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, 3D Viewer with Spreadsheet Layout

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, and access tools for changing preferences, taking a screenshot, toggling screen to fullscreen, and more.

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 to 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.

Edit DU Receptor

The Edit DU Receptor feature allows you to modify your receptor grid directly from the 3D Modeling page. Choose a design unit (DU), then select Edit DU Receptor on the Modeling drop-down menu.


Defining the grid enclosing a receptor

Once you open the Receptor Editor, you can adjust the size and position of an autogenerated box that defines the confines of the receptor grid. Simply make adjustments with the controls in the Setup Box. Click the “Setup Grid” button for additional options, then click “Build Grid” to build your receptor grid and see details about the contours and constraints. See the release highlights video for a demonstration.

From the list of molecules and design units, you can fine-tune constraints and inner and outer contours as shown in the figure below. These options are enabled by using the corresponding checkboxes. Contours can be adjusted with a slide bar. When adding a new constraint, you can adjust the interaction options using the toolbar on the right-hand side of the 3D Viewer. Click the plus sign to bring up the “Add a Constraint” box. As you hover over the binding site, circles will appear that correspond to atoms in your protein. To add a new constraint, either select one of these atoms or choose the “Custom” option to add a SMARTS pattern. Click the disk icon to save the DU.


Adding a new constraint

You can also add a new receptor to a DU if the DU does not have a receptor. The option to add a receptor will only appear if there is no receptor present. Most of the time, this step is not necessary.

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 about how to visualize small molecules, see Styling Small Molecules.

More tutorial videos

For more training videos on 3D features, see the 3D Features Video Tutorials.


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.