Visualizing molecular systems often feels like a balancing act—switching representations, adjusting colors, highlighting key atoms—before you’ve even started analyzing. For researchers and students dealing with increasingly large biomolecular structures, the time spent configuring these visualizations manually can quickly add up.
That’s where Visual Presets in SAMSON can make a real difference. Visual Presets offer a fast and flexible way to apply meaningful visual representations and color schemes to your model with just a few clicks. Whether you need quick publishing visuals or are preparing to present a mechanism at your next meeting, visual presets save valuable time and help maintain consistency.
What Are Visual Presets?
A visual preset is a predefined combination of selections, actions, visual models, and color schemes applied simultaneously to a molecular system. For example, a preset might highlight ligands with the licorice representation, shade the receptor ribbons per chain, and zoom in on the binding site.
These presets are available from SAMSON’s Home > Visual preset or Visualization > Visual preset menus. Simply select your molecular system (or nothing, to apply to the full document) and choose a preset.
Below is an example of the Protein-ligand preset applied to the PDB structure 1AA1. It simultaneously applies a ribbon and surface representation to the protein and a licorice model to the ligand.
Creating Your Own Visual Presets
One of the most useful features of SAMSON’s Visual Presets is the ability to create or tailor them to fit your workflow. Go to Home > Visual preset > Create… or Visualization > Visual preset > Create… to start editing or defining new presets from scratch.
Each preset consists of multiple steps, and each step offers four customizable options:
- Selection – define what part of the system the step applies to, like ‘Ligands’, ‘Receptor’, or even custom-defined selections through the Node Specification Language.
- Actions – such as hiding nodes, labeling, or zooming.
- Visual model – choose from styles like Van der Waals, Ribbons, or Licorice.
- Color scheme – select consistent coloring: per chain, constant, or per attribute like occupancy.
Want a semi-transparent protein shell to frame electron density? Or a color-coded set of ligands by charge? Each visualization choice is captured in steps that you can move, delete, or edit at any point.
Color palettes are fully adjustable too—simply double-click any default palette to customize it. These visual presets won’t just save time; they’ll help ensure reproducibility and consistency across your visual analyses and publications.
When Sharing Saves Time
If you’re working in a team setting or teaching, you can create instructional presets to help others start with an aligned view of their model. Presets can be reused, reviewed, and revised collaboratively, making them not just a visual time-saver but a communication tool as well.
To learn more about creating and applying visual presets, consult the full documentation page here: Visual Presets in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at www.samson-connect.net.