Jmol 13.0 released

Bob Hanson — Thu, 23 Aug 2012 15:45:15 -0000

Jmol 13.0 was released Aug 22, 2012. This major release brings to the stable release several very important new features in Jmol developed over the past year.

With well over 500,000 full application downloads (that is, distinct binary downloads by application users or developers, not simple applet downloads by users), full server-side Java support for non-Java (iPhone/iPad) or non-applet (Android) mobile devices, and a completely new JavaScript interface, Jmol is well-positioned for the next phase of development of a high-level scripted high-functional HTML5/WebGL user interface.

New features (see http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm\) include:

APPLET:
-- a new OOP JavaScript interface (Jmol-JSO)
allowing nonJava options such as ChemDoodle and GLmol
as well as JME/JSpecView connectivity (see http://wiki.jmol.org/index.php/Jmol_Javascript_Object\) to be seamlessly integrated into a web page in a platform-aware manner.
-- JmolData full "headless" operation for server-side processing allowing image-creation, server processing, and remote cross-domain sourcing for the unsigned applet and applet surrogates such as ChemDoodle and GLmol.

BIOPHYSICS:
-- COMPARE command

FILE READING:
-- reading of JCAMP-DX files having structure/spectra assignment data
using ##$MODELS and ##$PEAKS (see http://chemapps.stolaf.edu/jmol/jspecview\)
-- Gaussian log reading of Natural Transition Orbitals
-- automatic PNGJ file caching for immensely faster loading of PNGJ files from remote servers

FILE WRITING:
-- write PNGJ files encapsulate all model file data into one PNG file
-- write image 400 400 PNGJ "http://....." POSTs JMOL or IMAGE or structure to a server as application/octet-stream
-- write MOL adds partial charge data as > <JMOL_PARTIAL_CHARGES> in SDF format
-- multiple-scene PNGJ files allowing minimal or full data loading and scripted animations

ISOSURFACES:
-- isosurface caching
-- isosurface MOVE [[...matrix4f...]] moves/rotates an isosurface (for the state)

MINIMIZATION:
-- MMFF94/UFF minimization and energy calculation

MOLECULAR DATA:
-- show CHEMICAL
-- show NMR

MOLECULAR PLAYGROUND:
-- MolecularPlayground -- remote status and remote control

SOLID-STATE PHYSICS:
-- solid state physics support

SPECTROSCOPY:
-- integration of JSpecView into Jmol, including 2D spectral display and manipulation

STRUCTURE SEARCHING:
-- extended Jmol SMARTS searching
-- PubChem search for name (which can be a CAS number), cid, or SMILES using ":"

Jmol 12.2 released with over 100 new features

Bob Hanson — Sun, 30 Oct 2011 02:51:52 -0000

Jmol 12.2 introduces over 100 new features in a wide variety of disciplines. For details, see http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm

Some highlights include:

CONNECTIONS TO OTHER SYSTEMS:

direct access to NIH CACTVS server and IUPAC name recognition software for small-molecule structures

fully verified DSSP calculation of protein secondary structure

support for materials science surface first-principles computation visualization (CASTEP, CRYSTAL, QuantumEspresso, VASP, WIEN2K)

Molprobity file reading

SURFACES:

new CONTACT command

reversible and extensible isosurface slabbing

probability-based atomic orbitals

display of linear combinations of molecular orbitals

STRUCTURE ANALYSIS AND SEARCHING:

structure- and SMILES-based substructure searching using SMARTS

bioSMARTS/bioSMILES, and conformational SMARTS searching (Jmol innovations)

diasteriomer/enantiomer comparison and checking with structures or SMILES strings

ORGANIC CHEMISTRY:

easy mechanistic arrows

display of 2D drawing images, chemical names,

... and much, much more! The full list:

