Tired of Manually Styling Molecular Models? Try Visual Presets in SAMSON

If you’re a molecular modeler, chances are you’ve spent a lot of time adjusting representations and color schemes just to get your visualizations to look right. From ribbons to atoms, VDW surfaces to chain coloring — great visuals often take effort and time. And when you’re dealing with complex systems like protein-ligand interactions, getting everything styled clearly and consistently can become tedious.

Thankfully, SAMSON offers a way to reduce that friction: Visual Presets. These are pre-configured combinations of visual models, selection filters, and color schemes that you can apply in just a few clicks to obtain clean, informative visualizations tailored for specific tasks or systems.

Fast Visualization, Less Setup

Using visual presets, you can visually style a system in seconds. Whether you’re highlighting ligands, showing molecular surfaces or hiding solvent, there’s very likely a preset that does it for you — and if not, you can create your own.

Presets are accessible directly from the Home > Visual preset or Visualization > Visual preset menus. Once selected, a preset will automatically apply a set of styling rules to the whole document or the selected parts of your molecular model.

Visual presets menu

For example, here’s what the “Protein-ligand” preset looks like when applied to the protein with PDB code 1AA1:

Applying a visual preset

What’s Under the Hood?

Each visual preset consists of multiple steps, and each step includes:

  • a selection (such as “Ligands” or “Water”)
  • optional actions (e.g., hide or zoom)
  • an optional visual model (e.g., ribbons, licorice)
  • an optional color scheme (e.g., per chain)

Presets not only save time but help ensure consistency across your figures — useful when preparing publications or presentations.

Make Your Own Presets

SAMSON also lets you build your own visual presets with the Visual Preset Editor. This editor gives you full control over which nodes are selected, what actions to apply, and how elements should be visualized and colored.

Here’s a quick overview of what the editor looks like:

Visual presets window

You can add steps by clicking the plus icon next to the preset list:

Add a new visual preset

Then define each part of your custom step — from selecting atoms or groups using the built-in selectors, to labeling atoms, hiding other components, choosing a visualization model (like Van der Waals) and customizing the color through color schemes or constant color values.

You can even build your own selection filters with the Node Specification Language if the default options don’t match your use case.

When you’re ready, just hit “Apply” and save your preset to reuse it anytime.

Why It Matters

Saving time during visualization setup isn’t just a convenience — it allows researchers to focus more on interpreting results and less on manually configuring representations. The ability to share consistent visual styling across projects and teams is another big plus.

To discover more about customizing or applying visual presets in SAMSON, visit the documentation page: Visual Presets Documentation.

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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