Chemical search drawing tools: updating Java and security exceptions

Regular users of the Guide to PHARMACOLOGY will be aware that the site includes a ‘Chemical structure search’ function whereby users can draw chemical structures or parts of structures and use these to search against the database. Users can also paste in a non-isomeric SMILES string copied from another database and use this to search. The chemical drawing function is provided by the Marvin Sketch Java applet from ChemAxon.

In order to use this tool, a recent version of Java is required, and users may find they are prompted to update Java when attempting to access pages running Java applets. However, we have found that the latest version of Java (Version 7 Update 51) on Windows fails to run certain applets, including our chemical drawing tool, owing to enhanced security restrictions. In order to overcome these restrictions you need to add our website address to the Exception Site List for the version of Java your browser is running.

Instructions for how to add site exceptions can be found at this page, under the section “Adding a site to the Exception Site List”. Note that you should add both forms of the website address ( and

Other websites we use in our chemical curation work including Scifinder, OSRA and also run chemical drawing applets requiring Java therefore users may also wish to add security exceptions for these sites.

Feel free to contact us if you have any questions about the above. We expect in the future to be able to offer a JavaScript version of MarvinSketch which will bypass the Java requirement and should also run on tablet or mobile devices.

contributed by Joanna Sharman and Helen Benson

Posted in Technical

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