If you’re designing or analyzing molecular systems regularly, you’ve likely spent more time than you’d like adjusting atom sizes, tweaking colors, choosing rendering styles, and setting up views to get a clear and informative visualization. This overhead can be a silent time drain, especially under the pressure of publication deadlines or presentations. That’s where visual presets in SAMSON can make a real difference.
Visual presets in SAMSON are predefined templates that combine multiple representations and color schemes for fast and consistent molecular rendering. They are particularly helpful when dealing with complex systems such as proteins, DNA complexes, or virus structures, and they allow molecular modelers to focus more on science and less on tweaking styles.
What are Visual Presets?
At their core, visual presets are collections of visualization and colorization settings applied based on selectors. A good example is the default preset called “Protein-ligand,” which instantly sets up a visual representation suitable for protein-small molecule complexes. These presets suggest secondary structure ribbons, van der Waals radii adjustments, and chain-based coloring – all with a few clicks.
To apply a visual preset, go to Visualization > Visual preset and choose from the available presets. Here’s what the Protein-ligand preset looks like on PDB code 1AA1:
Save Time: Create Your Own Presets
SAMSON also allows users to create and save their own visual presets. This is helpful if you’ve developed a unique style for a project, or if you want to maintain consistent visualization standards across different models. You can start by adjusting an existing preset and then saving it to reuse later across other systems.
To learn how to create your own, see the detailed guide in the Visual Presets documentation.
Illustrative Presets Inspired by Goodsell
One highlight in SAMSON presets is the “Illustrate…” preset inspired by David S. Goodsell’s illustrative molecular style from RCSB PDB’s Molecule of the Month. This preset applies van der Waals representations, chain-based coloring, and adjusted rendering parameters to mimic that clean illustrative look used widely in science communication.
Preset Switching for Output Versatility
If you need to switch between styles for printing, presentations, or different audiences, navigate to Visualization > Presets to switch rendering modes. Whether you prefer high-quality soft shadows or a sharper cartoon look, switching presets saves time and avoids manual toggling.
Use Case: Protein Complex Snapshots
Let’s say you’re visualizing a protein-ligand system for a publication figure. Instead of manually setting up representations, colors, and lighting effects each time, visual presets let you apply the right setup instantly. Combining this with SAMSON’s F10 viewport capture features makes it easy to output publication-ready figures in seconds.
Conclusion
Visual presets offer a practical solution for molecular modelers who need speed, consistency, and quality in their visualizations. Whether you’re preparing figures or exploring a new structure, they are a handy feature that reduces time spent on repetitive tasks.
To learn more, visit the full documentation on Visualizing in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.