Create Bonds On The Fly

Say you load a pdb file and discover (to your dismay) that the heme's iron is not bond to the surrounding carbons. Here's how to add bonds between the atoms (to make it proper).

1. Click Picking Commands. It's the hand pointing to the upper left.

2. Choose 'addBondsGC' from the first drop-down menu that appears.

3. Click the unbound atom, a yellow ball should appear upon it along with a label.

4. Click the atom to which you think it should be bound. A line will be drawn betwixt the atoms.

5. Repeat until proper affect achieved.

note: if you would like to keep these changes, be sure to save the molecule with the connect records as well as the 'UserDefined' bond types: