The DCU Molecular Visualisation Pages

Developed and maintained by Albert Pratt, School of Chemical Sciences, Dublin City University

Click to go directly to the Table of Tutorials

  Chemists require an ability to visualise molecules, and reactions involving them, in 3-dimensional space. One of the earliest web-based systems, whereby 3D interactive visualisation of on-screen molecular models within a web browser became possible, involved the CHIME software plug-in. Further developments have led to 3D-visualisation and manipulation using the Jmol Java applet.

  These Dublin City University pages were originally developed (1997/99) to exploit the potential of the CHIME plug-in for teaching 3-dimensional aspects of organic chemistry using the Netscape browser. Since then they have been undergoing a series of updates to take advantage of the convenience which the Jmol Java applet provides.

  In principle the Jmol applet, pre-installed on the DCU web server, allows users of this website to load the molecular models and to manipulate them on their screens using Java- and Javascript-enabled browsers (the following sites may be useful in this regard: Java, Javascript).

  Currently (July 2014) the pages function as intended on the author’s Windows 7 laptop with the Chrome and Firefox browsers. They also function, but have not been fully tested, on a MacOSX laptop using the Chrome browser.

   Updated material will be made accessible from this page as it becomes available.

   For Jmol visualisation, your CHROME browser should be Java-enabled.  Nothing additional is required.

   A short Jmol tutorial, providing practice in manipulation of molecular models, is available on this site.

   Molecular Viewing Galleries containing about 400 interactive molecular models are available.

   Galleries of Annulenes  and related systems are currently available.

   A page illustrating the separation of a racemic mixture into its component enantiomers is also available.

  Chemists use a variety of conventions to represent 3-dimensional molecules on a 2-dimensional surface (paper/board/screen).  A Perspective Drawing tutorial which reviews some of these conventions is currently being updated to make it Jmol-compatible.

  Also being updated is a Conformational Analysis tutorial which uses on-screen interactive models to illustrate the basic principles.  The .pdb and .mol files used for the models on these pages have been obtained by editing the output files from commercial modelling programmes.

   A  gallery of Molecules of Irish Interest is under development on behalf of The Institute of Chemistry of Ireland,


Jmol-enabled Tutorials

How to use Jmol 

Molecular Viewing Galleries


Resolution of a Racemate

Molecules of Irish Interest

 Perspective drawing (being updated)

 Conformational Analysis (being updated)

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