117. LOAD trajectory extended to vibrations
116. write transparent-background PNG images
115. load "xxx.xxx" [ list of models to load ]
114. set minPixelSetRadius
113. CRYSTAL09 tensor quantities
112. unitcell {xxx yyy scale}
111. Application console commands UNDO, REDO
110. UNDOMOVE/REDOMOVE n
109. set isosurfaceKey
108. SurfaceTool
107. FEATURE CHANGE: "ligand"
106. MolProbity contact dot reader
105. new CONTACT command
104. select within(VDW, xxxx)
103. "picked" variable
102. select/display/hide GROUP ...
101. select/display/hide ADD/REMOVE
100. @n
99. {atomset}.x?
98. measure INTRAMOLECULAR/INTERMOLECULAR
97. measure VDW
96. set measurementUnits VDW
95. calculate HYDROGEN and set pdbAddHydrogens
94. load "==XXX"
93. more information with LOAD
92. isosurface slab n
91. show lighting
90. .count and .count(x)
89. JVXL files return state
88. arbitrary function surfaces
87. isosurface INTERSECTION
86. color isososurface {atom expression} [color]
85. select within(distance, $surfaceID)
84. isosurface slab within x.x {atom expression or point}
83. set defaultLablPDB and set defaultLabelXYZ
82. reversible isosurface slab
81. plane(r, theta, phi)
80. NCI surfaces
79. FEATURE CHANGE -- zshadePower default
78. set zSlab {atom expression or point}
77. quaternion()
76. isosurface PARAMETERS
75. color atoms property VECTORSCALE
74. appletReadyCallback
73. atomMovedCallback
72. connecting surfaces to atoms
71. simple curved mechanistic reaction arrows
70. pointilist atomic/molecular orbitals projected onto planes
69. pointilist molecular orbitals
68. pointilist atomic orbitals
67. loading of structure by IUPAC name
66. show chemical name/inchi/inchikey
65. isosurface remapping
64. set echo ID
63. show drawing
62. for (var x in [...]) {....}
61. for (var x in {...}) {....}
60. SPARTAN READER charge default changed
59. xxx.mass.sum
58. plane(<point>, <vector>, true)
57. frame TITLE @someArray
56. load MENU label "null"
55. write COORD XYZVIB filename
54. draw ARROW...BARB
53. isosurface... map property x WITHIN x.y
52. COMMAND-SHIFT-LEFT-DRAG (Macintosh only)
51. expanded XYZ file format
50. mo -n
49. loading of DCD files
48. linear combinations of molecular orbitals
47. write XXX.OBJ
46. intersection() function
45. x.sort, x.reverse
44. V2000 MOL reader reads partial charges
43. write xxxx.XYZRN
42. load filter "|" and "/=" options
41. isosurface spherical slab
40. isosurface MSMS xxxx.vert
39. isosurface/draw .length
38. draw SLAB
37. plane(pt1, pt2)
36. write SDF and write V3000
35. measure LIST
34. CIF file load defaults and load FILTER "MOLECULAR"
33. point(x.y)
32. label %{dataName}
31. set allowMoveAtoms
30. isosurface ROTATE
29. new auxiliaryinfo subset infoUnitCell
28. reset STRUCTURE
27. load OFFSET {x y z}
26. command aliases
25. set defaultStructureDSSP
24. structure HELIX310; structure HELIXPI; select HELIX310; select HELIXPI
23. "xxxx"%9999, "xxxx"%-9999 to upper/lower case
22. show state/xxxx
21. save STRUCTURE
20. calculate structure (DSSP)
19. show DSSP
18. calculate hbonds STRUCTURE
17. load SUPERCELL
16. measureCallback adds unrounded value
15. set structure helix/sheet/turn
14. hide/display bonds
13. color bonds directly using connected()
12. set multipleBondSpacing and set multipleBondRadiusFactor
11. set slabRange -- zoom-independent slab range
10. new SHAPE property
9. lcaoCartoon sp3d, sp3d2
8. "drill-down" properties
7. zSlab, zDepth; slab, depth
6. new NIH/SMILES load $XXXX service
5. new color() function and getProperty shapeInfo.isosurface[n].colorKey
4. isosurface display within 2.0 {...}
3. {*}.find("SMILES", SMILESstring)
2. compare(a,b,"ISOMER")
1. load ... unitcell [ax, ay, az, bx, by, bz, cx, cy, cz]

