A Quick Way to Instantly Enhance Molecular Visualizations in SAMSON

When working with complex molecular systems, presentation matters. Whether you’re preparing visuals for a publication, a lecture, or simply navigating intricate molecular networks, creating compelling representations that are both meaningful and accessible can take time. đź‘Ť

This is where Visual Presets in SAMSON can make a difference.

What are Visual Presets in SAMSON?

Visual presets are customizable templates that allow you to apply multiple visual styles, representations, selections, and color schemes all at once. Instead of manually setting up each aspect of the visualization, a visual preset handles it in one go. Think of it as a macro that transforms your model into a well-designed image in just a few clicks.

These presets are particularly helpful when dealing with molecular systems involving multiple proteins, ligands, water molecules, and more. They reduce manual work, ensure consistency across projects, and speed up image generation for publication or collaboration.

Applying a Visual Preset

To apply an existing visual preset:

  • Go to Home > Visual preset or Visualization > Visual preset
  • Select from the list of available visual presets

This action will create a folder in your document named after the selected preset, and automatically store the visual models and selections it generates.

Visual presets menu

Here’s what the Protein-ligand preset looks like applied to PDB code 1AA1:

Applying a visual preset

If you want a visualization that’s more tailored to your system or style, you can easily create your own visual preset.

Creating Your Own Visual Preset

The built-in Visual Preset Editor lets you define every step of how molecules are represented:

  • Which parts of the system to include (e.g., ligand, receptor, water)
  • What actions to perform (e.g., hide water, zoom on ligand)
  • Which visual models to use (e.g., ribbons, van der Waals)
  • How to color those models (e.g., per chain, constant color)

For example, you might create a preset that:

  • Hides water molecules
  • Applies a ribbons model to the receptor with per-chain coloring
  • Displays the ligand with van der Waals representation and constant color

Visual presets window

Steps can be added, removed, and reordered. You’re also free to select from default node groups (like “Receptor” or “Ligands”) or use custom selections through the Node Specification Language.

If you define a step with a visual model but don’t choose a color scheme, the model will use its default colorization. If you choose only a color scheme, it’s applied to the selected structural nodes.

Choose a visual model

Choose a colorization

Working Efficiently

Visual presets are a great way to maintain consistency across teams or projects. Once created, your custom presets are loaded every time you launch SAMSON. This ensures your visuals match your preferred style, even as your dataset changes.

Creating reusable templates also simplifies collaboration—share a preset with colleagues so everyone works with the same visualization language.

Want others to benefit from your preset? SAMSON even offers the possibility to submit it for inclusion in the default set of presets through the feedback system.

To learn more and see all the options available for editing and managing visual presets, visit the official documentation: https://documentation.samson-connect.net/users/latest/visual-presets/

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

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