Complete list of new Jmol script/JavaScript functionality in 11.0 relative to 10.2. 
See http://www.stolaf.edu/academics/chemapps/jmol/docs for details. Some of these 
commands are not documented because they are intended for serialization only -- for the
construction of a Jmol script describing the precise state of the applet or application.

axes command
bondOrder single|double|triple|hbonds  # *undocumented; for serialization
boundbox command
calculate hbonds
calculate structure
calculate surface [distance|+distance|distance%]
color altloc
color halos
color insertion
color measures
color molecule
color selectionHalos ....
color surfaceDistance
conformation [n]
console ON|OFF|CLEAR
data command
dipole command
dots +x.x
dots n%
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
halos ON/OFF
halos n% 
halos x.y
hbonds, cartoons: enhanced biomolecule DSSP hydrogen bond calculation
help command
hover "first line | second line | ...."
if;else;endif;
initialize  # *undocumented; for serialization
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:jmolLoadInLine([array of model strings])
javascript:jmolLoadInlineScript()
javascript:jmolRestoreOrientation()
javascript:jmolRestoreOrientationDelayed()
javascript:jmolSaveOrientation()
javascript:jmolScriptWait()
javascript:jmolScriptWaitAsArray()
javascript:jmolSetAtomCoord()
javascript:jmolSetAtomCoordRelative()
javascript:jmolSetCallback()
javascript:jmolSetLogLevel()
label "first line | second line | ...."
label formats: %A, %N, %o, %S, %u, %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
measure delete
measure "some label format"
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
moveTo [time-sec] front|back|left|right|top|bottom
pause
pmesh inline
polyhedra [# vertices] [basis] [selection sets] [display options]
quit [to quit currently running script]
restore bonds [name]
restore orientation [name] [timeSeconds]
restore selection [name]
restore state [name]
resume
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)
save bonds [name]
save orientation [name]
save selection [name]
save state [name]
select AL*  # * wildcard for PDB group names
select A*   # * wildcard for non-PDB/mmCIF atom names and atom names for all file types
select ({...})  # *undocumented; for serialization
select BONDS ({...})  # *undocumented; for serialization
select cell={1 j k}
select cell=555
select molecule=n
select PDB and mmCIF alternate location visualization
select site=n
select surfacedistance=xxx
select symop=n
select unitcell
select fractionalCharge
select [not] specialPosition
select [not] symmetry
select within(ELEMENT,expression)
select within(MOLECULE,...)
select within(SITE,expression)
set [any parameter name]
set animFrameCallback
set appletProxy
set axesMolecular
set axesUnitCell
set axesWindow
set backgroundModel N
set cartoonRockets
set dataSeparator
set defaultDirectory
set defaultLoadScript
set displayCellParameters
set dotsSelectedOnly
set dotSurface
set echo all
set echo none
set echo myecho 50  100
set echo myecho {1/1 1/1 1/1};echo (1 1 1)
set echo myecho (atomno=10) or (atomno=8);echo x
set echo somename 30% 50%
set forceAutoBond
set fractionalCharge
set frank
set hermiteLevel [-8 to 8]
set hideNotSelected
set highResolution 
set history n
set hovercallback
set labelAtom
set labelFront  # no parameters
set labelGroup  # no parameters
set labelPointer on/off/background
set loadStructCallback
set loglevel [0-5]
set measureAllModels
set measurements nm
set measurements pm
set measurements au
set measurements Bohr
set measturementNumbers
set messagecallback
set pickcallback
set picking SELECT ELEMENT
set picking SELECT MOLECULE
set picking SELECT SITE
set picking SPIN
set pickingStyle MEASURE
set pickingStyle MEASURE OFF
set pickingStyle SELECT toggle
set pickingStyle SELECT selectOrToggle
set pickingStyle SELECT extendedSelect
set rangeSelected
set refreshing [false/true]  # *undocumented; for serialization
set ribbonAspectRatio n
set showscript
set scriptQueue
set selectionHalos ON/OFF
set sheetSmoothing [0 to 1]
set showHiddenSelectionHalos
set showAxes //deprecated --  see "axes"
set showBoundBox //deprecated -- see "boundBox"
set showSelections //deprecated -- see "set display"
set showUnitcell //deprecated -- see "unitcell"
set statusReporting
set traceAlpha
set zoomLarge
show data "type"
show draw
show $drawObject
show history
show isosurface
show measurements
show mo
show [any parameter name]
show spacegroup
show spacegroup "Pmmn"
show state
show symmetry
show unitcell
show url
show url "url"
spin -x
spin 10 $axis1
spin 20 (atomno=8) (atomno=10)
spin y 10 (atomno=4)
spin y 10 molecular (atomno=4)
subset *:C
translateSelected command
unitcell command
write
zap  # allows echos and MUCH more
zoom (atom) +|-delta
zoom (atom) *|/factor
zoomTo [time-sec] (atom) +|-delta
zoomTo [time-sec] (atom) *|/factor