Click in the pathway window wherever you want a new node. Each click creates a new node.
All new nodes are labeled "Unnamed node" by default . You can change each one by setting a node label.

Selecting a node

Select a node in a pathway:

In the pathway window, click on on a node's box-shaped icon. The node is highlighted with a thick border around it.

Once selected, you can delete the node and get node information where you can change the node's label, compound, etc.

Deleting a node

Delete a node from a pathway:

Select a node.
Delete it by doing one of the following:
- Press the DEL key on your keyboard.
- Press the BACKSPACE key on your keyboard.
- Select "Delete" from the "Edit" menu.
- Right-click on the node to show a pop-up menu and select "Delete".
The deleted node is removed from the pathway.

Moving a node

Move a node within a pathway:

In the pathway window, click-and-drag the node to move it around. If the node is connected to any processes, the connections move with the node.

A "click-and-drag" is done by pressing the left mouse button down atop the node, then draging the mouse about while holding down the button. When you let go of the mouse button, the node stops moving.

Getting node information

The node information window shows the node's label, type, and compound information.

In the pathway window do one of the following:
- Select a node, then choose "Show node info..." from the "Edit" menu.
- Double-click on a node.
- Right-click on a node to show a pop-up menu and select "Show info...".

Setting a node label

Every node as a label shown in it's box on the pathway. Change the node's label:

Get the node information window for the node you want to change.
Type a new name into the box labeled "Label:".

Assigning a compound type

A node's compound type determines it's color and icon shape on the pathway drawing. You can assign a compound type without choosing a specific compound:

Get the node information window for the node you want to change.
Select the node's compound type from the pull-down menu labeled "Type:". Available choices are "Nucleic Acid", "Protein", "Small Molecule", and "Unknown."

Selecting a compound

A node represents the use of a compound in the pathway. The compound, and it's compound type, determines the node's color and icon shape on the pathway drawing. You can select a compound from the LIPID MAPS database:

Get the node information window for the node you want to change.

Press the "Select compound..." button. This presents a window for searching the LIPID MAPS compound database.

Select the type of compound to search for by using the pull-down menu labeled "Type:". Available choices are "Nucleic Acid", "Protein", and "Small Molecule".
Optionally, select a compound category using the pull-down menu labeled "Category:". The list of categories depends upon the type of compound.
Optionally, type in part of the compound name.
Press the "Search" button to search the database.

The search results are shown in the lower half of the window. If the search doesn't find what you want, change the pull-down menus and keyword and press "Search" again.
Select the compound you want and press the "Select" button. The node's compound, and compound type, are set to the compound you've chosen. You can get compound information about this compound.
Press the "Cancel" button if none of the compounds are what you want.

Getting compound information

The compound assigned to a node has information about it's name, synonyms, and chemical attributes:

Get the node information window for the node you want to change.
If the node doesn't have a compound assigned yet, select a compound first.

Press the "Show info ..." button. This presents a window with information about the node's compound.

When you are done with the window, press the "Done" button.

Clearing a node's compound

By default, a node has no compound assigned to it. You can select a compound, and later clear that selection:

Get the node information window for the node you want to change.
Press the "Clear compound" button. The node's compound choice is erased.

Adding comments

You can add your own comments about a node:

Get the node information window for the node you want to change.
Click on the "Comments" tab and type text into the box below.

Listing nodes

You can get a list of all nodes in a pathway:

In the "Tools" menu, choose "Manage nodes...". This presents a window showing a list of the pathway's nodes.

Select a node and press the "Show info..." button to show the node's information window.
When you are done with the window, press the "Done" button.