigate timeSeconds TRANSLATE $object

pause or wait 

pmesh pmeshID{default: all pmeshes}
pmesh pmeshID{default: all pmeshes} ON/OFF{default: ON}
pmesh pmeshID{default: all pmeshes} DELETE
pmesh pmeshID(optional) "filename"
pmesh pmeshID{default: all pmeshes} DOTS or NODOTS
    {default: NODOTS} "xyz.pmesh.gz"{default: current}
pmesh pmeshID{default: all pmeshes} FILL or NOFILL
    {default: FILL} "xyz.pmesh.gz"{default: current}
pmesh LIST
pmesh pmeshID{default: all pmeshes} MESH or NOMESH
    {default: NOMESH} "xyz.pmesh.gz"{default: current}

polyhedra 

ramachandran

refresh 

reset AUTOMATIC
reset FUNCTIONS
reset variableName
reset ALL

restore BONDS saveName
restore ORIENTATION saveName timeSeconds
restore SELECTION saveName
restore STATE saveName

restrict {default: ALL}
restrict [atom-expression]

ribbon ON/OFF{default: ON}
ribbon [ribbon-radius]

rocket ON/OFF{default: ON}
rocket [rocket-radius]

rotate
rotate X/Y/Z [number-of-degrees]
rotate AXISANGLE [xyz-coordinate] [number-of-degrees]

rotateSelected 

save 
save BONDS saveName
save ORIENTATION saveName
save SELECTION saveName
save STATE saveName

script [file-name]
script [file-name] CHECK
script [file-name] COMMAND n
script [file-name] LINE n
script INLINE [Jmol math expression]
script INLINE varName
script javascript:functionCall()

select 
select {default: ALL}
select [atom-expression]

selectionHalos 
selectionHalos ON/OFF{default: ON}

set
set xxx?

set (antialiasing) 
set antialiasDisplay OFF
set antialiasTranslucent ON
set antialiasImages ON

set (bond styles) 
set bondMode AND
set bondMode OR
set bondModeOr FALSE
set bondRadiusMilliAngstroms (integer)
set bondTolerance (decimal)
set dipoleScale (-10.0 to 10.0)
set hbondsSolid FALSE
set hbondsBackbone FALSE
set minBondDistance (decimal)
set showMultipleBonds ON
set ssbonds BACKBONE or SIDECHAIN
set ssBondsBackbone FALSE

set (callback) 
set AnimFrameCallback "function name"
set HoverCallback "function name"
set LoadStructCallback "function name"
set MessageCallback "function name"
set PickCallback "function name"
set ResizeCallback "function name"

set (debugging) 
set debugScript OFF
set historyLevel (integer)
set logLevel (0 - 5)
set scriptReportingLevel (integer)
set showScript OFF
set showScript milliseconds

set (ellipsoids)
set ellipsoidAxes ON
set ellipsoidArcs ON
set ellipsoidBall ON
set ellipsoidFill ON

set (files and scripts) 
set allowEmbeddedScripts
set appendNew TRUE
set appletProxy "URL"
set applySymmetryToBonds OFF
set autobond ON
set dataSeparator "separator text"
set defaultDirectory "directory path"
set defaultLattice {i j k}
set defaultLoadScript "script"
set forceAutoBond OFF
set history nLines
set loadFormat "URL"
set scriptQueue ON

set (highlights) 
set display SELECTED/NORMAL
set fontSize [font-size]{default: 8}
set frank

set (labels) 
set labelAlignment LEFT, RIGHT, or CENTER
set labelAtom (atom expression)
set labelFront (atom expression)
set labelGroup (atom expression)
set labelOffset [x-offset] [y-offset] (atom expression)
set labelPointer OFF (atom expression)
set labelPointer BACKGROUND (atom expression)
set labelToggle (atom expression)

set (language) 

set (lighting) 
set ambientPercent (integer 0 to 100)
set diffusePercent (integer 0 to 100)
set specular OFF
set specularExponent (integer 1 to 10)
set specularPercent (integer 0 to 100)
set specularPower (integer 0 to 100)

