The tool palette is located on the left-hand side of the Structure Drawing window. The Pencil tool is the default tool. To change to another tool, click the tool.
To adjust the position of the Tool Palette (or to hide it), select the appropriate option from the Preferences/Layout menu.
Using the tool palette is similar to using a drawing or paint program. Select the tool you want (for example, the ring tool), and then click inside the window to perform the action (for example, draw a ring).
Pencil Draw or Change Atoms and Bonds
To insert an atom, position the pencil where you want the atom to appear and click once. The current atom appears at the insertion point.
To draw a bond, position the pencil where you want the first node to appear and then drag to draw the bond. The values of the nodes and bond are those of the current atom and current bond.
To add a bond to an existing node, click the node and then drag to draw the bond.
To change an atom or bond, select a different atom or bond from the bottom of the window or select the Atom or Bond option from the Draw menu. Then click the existing node or bond to replace it.
- Select the Pencil tool to add variables, shortcuts, and G-groups to reactions.
Ring
Draw various ring systems.
In the Ring Description box, click a ring shape or select a ring size from the list, and then click OK.
Position the pointer inside the drawing window where you want the ring. Click once. The ring is drawn vertically upwards from the cross in the center of the pointer, and the current atom is placed at each node. Click again to draw another ring.
Spiro Rings - To draw two rings sharing a common node, position the pointer so that the cross in the center is over an existing node. Click to draw the spiro ring.
Fused Rings - To fuse one ring to another, position the pointer in the middle of a bond on an existing ring. Click to fuse a new ring to the existing ring.
To create a fused ring system, specify the ring sizes in order from left to right in the Ring Description box (for example, 65). You can also change direction by using U for up or D for down. For example, 66U6D5 draws a steroid skeleton.
Chain
Draw a chain of up to 30 nodes with the current atom and bond types.
Type the length you want in the Chain Length dialog box or select a number from the list, and then click OK. Click once in the Structure Drawing window to add a chain. To connect a chain to an existing node, point to the node and then click once.
Eraser Delete an atom or bond.
To erase, point to the atom or to the middle of the bond that you want to delete and click. (Notice that the pointer displays an A when positioned over a node and a line when positioned over a bond.) You can also use the Delete key to erase a fragment if you select it using the Selection tool.
Selection
Select nodes or bonds for subsequent operations.
Point to a node or to the middle of a bond and click. Selected nodes are highlighted by a box, selected bonds by a broken line.
To deselect, move the pointer away from the selected object and click again.
To make multiple selections, hold the Shift key down. Alternatively, drag to draw a rectangle around a fragment to select all nodes and bonds inside the rectangle. Use Select All on the Edit menu to select every node and fragment in the drawing window.
To modify a selected item, select an atom or bond from the bottom of the window.
- To copy and paste selected fragments, select Copy from the Edit menu to copy the fragment to the clipboard. Then select Paste to draw a duplicate of that fragment. The tool changes to the Lasso so that you can move the pasted object.
Lasso
Select and move part of a structure.
To move a fragment:
Hold down the mouse button and drag the lasso around the fragment you want to move.
Move the lasso pointer into the lassoed area so it changes to a hand pointer.
Drag the fragment to a new position.
To move a node to a different position:
Position the lasso so that the knot on the pointer is on the atom you want to move.
Click, and the lasso changes to a hand and the node is enclosed by a box. If the hand does not appear, move the lasso into the box.
Drag the node to a new position.
You can also copy, paste, and delete items selected with the Lasso tool.
Text
Type text inside the drawing window. This text is not searchable.
To change the font, open the Text! menu and make selections from the dialog box.
Do not use the Text tool to type in atom symbols. Select the symbol from the bottom of the window or from the Atoms option on the Draw menu. Then select the Pencil or Selection tool.
To delete text, select the Eraser tool.
Draw Reaction Arrow
Draw a reaction arrow.
Select an arrow type from the dialog box and click OK. The pointer changes to an arrow. To draw the arrow you selected, position the pointer where you want the arrow and drag it to the desired length.
Reaction roles (Product and Reactant) are automatically assigned when a reaction arrow is drawn between two structures.
Reaction Role Tool
Assign reaction roles.
Point to the structure whose role you want to change and click. Select a role from the dialog box, and then click OK.
Reaction roles (Product and Reactant) are automatically assigned to fragments on the screen when a reaction arrow is drawn between structures.
If roles don't appear, select Show Reactions from the Display menu. Alternatively, check the Show Reactions box under the Display tab in Preferences.
Reaction Site Tool
Assign reaction sites.
When this tool is selected, the pointer changes to an asterisk. Point to each node that you want to make a reaction site and click. To remove a reaction site label, point to the node again and click.
Reaction Mapping Tool
Use to map reactant and product nodes to specify the reaction mechanism.
Automatic Mapping maps reactant and product nodes automatically. You will be prompted to accept or reject the automatic mapping. Automatic mapping works well when large parts of the reactant and product molecules are the same.
Manual Mapping allows you to map atoms from reactant to product one at a time. When you select this option, the pointer changes to an X. Point to a node in a reactant and click. Then point to the corresponding node in the product and click. The two nodes are assigned the same mapping number. Mapping numbers are assigned sequentially, starting with 1. You can only map nodes of the same type (that is, a carbon in the reactant can only be mapped to a carbon in the product). If you try to map nodes of different types, you will receive this error message: "Nodes must be the same definition." Mapping can be overwritten by clicking a node that is already mapped.
To delete mappings, select the Eraser tool. Position the pointer on the number in the product and click. You will be asked to confirm the deletion. Both the reactant and the product mapping numbers are deleted. To delete all mappings, select the Delete Mappings command from the Edit menu.
Information About ...
- Atoms and Bonds
- Sample Reaction Query
- Toolbar Buttons
- Sample Reaction Query
- Using the Structure Drawing Plug-in
Structure Drawing Menus