When working with complex molecular systems, one of the earliest bottlenecks is often the time it takes to produce clear, insightful visualizations. Whether you’re preparing figures for publications or just trying to make sense of a complicated protein-ligand complex, customizing representations, color schemes, and viewpoint settings can quickly become tedious.
Visual Presets in SAMSON provide a practical solution to this challenge by letting you apply sets of visualizations and colorizations with just a couple of clicks. This feature is especially useful for researchers who frequently need to repeat visual styling tasks or want to maintain a consistent visual standard across projects.
What Are Visual Presets?
Visual presets are collections of visual styles that include:
- Selections (e.g., receptors, ligands, water)
- Optional actions (like hiding or labeling atoms)
- Visual models (e.g., ribbons, licorice, Van der Waals)
- Color schemes (e.g., per chain, constant colors)
You can find visual presets under both the Home > Visual preset and Visualization > Visual preset menus.
A Closer Look: Protein-Ligand Preset
Here’s an example using the Protein-Ligand preset on the structure with PDB code 1AA1:
The visual model and color scheme are applied automatically, organizing the scene and making important interactions easy to understand.
How to Apply Visual Presets
To apply a preset:
- Select the structure or leave it unselected to apply the preset to the whole document.
- Open the Visual preset menu.
- Choose a preset from the list.
Once applied, a folder is created in the document containing the new visual models, so everything is neatly organized from the start.
Why Use Visual Presets?
- Time-saving: Apply complex styles instantly.
- Consistency: Keep visualizations uniform across multiple systems or presentations.
- Customization: You can also create and save your own presets tailored to your preferences.
Create Your Own
Need something specific? SAMSON lets you modify existing presets or build new ones from scratch with the Visual Preset Editor, where you define steps for node selection, apply visual models, and even customize color schemes.
You can create multi-step workflows—e.g., highlight ligands in constant color while showing receptors in ribbons—all in one preset.
For a full guide on how to create and edit these presets, see the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.