set (measure) 
set defaultDistanceLabel "format"
set defaultAngleLabel "format"
set defaultTorsionLabel "format"
set dynamicMeasurements ON
set measurements [width-in-angstroms]
set measurements [linewidth-pixels]
set justifyMeasurements FALSE
set measurements DOTTED
set measurementLabels ON
set measurementUnits [distance-unit]
set showMeasurements TRUE

set (misc) 
set allowRotateSelected FALSE
set animationFps (integer)
set autoFPS FALSE
set axis1Color "color_name"
set axis2Color "color_name"
set axis3Color "color_name"
set backgroundModel (integer >= 1) or "filemodel"
set chainCaseSensitive FALSE
set colorRasmol FALSE
set defaultColorScheme JMOL or RASMOL
set defaultDrawArrowScale (decimal)
set defaults JMOL or RASMOL
set dotsSelectedOnly FALSE
set dotSurface ON
set drawHover OFF
set drawPicking OFF
set exportDrivers "driver_list"
set formalCharge (integer)
set helpPath "URL"
set hoverDelay (decimal)
set hoverLabel (string)
set isosurfacePropertySmoothing ON
set measureAllModels OFF
set percentVdwAtom (integer)
set pickingSpinRate (integer)
set propertyAtomNumberField (integer)
set propertyColorScheme "colorSchemeName"
set propertyDataField (integer)
set rangeSelected
set selectHetero ON
set selectHydrogen ON
set smartAromatic ON
set spinFps [frames-per-second]
set spinX [degrees-per-second]
set spinY [degrees-per-second]
set spinZ [degrees-per-second]
set stateVersion (integer)
set statusReporting ON
set stereoDegrees (decimal)
set syncMouse OFF
set syncScript OFF
set useNumberLocalization ON
set vectorScale (decimal)
set vibrationPeriod (decimal)
set vibrationScale (decimal)
set wireframeRotation OFF

set (navigation) 
set hideNavigationPoint FALSE
set navigationDepth (percent)
set navigationMode FALSE
set navigationPeriodic FALSE
set navigationSpeed (decimal)
set navigationSlab (percent)
set showNavigationPointAlways FALSE
set visualRange (angstroms)

set (perspective) 
set cameraDepth (positive number)
set perspectiveDepth ON
set perspectiveModel 11
set scaleAngstromsPerInch [viewing-distance]
set rotationRadius (Angstroms)
set windowCentered ON
set zoomEnabled ON
set zoomLarge ON
set zShade OFF

set (structure) 
set cartoonRockets OFF
set hermiteLevel (integer, -8 to 8)
set highResolution OFF
set ribbonAspectRatio (integer)
set ribbonBorder OFF
set rocketBarrels OFF
set sheetSmoothing (0 to 1)
set strandCount [strand-count]
set strandCountForMeshRibbon [strand-count]
set strandCountForStrands [strand-count]
set traceAlpha TRUE

set (visibility) 
set axes [line-width-or-type]
set axesMode 0, 1, or 2
set axesMolecular OFF
set axesScale (decimal)
set axesUnitcell OFF
set axesWindow ON
set backgroundColor [RGB-color]
set boundbox [line-width-or-type]
set defaultTranslucent (decimal)
set disablePopupMenu FALSE
set displayCellParameters TRUE
set greyScaleRendering OFF
set hideNameInPopUp FALSE
set hideNotSelected FALSE
set refreshing TRUE
set showAxes FALSE
set showBoundBox FALSE
set showFrank TRUE
set showHiddenSelectionHalos FALSE
set showHydrogens TRUE
set showSelections FALSE
set showUnitcell FALSE
set slabEnabled FALSE
set solventProbe OFF
set solventProbeRadius [probe-radius-in-angstroms]
    {default: 1.2}
set unitcell

set echo 
set echo user-named [horizontal-position]
    {default: left}
set echo user-named x-position y-position
set echo user-named %x %y
set echo user-named {x y z}
set echo user-named { [atom-expression] }}
set echo [vertical-position] ON
set echo user-named ON
set echo ALL
set echo NONE
set echo OFF

set picking 
set picking ON
set picking CENTER
set picking DRAW
set picking IDENT
set picking LABEL
set picking MEASURE
set picking MEASURE DISTANCE
set picking MEASURE ANGLE
set picking MEASURE TORSION
set picking NAVIGATION
set picking SELECT ATOM
set picking SELECT CHAIN
set picking SELECT ELEMENT
set picking SELECT GROUP
set picking SELECT MOLECULE
set picking SELECT SITE
set picking SPIN [frames-per-second]