Jmol 12.0 released

Bob Hanson — Fri, 30 Jul 2010 04:03:35 -0000

Jmol 12.0 was released today with over 170 new features compared to the previous release, Jmol 11.8. Full details may be found at

http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm

Generally new capability
-- 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
-- model kit mode allows rapid construction of simple models
-- extensive support for depiction of space groups
-- conversion of 2D models (SMILES, JME, MOL) to 3D
-- interface to JSDraw for 2D structure input
-- interface to Flot for plotting data
-- full implementation of Daylight SMILES/SMARTS
-- extension of Daylight SMARTS to 3D conformation
-- introduction of Jmol bioSMILES and bioSMARTS
-- new JmolSmilesApplet.jar.
-- 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

Jmol 11.8 released - over 215 new features

Bob Hanson — Sun, 30 Aug 2009 00:06:22 -0000

Jmol 11.8, released August 26, 2009, introduces over 215 new features compared to Jmol 11.6, which was released less than a year previously. Notable new features include greatly expanded scripting capability, extensive quaternion analysis and display capability, full support for working with cyrstallographic coordinates and planes, display of point group and cyrstallographic space group symmetry operations, display of Ramachandran planes and dihedral angles, creating of JPG and PNG files with embedded Jmol state so that the 2D image can also be dropped into Jmol and instantly become a 3D object, much expanded VRML and IDTF export capability, trapping of out-of-memory condition errors, and several new readers, including AIMS, Alchemy/3DNA, CASTEP, EFVET, Gromacs, isosurface OBJ, Materials Studio XML, and Wien2k.

Jmol 11.7 reads AMBER trajectories

Bob Hanson — Wed, 08 Oct 2008 18:08:07 -0000

The development prerelease of Jmol, Jmol 11.7, includes the capability to read AMBER topology and coordinate files. See the example scripts at http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm

Jmol 11.6 released -- over 200 new features

Bob Hanson — Wed, 01 Oct 2008 13:04:38 -0000

Jmol 11.6 is now available.

One of the most significant upgrades of Jmol to date, Jmol 11.6 includes over 200 new features introduced between January and October of 2008, including several totally new capabilities, such as point group identification and drawing of point group symmetry elements, thermal ellipsoid rendering, the capability to delete specific models from a set, 2D to 3D conversion and 3D minimization using the Universal Force Field (UFF), 3D Ramachandran plotting, quaternion maps for peptides and nucleic acids, and upgrading of the signed applet to enable file writing.

New features are discussed at http://chemapps.stolaf.edu/jmol/docs/examples-11/new6.htm.

Documentation for Jmol 11.6 is available at http://chemapps.stolaf.edu/jmol/docs?ver=11.6

