Representation

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

1. Fold All

Fold menus. Fold All/Unfold All

2. Binding Pocket Display

2-1. Configure Atoms and Residues for Binding Site Display: You can select which components to visualize within the binding site. The information displayed will vary depending on which options are checked. 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.

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: 약한 수소 결합을 표시합니다.

$r\ \ \le\ \ r_{HB}\ \ = 0.38\ nm$

$90^o\ \le\ \alpha\ \le\ 180^o$

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 Select the display style for the protein:

• Cartoon: Displays the ribbon structure

• Backbone: Displays only the backbone

• Ball and Stick: Displays atoms and bonds in a ball-and-stick format

• Rocket: Highlights alpha-helices and beta-sheets

• Surface: Displays the protein surface only

• Hide: Hides the protein structure

6-2. Color by Select the coloring scheme for the protein:

• Chain name: Colors based on chain identifiers

• Residue index: Colors based on residue order

• B-factor: Colors based on B-factor values (available only for 3D structure proteins)

• Confidence Level: Colors based on prediction confidence (available only for sequence-based proteins)

• Custom: For sequence-based proteins, you can assign a custom color per object in the Ligand Display panel. And for 3D structure proteins, a single color is applied across the entire structure.

6-3. Hydrogen: Show hydrogens

6-4. Water: Show water

7. Ligand

7-1. Structure Type Select the display style for the ligand structure:

• Stick: Displays the ligand as stick lines

• Ball and Stick: Displays atoms and bonds in a ball-and-stick format

7-2. Stick Radius Adjust the thickness of the sticks using the slider. You can make them thicker or thinner as needed.

7-3. Surface Type Choose how the ligand surface is displayed:

• Hide: Do not show the surface

• Solid: Display as a solid surface

• Mesh: Display as a mesh surface

7-4. Color by Determine how the ligand surface is colored:

• Electrostatic: Color based on electrostatic potential

• Custom: Apply a custom color

7-5. Opacity Adjust the transparency of the ligand surface using the slider.

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. Ligand Display

For more details, please refer to the Ligand Display page.

12. Show 2D Diagram

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

13. 2D Ligand View

2D image of Conformer.