Visualizing a Protein with its Ligand Instructions

Interactive Walkthrough

Prerequisites

1. Sign in so your generations can be downloaded and tracked.
2. Open the Generator from the top navigation.

Step 1: Search for and Load the Serotonin Receptor Protein

1. In the leftmost toolbar (the vertical tool rail along the left edge of the canvas), click the Add Protein Image button (protein icon). This opens the Protein Viewer modal.
2. In the search bar at the top of the modal, type the PDB ID 7E2Y and wait for the search suggestions to appear. Searching by name alone—for example, typing just serotonin—will not surface this structure, so search by its PDB ID.
3. Select the result showing 7E2Y: Serotonin-bound Serotonin 1A (5-HT1A) receptor from the suggestions dropdown.
4. Click on the suggestion or press Enter to load the protein. The protein will begin loading in the viewer.

Step 2: Configure the Protein Representation

1. In the representation menu (dropdown near the top of the modal), select Surface from the available options. This will render the protein as a surface area plot.
2. Ensure the Transparent Background checkbox is enabled (it should be checked by default). This creates a transparent background for the protein image, allowing it to blend seamlessly with other canvas elements.
3. Wait for the protein to fully render in the viewer. You can rotate and zoom the protein view if needed to get the desired orientation.

Step 3: Add the Protein to the Canvas

1. Once the protein is rendered to your satisfaction, click the Add to Canvas button. It is located near the top of the modal—just under the search bar and above the protein image.
2. The transparent surface area plot of the 7E2Y serotonin receptor will appear on your canvas. The Protein Viewer modal closes automatically once the protein has been added.
3. The protein image will appear as a placeholder initially and will be replaced with the high-resolution version once processing completes.

Step 4: Add Serotonin Molecule from the Top Toolbar

1. In the top toolbar above the canvas, locate the Add Molecule button (molecule icon). Click it to open the molecule picker.
2. Browse or scroll through the available molecules to find Serotonin.
3. Click on Serotonin to add it to the canvas. It will appear near the protein.

Step 5: Position the Serotonin Molecule Next to the Protein

1. With the serotonin molecule still selected, click and drag it to position it next to the protein surface plot.
2. You can resize the molecule by dragging the corner handles if needed to better match the scale of the protein visualization.
3. Rotate the molecule if desired by hovering over it and using the rotation handle that appears, or by using the rotate tool in the floating toolbar.
4. Adjust the positions of both the protein and molecule until you're satisfied with the layout. You can select and move either element independently.

Step 6: Download Your Composition

1. Once your composition is complete with the protein and serotonin molecule positioned as desired, click the Download button in the top toolbar above the canvas.
2. A download menu opens listing the available export formats.
3. Choose your preferred format—you can download the canvas as a PNG, JPG, PDF, or PowerPoint. For a shareable image of this protein-and-ligand layout, PNG or PDF works well.
4. The application processes the canvas content and generates the file in your chosen format.
5. The file automatically downloads to your computer, ready to open or share.

Tips and Notes

1. The protein surface representation shows the accessible surface area of the receptor, which is useful for visualizing binding sites and molecular interactions.
2. If the protein takes time to load, be patient—high-resolution protein renderings require processing time.
3. You can adjust the protein representation type (cartoon, surface, etc.) before adding it to the canvas by changing the selection in the Protein Viewer modal.
4. The transparent background ensures the protein blends well with other canvas elements and maintains a clean appearance when exported.
5. If you need to make further adjustments after downloading, you can always return to the canvas, make changes, and re-export.

Related reading

• Protein–ligand visualization in the generator
• Icon Tour: Protein structures

More product updates and walkthroughs are on the ChemIllusion blog.