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)

A more recent list of changes is compiled in SorceForge project pages, and listed and linked from the Jmol website: http://jmol.sourceforge.net/history/ (see 'History of Changes' section there).

New in version 10.2

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 atomype 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 h-bond, 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.

New in versions older than 10.2

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

Contributors

AngelHerraez, Pimpim