Jmol 12.0 new features 7/28/2010
New Jmol features introduced since the release of Jmol 11.8 on 8/26/2009 are highlighted here.
A PDF version of this file is Jmol-12.0-quickstart.pdf
Item links are to topics in examples-11/new.htm
Generally new capability
Graphical User Interface
New file readers
New file reading capabilities
New file output/export capabilities
Structure searching/matching
Atom properties
Jmol scripting functions and variables
New commands
New command options
-- customizable mouse button/action bindings
-- multi-touch/Kiosk capability using SPARSHUI adaptation (U-Tube video)
-- parallel multiprocessor capability for isosurface creation
-- drag-and-drop to signed applets and the application -- see drop.htm
-- model kit mode allows rapid construction of simple models
-- extensive support for depiction of space groups -- see Jmol Crystal Structure Explorer
-- conversion of 2D models (SMILES, JME, MOL) to 3D -- see JmeToJmol.htm
-- interface to JSDraw for 2D structure input -- see jstest.htm
-- interface to Flot for plotting data -- see jmol-flot.htm and jmol-flot-energy.htm
-- full implementation of Daylight SMILES/SMARTS
-- extension of Daylight SMARTS to 3D conformation
-- introduction of Jmol bioSMILES and bioSMARTS
-- new JmolSmilesApplet.jar. See JmolSmiles.htm, JmolSmilesTest.htm,
-- JavaScript-like flow commands and TIMEOUT
-- JavaScript-like TRY/CATCH error handling
-- direct reading of Uppsala electron density maps
-- natural bond orbital reading/rendering
-- direct logging to files using the LOG command
right-edge zoom
new mouse action: LEFT-DOUBLE-CLICK-DRAG
new multi-touch interface
SET command autocompletion in console
CRYSTAL reader
DGRID reader
isosurface DSN6/O electron density map readering
2D MOL reader to 3D
JME reader converts 2D to 3D
direct loading of SMILES strings to 3D
direct reading of Uppsala electron density maps
VASP vasprun.xml
XPLOR electron density reader
drag-and-drop to signed applet and from browsers
reading of polymer(1D) and slab(2D) unit cells
loading with option to save a local version (LOAD .... AS ….)
reading of Natural Bond Orbitals
reading of simple PDB trajectories
Spartan/Cygress FILTER "noOrient"
extended XYZ file format
reading specialized file data as property_xxxx
new LOG command
Jmol Archive Format (.jmol)
JVXL XML format
webExport enhancements
export of IDTF/laTeX for 3D-PDF files
full 3D-SEARCH SMILES/SMARTS and bioSMILES/bioSMARTS implementation
{*}.find("SEQUENCE")
{*}.find("smartsString",asArray)
{*}.find("SMILES”,"MF")
{*}.find("SMARTS","MF")
SMILES stereochemistry matching
SMILES-based conformational testing and alignment
light-weight JmolSmilesApplet.jar
SMARTS atropisomer matching
MEASURE search("...")
SET picking measure SEQUENCE
SHOW SMILES
better RNA hydrogen bond calculation
generalized hydrogen bond calculation
shapes: negative size implies ONLY
van der Waals default 23%AUTO
{xxx}.cartoon (etc.) Shapes: size testing and setting
{xxx}.eta for nucleic acids
{xxx}.polymer
{xxx}.selected
{xxx}.find("SEQUENCE")
{xxx}.find("smartsString",asArray)
{xxx}.find("SMILES”,"MF")
{xxx}.find("SMARTS","MF")
{xxx}.ionicRadius
{xxx}.theta for nucleic acids
{xxx}.volume("type")
{xxx}.x {xxx}.y {xxx}.z
x**y
associative arrays
acos(x)
compare()
hkl(a,b,c)
3x3 matrix math
4x4 matrix math
measure()
now()
prompt()
quaternion arrays
quaternion differences, means, and standard deviations
quaternion dot product q1.dot(q2)
symop(n)
symop(n,"...")
symop(n) * symop(m)
_multiTouchServer, _multiTouchClient flags
$SCRIPT_PATH$ script pre-processing variable
implicit SCRIPT command
BIND
COMPARE
FIX
LOG
MAPPROPERTY
PARALLEL
PLOT
PROCESS
PROMPT
STRUTS
SWITCH/CASE
TIMEOUT
TRY/CATCH
UNBIND
translucent color schemes
AXES CENTER {x y z}
AXES LABELS
AXES TICKS
BOUNDBOX $isosurface1
BOUNDBOX SCALE x.x option
BOUNDBOX TICKS
CALCULATE HYDROGENS
COLOR “BW”
COLOR “WB”
CONNECT XX% YY% ...
