One of the most common frustrations among molecular modelers is spending time repeatedly adjusting visualization settings to highlight the same structural regions—receptors, ligands, water molecules—across different molecular systems. Color schemes, visual styles, atom selections… it can all become time-consuming and error-prone.
If you’ve ever wished you could save and reuse specific visualization settings in one click, Visual Presets in SAMSON might be exactly what you need. This feature allows you to create custom visual styles that automatically apply your preferred colors, representations, and actions (like hiding atoms or zooming in), across any molecular system. It’s a great way to ensure consistency in your figures and save time while exploring complex structures.
What can a visual preset do?
Each visual preset is made up of one or more steps. Each step includes:
- A node selection (e.g., “Ligands”, “Receptor”, or a custom query)
- Optional actions like hiding structures or zooming in
- An optional visual model (e.g., ribbons, Van der Waals, licorice)
- An optional color scheme (per element, per chain, constant, etc.)
These steps are applied sequentially and allow fine-grained control over how different parts of a molecular system appear.
Creating your own visual preset
To create a new visual preset, go to Home > Visual preset > Create… or Visualization > Visual preset > Create…. You will be presented with the Visual Preset Editor:
Here’s how you can build your own visual preset step-by-step:
- Click the + Add Step button to create a new step.
- Select the node types to which this step should apply. Common options include “Ligands,” “Receptor,” or you can use the Node Specification Language for more advanced selections.
- (Optional) Add one or more actions, such as hiding, labeling, or zooming on the selection. Actions are executed in the order they appear.
- (Optional) Choose a visual model to apply—for example, “Ribbons” for proteins or “Licorice” for small molecules.
- (Optional) Pick a color scheme. If you use “Constant”, you can click the color block to choose any color. You can also select a full color palette for attributes like per-chain or per-residue colorization.
You can add as many steps as needed. Arrange their order using the “Move up” and “Move down” buttons, and delete steps with the “- Delete step” button. Once you’re satisfied with your visual preset, simply click Apply to use it, and you’ll be prompted to save it as well.
Best of all, saved presets are available every time you start SAMSON. You can apply them to a full molecular document, or only to selected nodes.
Why this matters
Whether you are preparing visuals for a presentation, publication, or internal sharing, consistency and clarity are key. Visual presets help streamline your workflow while making the result more reproducible. Instead of manually re-applying the same styles across different projects, create your own presets and apply them in seconds.
To learn more about creating and managing visual presets, visit the full page in the SAMSON documentation.
SAMSON and all SAMSON Extensions are now free for non-commercial use.