Copyright©2007 Antony Williams
A number of ChemSpider users have asked us to provide enhanced viewing of chemical structures and suggested that we use the JMol Open Source viewer. THis is an excellent example of a piece of Open Source software that has continued to advance in capabilities year on year with dozens of websites now taking advantage of this excellent piece of software. An example image is shown below for Bilirubin. In order to see any of the structures from ChemSpider displayed in JMol simply click on Jmol shown in the bottom right hand side of the structure image in the results set.
A set of expanded menus are available using a simple right hand click to display a long list of choices for alternative viewing options and other operations. Documentation is available online.
UNFORTUNATELY, if you rotate the displayed structures you will see that the structures are “flat”. All structures in ChemSpider are presently stored as 2D structures. We would like to offer our users the ability to view and download optimized 3D structures…so we are presently investigating the potential application of the CDK and the possibility to use the force field optimizer available in the developers kit. Watch this space.