DELETE HYDROGENS
DRAW BOUNDBOX
DRAW INTERSECTION $myIsosurfaceID PLANE|HKL
DRAW INTERSECTION BOUNDBOX PLANE|HKL
DRAW INTERSECTION UNITCELL PLANE|HKL
DRAW LINEDATA
DRAW POLYGON
DRAW SYMOP
DRAW UNITCELL
FRAME TITLE (from file-based model names)
FRANK OFF (local signed applet)
GETPROPERTY mouseInfo
GETPROPERTY SHAPEINFO
GETPROPERTY shapeInfo.isosurface
GETPROPERTY shapeInfo.pmesh
INVERTSELECTED STEREO option
ISOSURFACE ... COLOR "color1 color2 color3..."
ISOSURFACE color MESH [color]
ISOSURFACE ... map CONTOUR DISCRETE and INCREMENT
ISOSURFACE ... map MEP functionType
ISOSURFACE lattice {a b c}
ISOSURFACE "=nnnn"
ISOSURFACE ANISOTROPY generalized
ISOSURFACE CAP
ISOSURFACE color DENSITY
ISOSURFACE contour DISCRETE
ISOSURFACE contour INCREMENT
ISOSURFACE INLINE
ISOSURFACE FULLPLANE
ISOSURFACE OFFSET
ISOSURFACE SCALE3D
ISOSURFACE SIGMA
ISOSURFACE SLAB
ISOSURFACE WITHIN x.x {points}
LABELS DISPLAY
LABELS HIDE
LCAOCARTOON CPK
LOAD $CCC(C)C -- smiles string loading
LOAD @x where x is an array of file names
LOAD -n (single vibration)
LOAD DATA
LOAD INLINE "JME string" and load "@x"
LOAD "filename" AS "localFileName"
LOAD "somefilename" 0 (last-model loading)
MEASURE search("...")
MEASURE TICKS
MINIMIZE ADDHYDROGENS
MINIMIZE SILENT
PMESH ANISOTROPY generalized
PMESH OFFSET
PRINT symop(n,"...")
ROTATE (matrix variable)
ROTATE COMPARE option
ROTATE HELIX option
ROTATE TRANSLATE {x y z} option
SCRIPT LOCALPATH/REMOTEPATH
SELECT configuration=1
SELECT CYSTINE
SELECT POLYMER=n
SELECT RANGESELECTED extended
SELECT search() -- 3D-SMARTS
SELECT SPINE
SELECT within(BASEPAIR)
SELECT within(nResidues, GROUP, atoms)
SELECT within(POLYMER, {someAtoms})
SELECT within(SEQUENCE,"1-letter-code sequence")
SET allowGestures
SET allowModelKit
SET allowMultiTouch
SET cartoonBaseEdges
SET clickCallback
SET dotScale
SET HIGHLIGHT
SET isKiosk
SET minimizationSilent
SET ModelKitMode
SET mouseDragFactor
SET mouseWheelFactor
SET phongExponent
SET picking connect
SET picking deleteAtom
SET picking deleteBond
SET picking dragAtom
SET picking dragMinimize
SET picking dragMinimizeMolecule -- responsive docking
SET picking invertStereo
SET picking measure SEQUENCE
set picking select STRUCTURE
set picking select POLYMER
SET pickingStyle DRAG
SET preserveState FALSE
SET quaternionFrame "A", "C", and "P" for nucleic acids
SET saveProteinStructureState
SET slabByAtom
SET slabByMolecule
SET waitForMoveTo FALSE
SET zshade
SET zshadePower
SHOW BASEPAIRS
SHOW MOUSE [option]
SHOW SMILES
SHOW SYMOP
SHOW TIMEOUTS
SPACEFILL RESET
TRANSLATE SELECTED x/y/z
UNITCELL TICKS
WIREFRAME ONLY and wireframe -x.y
WIREFRAME RESET
WRITE MESH
WRITE PMESH
WRITE state LOCALPATH/REMOTEPATH
ZOOM IN|OUT
ZOOMTO IN|OUT