Draw Chemical Structures in JME Molecular Editor

Add a new structure to the drawing

By default, the JME tools add or change items in existing structures. To create a new structure in the drawing:

1. Click .
2. Add an atom, bond, ring, or carbon chain anywhere in the drawing area.

Add an atom of one of the following elements — C, N, O, S, F, Cl, Br, I, P — as a new structure

1. Click .
2. Click the element's symbol.
3. Click in the drawing area.

Add any atom as a new structure

1. Click .
2. Click .
3. In the popup window that is displayed, type the symbol of the atom you want to add.
4. Click in the drawing area.

Add an atom and its bond to an existing structure

1. Click a single bond , double bond , or triple bond .
2. Click the atom in the structure where the bond should be added.
3. Click the symbol of the atom that you want to add to the end of the bond, or click and type the symbol of the atom you want to add.
4. Click the end of the bond where the atom should be added.

Add a bond between existing atoms

1. Click a single bond , double bond , or triple bond .
2. Drag from one atom to another.

Change a bond type

1. Click a single bond , double bond , or triple bond .
2. Click the bond to be changed.

Replace an atom

1. Click the symbol of the new atom that you want to use, or click and type the symbol of the atom you want to use.
2. Click the atom to be replaced.

Set the charge for an atom

1. Click .
2. Click the atom to be changed. If needed, click the atom multiple times to see the possible charges suggested by the JME Editor.

Add a chain of carbon atoms

1. Click .
2. Starting from the atom to which the carbon chain attaches, drag in the drawing area until the number of carbon atoms you want to insert is displayed.

Add a carbon ring

1. Click the button that displays the kind of ring you want to add.

   

2. Click the atom to which the ring should be attached.

Add wedge bonds

1. Click .
2. Click the atom in the structure where the bond should be added.
3. If needed, click the wedge bond in the structure to change its type.

Delete a bond or atom

1. Click .
2. Click the item you want to delete.

Delete a structure

1. Move the pointer over the structure to be deleted until a portion of the structure displays a blue selection outline.
2. Click . The structure is deleted.

Delete a functional group

1. Click .
2. Click the bond connecting the group with the main skeleton.

Move a structure

1. Move the pointer over the structure to be moved until a portion of the structure displays a blue selection outline.
2. Move the pointer over an empty part of the drawing area.
3. Drag the pointer to move the structure.

Rotate a structure

1. Move the pointer over the structure to be moved until a portion of the structure displays a blue selection outline.
2. Hold down the Shift key and drag the pointer to rotate the structure.

Undo your last change

Click . You can undo only one change.

View the SMILES string for your drawing

Click . The SMILES string is displayed in a popup window.