If you’ve ever spent more time tweaking molecular renderings than actually analyzing your structures, you’re not alone. Molecular modeling is a visually intensive science, but producing an insightful, publication-ready representation can feel like an art project. The issue isn’t the complexity of the molecules—it’s how we visualize them. Fortunately, SAMSON offers a powerful and underused feature that can save you time and help you analyze structural data much faster: Visual Presets.
Visual presets in SAMSON are pre-defined collections of visual and rendering styles that you can apply with just a few clicks. Whether you’re exploring a protein-ligand interaction or preparing images for a presentation, visual presets make it easy to jump from raw structure to clear visualization—instantly. What’s more, you can customize and save your own presets to streamline your workflow.
Why Visual Presets Matter
Imagine opening a PDB structure and immediately seeing atoms, bonds, and chains styled in a meaningful and visually coherent way. Instead of toggling model types or adjusting colors manually, you simply pick a preset—like “Protein-ligand” or “Illustrate…”—and focus your energy on understanding the data. This is especially useful for educators, structural biologists, and anyone under a deadline.
How to Apply a Visual Preset
Start by opening your molecular system in SAMSON. Then, go to Visualization > Visual preset and select one of the available options. That’s it. The preset automatically applies one or more visual models (like ribbons or van der Waals spheres), color schemes, and rendering parameters to your structure.
For example, the “Protein-ligand” preset might show the protein as a surface and the ligand as sticks, colored distinctly for clarity—perfect for spotting surface accessibilities or binding pockets at a glance.
Creating Your Own Presets
If you often use a specific color scheme or prefer a particular orientation of visual models, you can create and save your own visual presets. Just tweak the existing visual models and settings as desired, then go to Visualization > Visual preset > Create new…. Name your preset and use it anytime in future projects.
This is particularly useful if you work with recurring structure types or want consistent visuals across multiple figures or publications.
Illustrative Styles for Teaching and Communication
For those aiming for textbook or presentation-style images, SAMSON offers an illustrative preset inspired by the visual style of RCSB PDB’s Molecule of the Month. This preset applies a hand-drawn look with simplified surfaces, clear chain coloring, and specialized lighting to emphasize shape and topology. It’s a great tool for educators and science communicators.
Pro Tip: Reset When Needed
If you ever wish to return to a cleaner, more neutral view, you can quickly switch back to “Default” or “High quality” rendering under Visualization > Presets. Removing applied visual models in the Document View will also help you reset to baseline visuals.
Whether you’re analyzing, teaching, or creating images for publication, reducing time spent on repetitive visual styling lets you focus more on meaningful scientific questions.
To learn more about visual presets and other visualization options, visit the official SAMSON documentation page: https://documentation.samson-connect.net/users/latest/visualizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.