Jmol / News: Recent posts

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. ... read more

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)... read more

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 ... read more

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.

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 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. ... read more

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) ... read more

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 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. ... read more

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.... read more

We recommend that all developers of new web pages utilizing Jmol upgrade to Jmol 11.0 if currently using Jmol 10.2.

Jmol 11.0 is a significant advance over version 10.2, including an extraordinary set of new features such as the ability to save and restore the state of the model, the ability to annotate a model by placing text at any {x y z} coordinate, the ability to select and remove atoms based on one or more defined planes, the capability to designate a particular model as a "background" model, custom stereo viewing coloration, the ability to define arbitrary space groups and unit cells for any model from any file format, even if that information is not contained in the file and the coordinates are not fractional, the option to recalculate secondary structure on the fly after selecting a specific set of alternative atom locations, and if/else/endif constructs in scripts. ... read more

After a long period of only development releases, the first stable release after 10.0 is out now. Many bugfixes and new features.

The source code is being moved into a Subversion based repository, and the CVS repository will no longer be used. The migration is expected to complete within in the next 6 hours.

Ofcourse the www.jmol.org has many live demo's, but since SF project pages now have a screenshot section, added some static images of the lives demo's at the Jmol webpage.

A Wiki website has been set up to enable Jmol users to share experiences. Go to http://wiki.jmol.org.

After a year of hard work by mostly one developer (Miguel) a new stable release is nearing completion. An active user community with lots of suggestions, ideas, questions, requests, patches helped a lot during the last year.

The new release features a completely rewritten Jmol while most of the old features are again available, including a much faster rendering engine, and much better scripting engine. ... read more

As of yesterday, a preview of the new Jmol applet can be examined at Jmol's website:
http://jmol.sf.net/preview.html

New versions of the Jmol application and Jmol applet have been released. Mostly bugfixes, but also a few new features. See the jmol.sf.net website.

This release offers a much faster implementation of the rebonding algorithm is now used, VASP and Gaussian 03 readers were added, and reading of Jaguar 4.2.77, ABINIT, and, AcesII files was fixed.

A few weeks ago version 6 of Jmol was released. Download it from SourceForge's Jmol Project page.

The Jmol team is proud to announce that Jmol has been downloaded over 20,000 times from our SourceForge website. This excludes the distribution of the software through other channels, like comilation CDs. The latest version has been downloaded about 300 times so far.

Jmol version 5 has been released. 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.

The following is a brief list of changes:

- Jmol now views the unit cell axes of crystals
- Dutch and Spanish translations of the GUI have been
added.
- The PDB reader now no longer parses CONECT fields as it
had too many bugs
- Addition of a ShelX97 reader.

Jmol version 4 has been released. 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.

The following is a brief list of changes:

- Reading of MOPAC 97 and 2002 files. Formerly, only MOPAC 7 files worked.
- Jmol can now also read files in non-CML with the command "jmol <filename>".
- The PDB reader now also parses CONECT fields and implements Rasmol's perception of bond orders.
- Atoms can now also be colored by their partial atomic charge.
- Addition of a ABINIT reader.
- PDF export.

Jmol version 3 has been released. The following is a brief list of changes:

- Export of BMP and PNG images.
- Rendering of multiple bonds.
- Scaling of vector arrowheads by magnitude which shows significant vectors more clearly.
- Fixed bugs 547574 and 548591.
- Adjustable scaling of vector length from -2.0 to 2.0 times length.
- Import of Ghemical MM files.
- Automatic file type determination used for all loading of files.

Jmol can now be run via Java Web Start. The link can be accessed via the download page http://jmol.sourceforge.net/download.html or directly at http://jmol.sourceforge.net/jws/jmol.jnlp.

Thanks to Christian Ribeaud for helping develop this feature.