Representation

• This page explains all the functions of the 3D viewer.

3D Viewer page

1. Fold All

Fold menus. Fold All/Unfold All

2. Binding Pocket Display

2-1. Sidechains: Display all side chains that interact with your molecule. If you clear the checkbox, you will not be able to see the residue.

2-2. Surface near Clipping: A computer graphics technique that restricts rendering to a defined region of interest on a surface. 2-3. Surface radius Clipping: A computer graphics technique used to restrict rendering to a radius of side chains, defining the surface region of the binding site. 2-4. Surface opacity: Surface view: If you want to see the binding site surface, move the bar to over 50%. This function is used for the repulsion of the molecule. 2-5. Pocket radius: The binding pocket radius from your molecule. You can see the interactions and side chains within 5 angstroms (the default) from your molecule. 2-6. Residues with ligand interactions: If you want to see only the interaction residues with your molecule. By clicking the checkbox, you can clearly see the residues that interact with your molecule.

3. Interaction Entities

3-1. Receptor-Ligand: Receptor-ligand interaction (default) 3-2. Ligand-Ligand: Ligand-ligand interaction (intermolecular interaction) will be displayed. 3-3. Receptor-Receptor: Receptor-receptor interaction will be displayed. 3-4. Ligand-water: Ligand-water interaction will be displayed. In case water exists in your system. 3-5. Receptor-water: Receptor-water interaction will be displayed. In case water exists in your system.

4. Interaction Types

4-1. Covalent: Covalent interaction will be displayed. 4-2. Clash: Residue and ligand clashes will be displayed. 4-3. Vdw: van der Waals interaction will be displayed. 4-4. Hydrogen bond: Hydrogen bond interaction will be displayed. criteria: $r\ \ \le\ \ r_{HB}\ = 0.34\ nm$

$90^o\ \le\ \alpha\ \le\ 180^o$ 4-5. Week Hydrogen bond: $r\ \ \le\ \ r_{HB}\ \ = 0.38\ nm$

$90^o\ \le\ \alpha\ \le\ 180^o$ 4-6.Ionic: Electrostatic bond, also known as a salt bridge. e.g.) GLU-LYS 4-7.Metal: Molecule interaction with metal atoms in the protein near your molecule. 4-8. Hydrophobic: Hydrophobic interaction. This is a type of van der Waals (vdW) interaction. The interaction between the hydrophobic moiety of your molecule and hydrophobic residues will be displayed. 4-9. Cation-Pi: This is a Cation-Pi interaction. Interactions between the positively charged moiety of your molecule and residues with an aromatic ring (TYR, PHE, TRP) or positively charged residues (ARG, LYS) and the aromatic ring moiety will be displayed. 4-10: Pi-Pi: This section displays interactions between residues with an aromatic ring (TYR, PHE, TRP) and the aromatic ring moiety of your molecule.

5. Binding Pocket Residues

5-1. Structure Type: Stick/Ball and Stick. Residue display type.

5-2. Structure Stick radius: If you want to see thicker or thinner sticks, you can control it with the bar. 5-3. Label Type: Residue letter. Amino acid letter representation. 1-letter or 3-letter. 5-4. Label size: Label size control. 5-5. Label color: Black/white. This will be controlled automatically in dark mode. 5-6. Background: None/Hollow rectangle/Filled rectangle. 5-7. Background color: Black/White. This will be controlled automatically in dark mode.

6. Protein

6-1. Type: Cartoon/Backbone/Ball and Stick/Rocket/Surface/Hide

6-2. Color by: Chain name/Residue index/B-factor/Element/Custom

6-3. Hydrogen: Show hydrogens

6-4. Water: Show water

7. Ligand

7-1. Structure Type: Stick/Ball and Stick

7-2. Stick radius: If you want to see thicker or thinner sticks, you can control it with the bar.

7-3. Surface Type: Hide/Solid/Mesh

7-4. Color by: Electrostatic/Custom 7-5: Opacity: Ligand surface opacity. This can be controlled with a slide bar.

8. Screen Shot

Export an image from the current viewpoint within the viewer.

9. Close/Open Tab

Show Tab or close tab

10. Fullscreen

Make full screen or exit full screen.

11. Show 2D Diagram By clicking the slider, you can view the 2D molecular interaction tab.

12. Molecule List

Please refer to the Molecule List page.

13. 2D Ligand View

2D image of Conformer.