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Atom Mapping Tool

The Atom Mapping tool is used to specify a correspondence between atoms in the reactant and atoms in the product.

To use this tool:

1. Click the Atom Mapping tool from the Vertical Tool Palette.

2.  In the dialog box, select either the Manual Mapping or the Automatic Mapping option to get a message telling you how to use the selected option.

Manual Mapping - Using the cross cursor, point to an atom in the reactant and click and then point to the corresponding atom in the product. The atoms will be assigned a mapping number 1. Repeat for subsequent pairs of reactant and product atoms.

Automatic Mapping - This option causes the fragments to be automatically mapped where possible.

To delete mappings, use the Eraser Tool or the Delete Mappings command from the Edit Menu.

Reactant atoms can only be mapped onto product atoms (and vice-versa), and two different atoms cannot be mapped.


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