JSME 2-D Line Editor
JSME (JavaScript Molecular Editor) is a 2-D line editor that interfaces with the built-in 3-D WebMO molecular editor. It allows one to draw a molecular structure using line structures familiar to organic chemists, which are then converted into a 3-D structure for WebMO.
JSME 2-D Line Editor
Using the Line Editor
Building a Structure
From an empty WebMO Editor window, invoke the line editor with Build: Line Editor... This brings up the JSME 2-D Line Editor.
Build the backbone structure of the molecule by selecting the single, double, or triple bond tool (second row) and clicking in the drawing area. Add additional bonds by selecting a different bond type if needed and clicking on the end of an existing bond. Wedged bonds are used to indicate stereochemistry.
Carbon-carbon bonds are created by default. Convert C atoms into other elements by selecting the desired element (left column) and then clicking on the end of a bond
Rings can be added by selecting the desired ring and clicking on the end of a bond. Fused rings are formed by clicking on the center of a bond.
The black X tool allows one to define non-standard atoms. The FG tool contains various functional groups.
Editing Atoms and Bonds
Atoms can be redefined by selecting a new element and clicking on an exiting element. Bonds can be edited into other types by selecting a new bond type and clicking on the middle of an existing bond.
Atoms and bonds can be deleted by selecting the red X tool and clicking on parts of the displayed structure.
Non-zero atomic charges can be specified with the +/- tool.
Translation and Zoom
Translate the line structure by dragging anywhere in the background. Zoom the line structure by scrolling up or down.
First draw carbon-carbon bonds for the overall structure. Then convert carbon atoms into other elements.
Importing Line Structure into WebMO
When the line structure is complete, click the Save button. The structure is then translated into a 3-D structure and imported into WebMO. Stereochemistry is preserved during this process.
Optionally, one might want to perform a Cleanup: Comprehensive Mechanics on the structure before subsequent calculations.
Imported Line Stucture
Limitations
While it is possible to send a structure from WebMO Editor into the 2-D Line Editor, when doing so all H atoms are explicitly included and stereochemistry is not preserved.
The 2-D to 3-D translation process relies on NCI/CADD Chemical Identified Resolver. Therefore, the WebMO server must have access to the internet to be able to import line structures.
Reference
WebMO uses the JSME Editor: B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, J. Cheminformatics 5:24 (2013).