Features since version 10

Jmol + JSmol Documentation

Description of files in Jmol+JSmol distribution
File formats read or written by Jmol
The Jmol scripting interface
- Scripting as a programming language
- Complete reference of scripting commands:
  - at St Olaf (primary site)
  - at Jena3D (mirror)
Loading models directly from databases
Mouse manual
Default colors used by Jmol
Atom sets predefined in Jmol
Support for bond orders · isotopes · stereochemistry · hydrogen bonds
Jmol as editor
Multi-touch support
Copying and pasting state scripts between applets.
Backward compatibility (changes of behavior across versions)
Features added since version 10
Users mailing list (and a mirror)

The latest list of changes is compiled in SorceForge project pages.

New in version 14.4

(June 2014 - October 2015)

New MUTATE command allows easy modification of protein residues, which along with set picking dragMinimize allows easy tweaking of the mutated group.
Biomolecule annotations including DSSR, RNA3D, EBI sequence domains, and PDB validation data.
Additional math functions for working with arrays, data tables, planes and polyhedra.
Simplified JmolSQL for working with annotations and other array-based data.
New DRAW and CGO options, including simple PostScript graphics reading.
New capability to display images in pop-up windows or within locations on a web page.
Integration into NBO (still in development).
Several important new load options, including volume filling (rather than unit cell filling) of crystal data, lattice scaling.
Significant enhancements in relation to polyhedra, including extension of stereochemical SMILES and SMARTS to atom environments, polyhedra matching, and the polyhedra() function.
Addition of Legendre polynomials for modulated structure CIF file loading.
Integration into AFLOW computational solid state physics project.

For more details, please see the properties file.

Click here for interactive examples of the new features in 10.2

Easier zoom, perspectiveDepth on or off switching
'hbonds on' does not calculate hbonds anymore. Instead, use 'hbonds calculate'. This enables the separation of hbonds data present in the pdb file (e.g. calculated by a separate algorithm) and hbond information as calculated by the Jmol hbond algorithm.
Extended label formatting options, printing three-letter, one-letter amino acid codes possible, also including all available atom information (e.g. coordinates) in the label.
The pop-up menu when right-clicking the applet can be disabled with 'set disablePopupMenu TRUE'. The pop-up menu itteself also can be tweaked.
An advanced selection option based on connectivity is introduced: select connected It can for example select based on the amount of connections an atom has, or to which atom it is connected.
Default atomtype coloring within a running applet can be changed by e.g. 'color hydrogen yellow'. Coloring of specific selections overrides the default coloring, as before.
Complete control of drawing bonds between (selected) atoms is now possible with the 'connect' command. Drawing of hydrogen bonds, double, triple, aromatic bonds is possible.
Orbitals and electron density and other information can now be drawn as isosurface or pmesh.
Advanced polyhedra bonds are introduced.
The stars command creates better visibility of selected atoms.

Check the main Jmol website for the changelog of the older versions.