Structure Diagram Structure Diagram icon

Structure Diagram generates 2D images of small organic molecules using a web service provided by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). This web service is implemented in Java using the Chemistry Development Kit.

Use is only recommended for small organic molecules, on the order of 50 or fewer nonhydrogen atoms. See also: ViewDock, using open to fetch by SMILES string or PubChem CID.

There are several ways to start Structure Diagram, a tool in the Utilities category.

Information sent to the server can be a SMILES string or a 3D structure (Molecule) already open in Chimera. Clicking Apply sends the information to the server and displays the resulting 2D diagram (image in PNG format). Hydrogen atoms are inferred by the server. Image dimensions are set by the size of the Structure Diagram dialog when Apply is clicked, and the PNG file can be saved to disk with Save. Close dismisses the dialog, while Help opens this manual page in a browser window.

UCSF Computer Graphics Laboratory / July 2010