Structure Diagram Structure Diagram icon

Structure Diagram generates 2D chemical diagrams using the GIF Creator for Chemical Structures web service (courtesy of Dr. W. D. Ihlenfeldt and hosted by the Resource for Biocomputing, Visualization, and Informatics at UCSF). Please see the usage conditions below.

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.

Usage conditions

Images generated by this service can be used free of charge for almost every purpose. If you put them on a Web site, the HTML document embedding the image must contain a link to A small footnote is sufficient.

However, you are explicitly forbidden to include these images in any CD or other medium you charge for without prior contact with Dr. Ihlenfeldt and an agreement in writing. The images contain embedded, invisible copyright information which can be read back by suitable tools.

UCSF Computer Graphics Laboratory / April 2008