3D Modeling Page

The 3D Modeling page allows users to manipulate structures in 3D. It includes the perception of protein and ligand interactions as well as editing facilities for ligands in the context of the active site.

Badges such as badge identify molecules, proteins, and other components.

3D Modeling Page Layout



3D Viewer

Displays 3D structures of small molecules and receptors.

The Side Toolbar

Allows users to change mouse map modes, switch to distance measurement mode, change the residue selection model, access tools

for, e.g. changing preferences, taking a screenshot, and toggling screen to fullscreen.

Visible Objects List

Displays structures that are currently marked as “active”.


Allows users to render structures using different color schemes and styles.

Structure Rating

Allows users to rate a structure on a 1 - 5 scale by hovering over the Rating icon next to each structure.


Allows users to add an annotation to a structure by hovering over the Notes icon next to each structure.

Structure Editing

Allows users to edit a structure by clicking the Side Arrow next to each structure, then selecting the Pencil icon.

Binding Site View

Allows users to generate a binding site view of a selected receptor using a cocrystallized ligand as the site marker.

Protein editing video

For a tutorial on protein editing, see Protein Editing: 3D Modeling.

Receptor constraints video

Features for enabling and modifying constraints are covered in the 2023.1 video.

Styling small molecules video

For a tutorial, see Styling Small Molecules.

More tutorial videos

For more training videos on 3D features, see Videos about 3D features.


Selected objects are listed in the Visible Objects sublist at the top of the parent Active Objects list. Selecting any or all objects from this list places them in the Selected bucket list.