If you’ve ever opened a complex biomolecular structure only to be overwhelmed by a tangle of atoms and bonds, you’re not alone. Structural biologists, computational chemists, and anyone working with molecular systems often face the challenge of understanding 3D molecular structures hidden in messy visuals. While precise, raw PDB renderings are rarely intuitive at first glance.
Visual presets in SAMSON offer a practical and fast solution to this. With just a few clicks, visual presets transform your molecular data from overwhelming to insightful using combined representations and contextual color schemes.
What Are Visual Presets?
Visual presets in SAMSON are saved configurations that include specific combinations of visual models and color schemes. Rather than adjusting each element manually, you can apply a preset—such as “Protein-ligand” or “Illustrate”—to instantly restructure your visualization according to best practices for a particular molecular setup.
Why This Matters
Imagine you’re analyzing a protein-ligand interaction. You need to identify binding sites quickly without spending 15 minutes changing representations for atoms, residues, and chains. A single visual preset arranges the protein as ribbons, colors chains distinctly, and emphasizes the ligand in van der Waals representation—and you’re ready to think scientifically within seconds.
This approach is especially beneficial when preparing imagery for publications, presentations, or collaborative discussions. The result is not just better understanding, but also more readable and compelling visuals—and less time editing.
How To Apply Visual Presets
To apply a visual preset in SAMSON, navigate to Visualization > Visual preset, and choose one from the existing list. That’s it.
For example, here is how the “Protein-ligand” preset appears when applied to PDB 1AA1:
This preset sets the receptor and ligand in appropriate representations and chain-based colors—perfect for rapidly spotting protein-ligand contacts.
Customizing Your Own
Need something specific? You can duplicate an existing visual preset and tweak it to your liking, then save it for future use. Maybe you always want to show ions as yellow spheres, or fade out solvent molecules. Personalized presets boost your productivity without the overhead.
A Special Case: The Illustrative Style
If you’re inspired by David S. Goodsell’s visual storytelling (e.g., the RCSB’s Molecule of the Month), SAMSON offers a special “Illustrate…” preset which mimics this well-known illustrative style. Ideal for educational or explainable visuals, this preset applies van der Waals representations with chain-specific colors, soft shading, and silhouette edges for clarity.
Combine it with the illustrative rendering style via Visualization > Presets > Illustrative for finely tuned lighting, fog, ambient occlusion, and more:
Start with What You Need
Whether you’re modeling an enzyme active site or presenting a virus particle, visual presets simplify the start and amplify the insight. Customized, shareable, and reproducible views are only a few clicks away.
📖 To learn more about visual presets and other visualization tools in SAMSON, visit the original documentation page: https://documentation.samson-connect.net/users/latest/visualizing/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.