Normal modes can be used to generate an ensemble of protein structures. For example the method can be used to represent flexibility in the pocket.

To generate an ensemble of structures using normal modes.

• Convert your protein to an ICM object.
• MolMechanics/Generate NM stack
• Enter the number of normal modes to sample
• Enter the relative amplitude of the normal modes.
• Optional: select to make random combination of modes.
• Optional: select Fast GAP model only.
• Optional: run the normal mode generation locally.