Molecule List

• This section is about the molecule list in the 3D viewer.

• There are several functions for handling your molecules.

• These functions will help provide insight.

Molecule list in 3D viewer page

The 3D viewer page is divided into four parts. (Other parts will be mentioned later)

• 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.

• This is the basic page that you will see every time you access the 3D viewer page.

• The highlighted part is the molecule list. There are five columns:

  • 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.

  • Paint: Color of your molecule. It will be applied to the carbon atoms.

• 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.