Saving Time and Keeping It Clean: Using Visual Presets in SAMSON

One of the recurring challenges in molecular modeling is ensuring visual consistency across figures and animations, especially when working with large, multi-scale systems or preparing presentations and publications. If you’ve ever spent too much time adjusting rendering settings, tweaking atom colors, or manually replicating visualization styles, you might benefit from exploring Visual Presets in SAMSON.

Visual presets in SAMSON provide a quick way to apply predefined (or custom) visual styles to your molecular systems. Whether you want to immediately highlight secondary structure elements in a protein, emphasize electrostatics on a surface, or generate publication-ready images with the right color schemes and lighting, presets can help streamline your workflow.

What are Visual Presets?

Visual presets are essentially collections of visualization settings that define how different elements (atoms, bonds, surfaces, etc.) are displayed. They can encapsulate lighting parameters, atom coloring rules, rendering styles, and even camera settings or background colors.

Instead of manually adjusting each of these settings, you can apply a preset with one click. SAMSON comes with a number of default presets, but you can also create and save your own.

Common Modeling Scenarios where Presets Help

  • Protein-ligand interactions: Visualizing ligands with distinct coloring and transparency to highlight binding interfaces.
  • Presentation slides: Maintaining consistent visual style across all images or animations.
  • Publication figures: Applying muted or high-contrast styles as required by different journals.
  • Data Sharing: Sharing standardized presets across teams for consistency.

How to Use Visual Presets in SAMSON

  1. Navigate to the Visual Presets section in SAMSON using
    Visualization > Visual Presets in the interface (or refer to the corresponding button in your version).
  2. Select any of the default presets (e.g., “Cartoon with rainbow coloring” for secondary structure).
  3. To create your own preset:
    1. Customize your scene (colors, lighting, rendering styles).
    2. Save the current settings as a new preset through the interface.
  4. To apply your preset to another system:
    1. Load the molecular model.
    2. Apply your saved preset immediately to restore consistency.

Tip: Combine with Visual Presets with Selections

Visual presets in SAMSON can be layered with advanced selection techniques using the Node Specification Language (NSL). This allows power users to apply styles to very specific parts of a system—for example, coloring only the side chains of charged residues differently or rendering a surface around a particular subset of atoms.

When Consistency Matters

For molecular modelers working in collaborative environments, educational settings, or for publications, ensuring that visuals are clean, consistent, and compelling can be just as important as the results. Visual presets are a quiet but powerful feature that makes this job easier. And since they are user-defined, they also reflect your style and preferences. Don’t underestimate the relief of applying a preset and getting exactly what you expect, with zero tweaking.

To learn more about this feature, visit the original documentation page: SAMSON Documentation – References.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.

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