set pickingStyle 
set pickingStyle SELECT toggle
set pickingStyle SELECT selectOrToggle
set pickingStyle SELECT extendedSelect
set pickingStyle SELECT NONE
set pickingStyle MEASURE ON

set userColorScheme 
set userColorScheme colorName colorName �

show BOUNDBOX
show CENTER
show COLORSCHEME "name"
show DATA "type"
show DRAW
show FILE
show FILE filepath
show ISOSURFACE
show FUNCTIONS
show HISTORY n
show MEASUREMENTS
show MO
show MODEL
show ORIENTATION
show PDBHEADER
show SET
show SPACEGROUP "name"
show STATE [optional name]
show SYMMETRY
show TRANSFORM
show UNITCELL
show URL
show URL URL
show ZOOM
show $objectID

slab ON/OFF{default: ON}
slab [slab-percent]
slab HKL {h k l} or NONE
slab -HKL {h k l}
slab PLANE plane_expression or NONE
slab -PLANE plane_expression
slab RESET
slab SET

spacefill ON/OFF{default: ON}
spacefill [radius-in-angstroms]
spacefill [radius-percent-vdw]
spacefill +(solvent probe radius)
spacefill IONIC
spacefill TEMPERATURE

spin 
spin ON/OFF{default: ON}

ssbonds ON/OFF{default: ON}
ssbonds [width-angstroms]
ssbonds [width-Rasmol]

star ON/OFF{default: ON}
star [length-in-angstroms]
star nn%

stereo [stereo-viewing-angle]{default: 5}
stereo {default: ON}
stereo OFF
stereo REDBLUE [stereo-viewing-angle]{default: 3}
stereo REDCYAN [stereo-viewing-angle]{default: 3}
stereo REDGREEN [stereo-viewing-angle]{default: 3}
stereo [RGB-color] [RGB-color] [stereo-viewing-angle]
    {default: 3}

strands ON/OFF{default: ON}
strands [strand-radius]

subset 

sync &PER;|>|*|appletId|appletId[syncId] ON
sync &PER;|>|*|appletId|appletId[syncId] SLAVE
sync &PER;|>|*|appletId|appletId[syncId] OFF
sync &PER;|>|*|appletId|appletId[syncId] "command"

trace ON/OFF{default: ON}
trace [trace-radius]

translate 
translate X or Y [percent-translation]

translateSelected 
translateSelected {x y z}

unitcell ON/OFF{default: ON}
unitcell (decimal)
unitcell DOTTED
unitcell {i j k}

vector ON/OFF{default: ON}
vector [diameter-pixels]
vector [radius-in-angstroms]
vector SCALE [vector-scale]

vibration ON/OFF{default: ON}
vibration [time-period]
vibration PERIOD [time-period]
vibration SCALE [vibration-scale]

wireframe ON/OFF{default: ON}
wireframe [radius-in-angstroms]
wireframe [radius-Rasmol]

write 
write fileName
write COORDS SPT|XYZ|MOL|PDB "fileName"
write FILE "fileName"
write FUNCTIONS "fileName"
write HISTORY "fileName"
write IMAGE JPG|JPG64 n "fileName"
write IMAGE PNG n "fileName"
write IMAGE PPM "fileName"
write ISOSURFACE "fileName"
write MO "fileName"
write STATE "fileName"
write VAR [variable name] "fileName"

zap 

zoom ON/OFF{default: ON}
zoom [percent-zoom]
zoom (atom expression) or {x y z} [percent-zoom]
zoom (atom expression) or {x y z} + or - delta
zoom (atom expression) or {x y z} * or / factor

zoomto
zoomto OUT
zoomto [time-in-seconds] (atom expression) or {x y z}
zoomto [time-in-seconds] (atom expression) or {x y z}
    [percent-zoom]
zoomto [time-in-seconds] (atom expression) or {x y z}
    + or - delta
zoomto [time-in-seconds] (atom expression) or {x y z}
    * or / factor
zoomto [time-in-seconds] (atom expression) or {x y z} 0