Features since version 10

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Revision as of 11:51, 7 June 2007 by Pimpim (talk | contribs) (summarized new stuff in version 10.2)
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Jmol + JSmol Documentation

New in version 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.

click here to see interactive examples

Contributors

AngelHerraez, Pimpim