Bob Hanson, Oct. 8, 2008
hansonr@stolaf.edu

# new feature: // at beginning of a line marks comments
# new feature: "%T" label format for straightness
# new feature: "load" of Jmol state scripts works same as "script" command
# new feature: "quaternion derivative" --> "quaternion difference", which is more
# new feature: $"xxx" quotations or $@{...} allows variable definition of object id reference
# new feature: $*xx* double wild cards
# new feature: (popup menu) Biomolecules submenu added within title menu
# new feature: .sub(), .add(), .mul(), .div() extended to all operand types
# new feature: /*SPLIT*/ in a command string allows it to be processed by
# new feature: [dots|stars|spacefill] ADPMAX [percent]
# new feature: [dots|stars|spacefill] ADPMIN [percent]
# new feature: [draw|pmesh|isosurface] xxx* [on|off|delete]
# new feature: _applet boolean
# new feature: _signedApplet boolean is available:
# new feature: {point1} == {point2} if distance < 0.000001
# new feature: {quaternion} == {quaternion2} if distance < 0.000001
# new feature: allows zip files to be designated as default directories
# new feature: applet console has "help" menu item, which includes several hundred items.
# new feature: applet message regarding help and command entry
# new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value
# new feature: application [>|] button
# new feature: application measure button tied to picking style
# new feature: application pick button reinstated
# new feature: application select button reinstated
# new feature: axes labels change subtly for set axesMolecular and setAxesOrientationRasmol
# new feature: axes position [x y] and axes position [x y %]
# new feature: background IMAGE "filename"
# new feature: better draw pointgroup
# new feature: calculate pointGroup
# new feature: calculate pointGroup -- preliminary only -- untested
# new feature: CIF reading of B factors for thermal ellipsoids
# new feature: cross(a,b)
# new feature: DATA "data2d_xxxxx"..... end "data2d_xxxxx"
# new feature: DATA "property_x i j" .... END "property_x i j"
# new feature: data() and DATA expanded to allow fixed-column entry
# new feature: DELETE $xxx
# new feature: delete {atom expression} NEEDS TESTING
# new feature: dipole/draw/ellipsoid/isosurface/pmesh/mo/lcaocartoon ID keyword optional
# new feature: DISPLAY $xxx
# new feature: draw .... ">xxx" first character of title ">" forces title to
# new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows
# new feature: draw {point} {plane}
# new feature: draw {point} PLANE [plane def, including xy, yz, x, etc.]
# new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
# new feature: draw arrow {point} {plane}
# new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
# new feature: draw CIRCLE
# new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive open/filling syntax
# new feature: draw CYLINDER
# new feature: draw pointGroup
# new feature: draw pointGroup [type] [index] SCALE [x]
# new feature: draw quaternion [w|x|y|z|a|r] [difference][2]
# new feature: draw RAMACHANDRAN
# new feature: draw ramachandran includes planes connecting atoms.
# new feature: draw Vector [x y] or [x y %] {x' y' z'}
# new feature: draw VECTOR {atom center} {dx dy dz}
# new feature: draw vector {point} {plane}
# new feature: draw with mixed types processes them in order
# new feature: echo myecho DEPTH xx
# new feature: echo myecho IMAGE "filename"
# new feature: echoCallback
# new feature: ellipsoid ball rendering tied to "set wireframerotation" option
# new feature: extended quaternion math
# new feature: float1 == float2 if |float1 - float2| < 0.000001
# new feature: font [type] [size] [face] [weight] [scaleReference (Angstroms per pixel)]
# new feature: four optional defaults for Van der Waals radii:
# new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed.
# new feature: full math on individual atom properties using
# new feature: GamessUK reader
# new feature: generally for objects (draw,pmesh,isosurface,etc.) use DISPLAY/HIDE rather than ON/OFF
# new feature: getproperty menu current
# new feature: getProperty minimizationInfo
# new feature: getProperty PointGroupInfo
# new feature: getProperty("appletInfo") includes a key "registry" for which
# new feature: HIDE $xxx
# new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
# new feature: in Java 1.6.0_10, right-click activates the console, and the
# new feature: inline math @{x+3} extended to all commands
# new feature: integration of star, halo, and spacefill code so all behave the same.
# new feature: isosurface DOWNSAMPLE n # down-factors the number of points in a CUBE file by a factor of n
# new feature: isosurface ELLIPSOID id
# new feature: isosurface FunctionXY "data2d_xxxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
# new feature: isosurface FunctionXY "data2d_xyz_xxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
# new feature: isosurface functionXY can be used for mapping.
# new feature: isosurface MAXSET n # removes larger fragment sets
# new feature: Jmol math within("branch", {atom1}, {atom2})
# new feature: jmolSetCallback("evalCallback", "someFunction")
# new feature: jmolSetCallback("evalCallback", "someFunction")
# new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting
# new feature: load [file info] FILTER "[filter string]"
# new feature: load [file info] FILTER "[filter string];BIOMOLECULE n"
# new feature: load [file info] FILTER "BIOMOLECULE n"
# new feature: load [file info] FILTER "BIOMOLECULE n;NOSYMMETRY"
# new feature: load menu items for signed applet
# new feature: load of molecular dynamics topology file and coordinates
# new feature: measure {atomExpression or point} {atomExpression or point} ...
