Understanding how your ligand interacts with a receptor at the atomic level is key to rational drug design. However, many molecular modelers spend a surprising amount of time just trying to generate clear, informative visuals of binding sites. If you’re tired of juggling PyMOL scripts or aligning residues by hand, SAMSON’s built-in visualization tools can simplify your workflow without compromising detail.
This post walks you through how to rapidly visualize the binding pocket of a ligand using SAMSON after a docking run with the FITTED Suite Extension. From selecting surrounding residues to coloring and labeling key atoms, you’ll reduce your visualization prep time and enhance your interpretability. Let’s dive in. 🧪
Step-by-step visualization of the binding site
Once you’ve performed a docking calculation (for example, the 1E2K + TMC 500 example in the FITTED Suite tutorial), SAMSON gives you tools to focus directly on the binding site and see how your ligand fits in context.
1. Visualize the secondary structure of the receptor
In the Document view, select the processed receptor (e.g. 1E2K_pro) and use the Visualization menu to add a Ribbons visual model. This makes it easier to appreciate how the ligand fits into the receptor’s folds.
2. Highlight residues around the ligand
Select the docked ligand (e.g. 1E2K_log.mol2_DockingRun_*), then navigate to Select > Biology > Binding sites and define parameters to capture surrounding residues (e.g., 4 Ă… cutoff). These residues will be auto-highlighted.
Group them for easy access via Document view > Current selection > Create group.
3. Add licorice visuals
While the binding site residues are selected, apply a Licorice rendering from the Visualization menu. This visually distinguishes covalent framework atoms.
Want to go further? Customize color schemes. For example, select all carbons in the receptor and color them according to residue index to mimic standard secondary structure coloring:
Then apply the Material > Per attribute visualization and choose Residue index.
Final result
By hiding the original receptor model (to avoid double visuals), you get a clean, clear depiction of the ligand inside its binding pocket—colored, labeled, and ready for publication or presentation.
With a few clicks, you’ve gone from raw docking result to an annotated, visually clear binding site. No Python scripts, no exported files, no jumping between programs.
Conclusion
If you often find yourself in front of messy or ambiguous visuals of protein-ligand complexes, investing a few minutes to learn SAMSON’s visualization flow can drastically cut down your time and raise the clarity of your data.
To learn more and follow the full tutorial with interactive examples, visit the official documentation: FITTED Suite SAMSON Extension Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.