For molecular modelers juggling complex structures, creating beautiful and informative molecular visualizations can feel like a time-consuming process. Manually setting colors, choosing the right visual models, and fine-tuning rendering effects is often repetitive and error-prone, especially under tight publication or presentation deadlines.
Visual presets in SAMSON offer a solution to this challenge by letting users apply predefined (or custom-made) visualization settings in just a few clicks. In this blog post, we’ll take a closer look at how visual presets work, what they change, and how they can help speed up your workflow without sacrificing visual quality.
What are Visual Presets?
Visual presets in SAMSON are essentially bundles of visualization settings. They can quickly apply combinations of visual representations (like cartoon ribbons or ball-and-stick) and color schemes based on molecular features like chain ID, element type, or residue.
You can choose from several pre-installed presets, such as:
- Protein-ligand: A commonly used preset showing ligands distinctly within a protein context.
- Illustrate…: Inspired by the scientific style of Molecule of the Month artwork by David Goodsell.
How to Apply a Visual Preset
You can apply a visual preset with a few menu clicks:
- Load your molecular system.
- Navigate to Visualization > Visual preset.
- Select from the available presets.
The changes happen instantly. You’ll get an appropriate set of visual models applied across your molecule, including meaningful coloring and helpful representations.
Here’s what the Protein-ligand visual preset looks like when applied to a molecular system (PDB ID: 1AA1):
Tailoring and Saving Your Own Presets
The best part? You’re not limited to the presets provided by default. SAMSON allows you to customize them:
- Add or remove visual models (e.g., Ribbons, Licorice, Van der Waals).
- Change color schemes using the Inspector, the context toolbar, or the Visualization > Color menu.
- Adjust rendering effects like ambient occlusion, shadows, and silhouettes.
Once you’re satisfied with your setup, navigate to the Create visual presets section to save it for later use, or even share it with collaborators.
When Should You Use Visual Presets?
Visual presets are particularly helpful when you:
- Need a consistent look across a series of molecular systems.
- Want to focus on ligand-receptor interaction visualization.
- Are preparing educational content or slides for teaching or outreach.
- Need to quickly prepare illustrations for publication or communication.
Tips for Better Results
- Try using the Illustrative rendering style for a science-art look reminiscent of print publications.
- Create your own preset templates for different structure types — for example, one for nucleic acids and another for protein complexes.
- Combine visual presets with quick viewport captures (using F10 or Ctrl/Cmd + F10) to generate clean, reproducible figures quickly.
Taking advantage of visual presets in SAMSON doesn’t just make your molecules look better — it also helps you spend less time fiddling with settings, and more time analyzing and communicating your results.
Want to dive deeper? You can read the full documentation on visualizing in SAMSON here: 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.