# new feature: measureCallback
# new feature: menu includes all standard color scheme options
# new feature: minimization CONSTRAINTS {xx} {xx} [{xx} [{xx}]] x.y
# new feature: minimization FIX {atom expression}
# new feature: minimizationCallback
# new feature: minimize CLEAR # flushes logged info and saved atom info
# new feature: minimize command -- mostly untested
# new feature: minimize CRITERION x.y
# new feature: minimize ENERGY # no stepping
# new feature: minimize menu item
# new feature: minimize STEPS n
# new feature: MODEL/ENDMDL records in write PDB (still no TER records)
# new feature: MODEL/ENDMDL records in write PDB (still no TER records)
# new feature: mol file bond type 8 as partial
# new feature: MOL2 reader is PDB-enabled.
# new feature: more load FILTER options:
# new feature: new command:
# new feature: no saving of point group -- just recalculated each time
# new feature: Numerical left division (integer divide)
# new feature: pmesh BINARY "filename"
# new feature: pointgroups with vibration vectors
# new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type -- set to 0 for now
# new feature: print getProperty("modelInfo.models[3].file") syntax
# new feature: q = axisAngle("{x y x theta}")
# new feature: q = axisAngle({x y z}, theta)
# new feature: q = axisAngle(x, y, z, theta)
# new feature: q = quaternion("{x y z w}")
# new feature: quaterion % point4f --- "thetaDirected" --
# new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw]
# new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental]
# new feature: quaternion({atom expression}) -- returns calculated
# new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent
# new feature: random(a), random(a,b) where a is lower bound and b is upper bound
# new feature: reading COMPND and HEADER records of PDB file
# new feature: reading of Spartan spinput files (uses Odyssey reader)
# new feature: reset VARIABLES (replaces "reset ALL")
# new feature: rotate @{axisAngle(....)}
# new feature: rotate @{quaternion(....)}
# new feature: rotate axisAngle {x y z theta}
# new feature: rotate branch {atom1} {atom2} ...
# new feature: rotate quaternion {x y z w}
# new feature: save menu items for signed applet
# new feature: save/restore coordinates
# new feature: script APPLET appletName "some script"
# new feature: scriptCallback
# new feature: select whatever; quaternion draw
# new feature: select within(branch, {atom1}, {atom2})
# new feature: set atomPicking TRUE/FALSE
# new feature: set bondPicking TRUE/FALSE
# new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for testing scripts
# new feature: set dotDensity [-3 to 3]
# new feature: set drawPicking now enables measuring among atoms and DRAW points
# new feature: set echo myecho [x y] and set echo myecho [x y %]
# new feature: set ellipsoidArcs [true]
# new feature: set ellipsoidAxes [true]
# new feature: set ellipsoidAxisDiameter x.y
# new feature: set ellipsoidBall [false]
# new feature: set ellipsoidDotCount [200]
# new feature: set ellipsoidDots [false]
# new feature: set ellipsoidFill [false]
# new feature: set fontScaling TRUE/FALSE
# new feature: set loglevel 6 allows a "debugHigh" setting
# new feature: set messageStyleChime
# new feature: set pdbGetHeader TRUE # to get the header when loading (for Protein Explorer)
# new feature: set pdbSequential (default FALSE) for custom PDB files
# new feature: set PICKLABEL "xxx" -- allows customized pick reports
# new feature: set pointGroupDistanceTolerance (default 0.2 angstroms)
# new feature: set pointGroupLinearTolerance (default 8 degrees)
# new feature: set quaternionFrame "c" "p" "q"
# new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame
# new feature: settable Van der Waals radius using {carbon}.vanderwaals = 1.7
# new feature: show atom(s)
# new feature: show chain(s)
# new feature: show group(s)
# new feature: show info
# new feature: show minimization
# new feature: show orientation moveto # just the moveTo; no comments
# new feature: show residue(s)
# new feature: show rotation aka show orientation rotation
# new feature: show selected
# new feature: show sequence
# new feature: show translation aka show orientation translation
# new feature: show vdw shows a listing of the currently set VDW radii
# new feature: signed applet allows "load ?" and includes previewer
# new feature: signed applet may write file, images, scripts, variables to disk. User dialog is required.
# new feature: signed applet shows frank "Jmol-S" which is NOT removable.
# new feature: signed applet/application load ?xxx uses load dialog
# new feature: sin(x), cos(x)
# new feature: spacefill/dots/geosurface/cartoon/trace/etc. ONLY
# new feature: spacegroup/symmetry for CML files with <module> tags
# new feature: Spartan archive reader now reads aromatic bonding
# new feature: Spartan archive reader now reads aromatic bonding
# new feature: Spartan input files read as Odyssey format
# new feature: sqrt(x)
# new feature: State save of property_xxx now in easily readable Jmol Data Format
# new feature: straightness, defined as:
# new feature: support for application transparent background -- "-b" command switch (testing only)
# new feature: syncCallback -- intercepts messages that would otherwise go to applets for syncing
# new feature: threaded option for command processor
# new feature: webexport now cleans up scratch files on deletion of instances and program exit.
# new feature: webexport now compresses data files over 512 MB
# new feature: wildcard at beginning for draw/pmesh/isosurface/etc. *xxx on/off/delete allowed
# new feature: within(structure,atom_expression)
# new feature: write GIF
# new feature: write pointGroup
# new feature: write pointgroup draw delivers draw commands
# new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw]
# new feature: write RAMACHANDRAN draw
# new feature: write/show pointgroup gives counts and tab-separated listing;
# new feature: x = getProperty("minimizationInfo")
# new feature: x = quaternion({center_or_point}, {atomX_or_point}, {atomXY_or_point})
# new feature: x = quaternion(q, "id", {center})
# new feature: x = script("some script", "appletName")
# new feature: xyz reader reads partial charge in 5th field
# new feature: zap {atom expression} # zaps models associated with given atoms.
# new feature: ZAP clears undo stack
# new feature: zip file reading extended to write FILE

