Knowledge Base

The Ligand Interaction Diagram uses Maestro's automatic ligand detection parameters (e.g., molecule size range, excluded residue types), which you can change via the Maestro Preferences panel.  On Linux/Windows:

Edit → Preferences → Ligand Detection

On Mac:

maestro → Preferences → Ligand Detection

Note that these changes affect all ligand detection throughout Maestro, not just in the Ligand Interaction Diagram.

Below are some reasons that your ligand might not be detected, and the changes in the settings you can make:

• Your ligand may be larger than the default size. In this case, increase the "Maximum atom count" to larger than the number of atoms in your ligand.
• If you have a peptide ligand, select the "Allow molecules containing only amino acids" option.

You can find more information in the Maestro Help for the Preferences Panel.