Ligand Display

• This section is about the Ligand Display in the 3D viewer.

• There are several functions for handling your molecules.

• These functions will help provide insight.

Ligand Display

Ligand Display displays up to 7 entries. If the protein Type is 3D Structure, the same protein structure is shown for all molecules. If the Type is Sequence, each row may display a slightly different structure. Therefore, an additional Protein color customization feature is provided for sequence-based proteins.

• Mol ID: Molecule Name

• Conf. ID: Conformer ID generated by Hyper Binding

• BS (kcal/mol): Binding Score

• Magnifying Glass: Zoom

• Eye Mark: Activate/deactivate your molecule. You can also pin the molecule.

• Ligand: Set the color of the molecule. Applied to carbon atoms.

• Protein: Set the color of the protein.

• The arrow right next to Mol ID means to hide conformers (9 out of 10).

• When you click it, you can see the whole conformers with their binding score.

• To see each conformer, click the eye mark.

• To see the details of the residue-ligand interaction (3D), click the magnifying glass on the left.

• To pin a specific conformer/molecule, click the eye mark until the lock icon appears.

• While the lock icon is displayed, you can click another conformer’s eye mark to see the difference.

• If you want to view all conformers, click the eye mark at the top of the column.

3D viewer display mode settings

• If you want to change to a black background, you can use dark mode.

• To set dark mode, click the slider in the top-right corner.