Jmol users -- I'm developing a list of new Jmol script/JavaScript
functionality in 11.0 relative to 10.2. Please let me know if I've
missed something. --Bob Hanson
axes command
boundbox command
color altloc
color insertion
color measures
color molecule
conformation [n]
console
data command
dipole command
dots +1.2
draw arrow
draw line
draw plane
draw point
echo "first line | second line | ...."
exit [to stop all script execution and clear script queue]
fractional coordinates
frame play
frame playrev
frame prev
frame range
frank command
geosurface command
getproperty animationInfo
getproperty appletInfo
getproperty atomInfo
getproperty auxiliaryInfo
getproperty bondInfo
getproperty boundBoxInfo
getproperty centerInfo
getproperty chainInfo
getproperty dataInfo
getproperty extractModel
getproperty fileContents
getproperty fileContents
getproperty fileHeader
getproperty fileName
getproperty jmolStatus
getproperty measurementInfo
getproperty modelInfo
getproperty moleculeInfo
getproperty orientationInfo
getproperty polymerInfo
getproperty shapeInfo
getproperty transformInfo
hbonds calculate
hbonds on [initially shows file-only hbonds]
hbonds, cartoons: enhanced biomolecule DSSP hydrogen bond calculation
help command
hover "first line | second line | ...."
isosurface [atomic orbitals]
isosurface [ellipsoids]
isosurface [lcaoCartoon hybrid orbitals]
isosurface [molecular orbitals]
isosurface [spheres]
isosurface [user-defined functions]
isosurface JVXL file creation/reading
javascript:jmolAppletAddParam()
javascript:jmolDecodeJSON()
javascript:jmolGetPropertyAsArray()
javascript:jmolGetPropertyAsJavaObject()
javascript:jmolGetPropertyAsJSON()
javascript:jmolGetPropertyAsString()
javascript:jmolGetStatus()
javascript:jmolLoadAjax_MSA()
javascript:jmolLoadAjax_STOLAF_ANY()
javascript:jmolLoadAjax_STOLAF_RCSB()
javascript:jmolLoadAjaxJS()
javascript:jmolLoadInlineScript()
javascript:jmolRestoreOrientation()
javascript:jmolRestoreOrientationDelayed()
javascript:jmolSaveOrientation()
javascript:jmolScriptWait()
javascript:jmolScriptWaitAsArray()
javascript:jmolSetAtomCoord()
javascript:jmolSetAtomCoordRelative()
javascript:jmolSetCallback()
javascript:jmolSetLogLevel()
label "%o" # space group operation
label "first line | second line | ...."
label formats: %A, %N, %o, %S, %X, %Y, %Z
lcaoCartoon command
load "fileset" "file1.xyz" "file2.PDB" "file3.CIF" ...
load "myfile.cif" n
load "myfile.cif" {i j k}
load "myfile.pdb" {i j k} spacegroup "[Hall Symbol]"
load "myfile.pdb" {i j k} spacegroup "[H-M Symbol]"
load "myfile.pdb" {i j k} spacegroup "[Jones-Faitful operator set]"
load "myfile.xyz" {i j k} unitcell {a b c alpha beta gamma}
load argusFile limited capability
load CML expanded functionality
load DOM node expanded functionality
load file with embedded "#jmolscript:"
load gamess output basis/orbital coefficients
load gaussian output basis/orbital coefficients
load spartan output basis/orbital coefficients
load TRIPOS/SYBYL mol2 data file viewer support
load Wavefunction Odyssey file viewer support
load Wavefunction Spartan 06 file viewer support
load WebMO file basis/orbital coefficients
measure RANGE [min] [max] (atomset) (atomset) .....
measure all
measure allConnected
measures delete
measures off
message command
mo [JVXL file creation]
mo color
mo cutoff
mo next
mo noplane
mo plane "xy"
mo plane {1 1 1 0}
mo prev
mo resolution
mo TITLEFORMAT
mo translucent
pmesh inline
polyhedra [# vertices] [basis] [selection sets] [display options]
quit [to quit currently running script]
rotate -x
rotate 10 $line1
rotate 20 (atomno=8) (atomno=10)
rotate y 10 (atomno=4)
rotate y 10 molecular (atomno=4)
rotate/zoom enhancement of mouse action with SHIFT-LEFT (zoom/rotate)
select [not] specialPosition
select [not] symmetry
select cell={1 j k}
select cell=555
select molecule=n
select PDB and mmCIF alternate location visualization
select site=n
select symop=n
select within(ELEMENT,expression)
select within(MOLECULE,...)
select within(SITE,expression)
set animFrameCallback
set appletProxy
set axesMolecular
set axesUnitCell
set axesWindow
set cartoonRockets
set defaultDirectory
set defaultLoadScript
set displayCellParameters
set dotsSelectedOnly
set dotSurface
set echo myecho 102 100
set echo myecho 30% 50%
set hovercallback
set labelsFront
set labelsGroup
set loadStructCallback
set loglevel [0-5]
set measureAllModels
set measurements nm
set measurements pm
set measturementNumbers
set messagecallback
set pickcallback
set picking ELEMENT
set picking SITE
set pickingStyle
set rangeSelected
set scriptQueue
set showAxes //deprecated -- see "axes"
set showBoundBox //deprecated -- see "boundBox"
set showSelections //deprecated -- see "set display"
set showUnitcell //deprecated -- see "unitcell"
set statusReporting
set windowCentered
show data "type"
show draw
show $drawObject
show isosurface
show measurements
show mo
show spacegroup
show spacegroup "Pmmn"
show symmetry
show url
show url "url"
spin -x
spin 10 $line1
spin 20 (atomno=8) (atomno=10)
spin y 10 (atomno=4)
spin y 10 molecular (atomno=4)
translateSelected command
unitcell command
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