new Jmol 11.4 capabilities

Bob Hanson — Sun, 30 Dec 2007 23:19:35 -0000

Jmol 11.4 includes over 70 new features since Jmol 11.2, including:

%l -- element (atomic) number
****Jmol Embedded Script**** in comments (/* ... */)
****Jmol Embedded Script**** in super-comments (/** ... **/)
.type math function
@{mathExpression}
\ marks continuation lines in scripts
_1 parameter for "first atom" in CONNECT
_slabPlane and _depthPlane
adjustable scale for unit cell
antialiasing in Jmol
automatic calculation of alternating single/double aromatic bonds
calculate surfaceDistance FROM or WITHIN
color [object] property [property] "schemename" range [min] [max]
colors in Jmol math
connect aromatic auto
customizable menus
direct string replacement in atom expressions
draw object title lines specific for models
expanded "within" capability
export of VRML
extended bond orders
extended boundbox command
extended show boundbox command
frame titles
getproperty stateinfo TYPE
gOpenMol formated plt files for isosurfaces
helixes as barrels, not rockets
if/while/for capability
inline SCRIPT command
isosurface CAP
isosurface mapping of MEP and MO data onto planes
isosurface SQUARED
Jmol math .boundbox qualifier
Jmol math getProperty() function
jmolLoadInlineArray([line1, line2, ....])
jmolLoadInlineArray([model1, model2, ....])
jmolLoadInlineString("line1\nline2\n....")
load symmetry range
load TRAJECTORY
local/global functions (applet)
Mac Spartan06 DIRECTORY reading
model-based parallel array calculations
model-specific echos
MOLDEN reader
POV-Ray EXPORT (application only)
programmatic color definition
quaternion command
ramachandran command
reading models from ZIP files
reading text-based content of ZIP and JAR files
Remdiated PDB support
select ISAROMATIC
select within(x.x,"plane",$plane)
set ?
set atom properties directly using Jmol math
set atom properties with an array
set drawPicking
set isosurfacePropertySmoothing ON/OFF
SET RESTRICTED TO JMOL VARIABLES ONLY
set wireframeRotation
Settable atom colors using Jmol math
show FRAME option
show spacegroup "X,Y,Z;-X,Y,Z;..."
Spherical Basis Set Molecular Orbitals
support for prime in nmes
support for SITE records in PDB and CIF
sychronize command
user-defined macros, subroutines, and functions capability
VALENCE property
WebExport (application)
write FILE (applet)
write FILE [filename] (application)

