Bond
bond creates a new bond between two selections, each of which should contain one atom. You can easily create a new bond by selecting two atoms, each with the CTRL-MIDDLE-MOUSE-BUTTON and typing "bond" on the command line.
In order to visualize the newly created bond, lines or sticks have to be shown for both atoms.
USAGE
[edit]bond [atom1, atom2 [,order]]
atom1 and atom2 must either be selections (created by the select command, for example) or chosen using the PkAt mouse action (Ctrl+Middle mouse button). order is an optional integer (default is 1).
Example usage:
bond resi 1 and name NE2, resi 10 and name ND1
PYMOL API
[edit]cmd.bond(string atom1, string atom2)
where atom1 and atom2 are selections.
NOTES
[edit]The atoms must both be within the same object.
The default behavior is to create a bond between the (lb) and (rb) selections.