see http://chemapps.stolaf.edu/jmol

Jmol 11.2 released -- over 50 new features

Bob Hanson — Fri, 10 Aug 2007 15:11:39 -0000

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

Jmol 11.2 introduces many new capabilities, including "flying" through the molecule in "navigation mode", internal (arbitrary plane) slabbing, surface cavity depiction, mapping of user-derived data onto surfaces, loading of files without replacing already-loaded files, variable translucency, the translating, rotating and inverting of selected atoms, the use of calculated mathematical values in all commands, and the writing of JVXL surface data directly to files.

Jmol 11.1 beta testing requested

Bob Hanson — Fri, 23 Mar 2007 12:16:27 -0000

Jmol 11.1 prelease development versions for Jmol 11.2 are in active late-stage beta testing. We encourage developers interested in the broader range of capabilities listed below to try Jmol 11.1.

Jmol 11.1 represents a revolutionary new way to work with and visualize molecular data.

A new navigation mode for Jmol 11.1 allows scripted or unscripted "fly-throughs" of the model. Fasten your seat belt and take a ride on a protein's backbone from one end to the other.

Jmol 11.1 introduces a whole new vocabulary of scripting. Fully backward-compatible with Chime and RasMol, Jmol scripts now allow for a broad range of user-defined data types and selective application of external file atomic data to a model for color-based visualization of properties. Variables can be defined and manipulated using a simple arithmetic involving boolean (true/false), integer, decimal, string, array, point, and plane data types.

Jmol 11.1 introduces full support for multiple file loading, with the option of multiple models within the various loaded files. Files can be loaded sequentially into new "frames" or appended into the current frame so as to merge two datasets into one.

Jmol 11.1 supports translation, rotation, spinning, and point/plane inversion of selected atoms, allowing a completely new way of working with a model.

Jmol 11.1 introduces industry-standard translucency of objects, producing vivid rendering of multiple translucent objects at eight levels of translucency.

Jmol 11.1 allows on-the-fly creation of variable-scale JPEG "snapshots" of the displayed window both by the application and the applet. Scripted writing of these snapshots allows creation of AVI movies using commonly available tools such as Microsoft Movie Maker.

Jmol state "snapshots" can now be used to clone a model from the applet or application in order to view it in a pop-up window, save it for later retrieval, send a specific view of a specific model via email to a colleague.

Additional new features of Jmol 11.1 can be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm

Jmol Voxel File Format (JVXL)

Bob Hanson — Fri, 23 Mar 2007 11:57:06 -0000

Jmol 11.0 introduces a revolutionary way of delivering molecular surfaces over the web -- the Jmol Voxel File Format (JVXL). With a compression ratio on the order of 300-600:1 over color-mapped CUBE files, the JVXL format allows delivery of full protein color-mapped solvent-accessible and solvent-excluded surfaces in 30-60 Kb instead of 10-20 Mb, making practical delivery of molecular surfaces available on the web for the first time ever.

The Jmol application can write these surface files to disk. After transferring the JVXL file to a web-site directory, applets at that site can display the surfaces almost instantly. Command line options for the application allow surfaces to be created automatically if desired.

Supported surface types in Jmol 11.1 development versions include:

fixed-atomic-radius surfaces
adjustable-radius van der Waals surfaces
solvent-accessible surfaces
solvent-excluded surfaces
biomolecular cavities

molecular orbitals
molecular electrostatic potential maps

color-contour-mapped planes
arbitrary f(x,y) surfaces
color-contour-mapped arbitrary f(x,y) surfaces

Details relating to the JVXL file format can be found at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf with numerous illustrated examples at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm
and http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm

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