In molecular modeling, a common challenge is consistently generating clear, informative visualizations—especially when dealing with complex systems such as protein-ligand complexes, solvated structures, or multi-chain systems. Adjusting representations, selecting relevant atoms or molecules, setting color schemes, and choosing visualization models are repeated tasks that can be both time-consuming and error-prone.
SAMSON offers a solution through its Visual Presets system. What makes this especially useful is not just its default presets, but the ability to create and save your own—allowing for fast, one-click visual representations of molecular systems tailored entirely to your preferences or team standards.
Why Create Your Own Visual Presets?
Custom visual presets are especially helpful if:
- You frequently work with similar types of molecular systems (e.g., ligand-receptor complexes, DNA-protein interactions).
- You want to maintain a consistent look and feel for figures or animations in publications or presentations.
- You need to repeatedly apply specific viewing angles, color schemes, or hidden components.
How a Visual Preset Works
A visual preset in SAMSON is made up of a list of steps, and each step contains:
- A node selection (e.g., all amino acids, ligands, water molecules).
- Optional actions (e.g., zoom to selection, hide, label atoms).
- A visual model (e.g., ribbons, van der Waals spheres, licorice).
- An optional color scheme (e.g., per chain, by element, a constant color).
Steps are executed in the order they’re added, and multiple steps can be used to compose elaborate, layered visualizations.
Creating Your First Preset
To create a new preset:
- Go to Visualization > Visual preset > Create… or Home > Visual preset > Create….
- Click the “+” button next to the list to add a new preset.
- Use the Add step button to define each visualization step.
Each step allows you to pick a predefined selection like “Receptor” or “Ligands”, or define your own using SAMSON’s Node Specification Language (NSL)—a powerful feature for expert users looking to capture highly specific structural selections.
You also get fine-grained control over color schemes and palettes. Selecting a constant color is as simple as double-clicking the color block next to the scheme. Customizing these options can help you align molecular visuals to journal requirements or presentation themes.
Reuse, Edit, Share
Once you’ve created your custom visual preset, you can:
- Apply it to any document in one click.
- Edit it anytime, duplicating a preset or changing steps as your focus evolves.
- Save and share it with collaborators or students.
If you’ve created a visual preset that you believe could benefit others, SAMSON offers the possibility to submit it for inclusion in the list of default presets. This is especially helpful in academic or collaborative environments where standardization enhances reproducibility.
By investing a few minutes to set up custom visual presets, you can potentially save hours over time, reduce variability across your molecular visuals, and simplify your workflow considerably.
To learn more about visual presets in SAMSON, including detailed steps and examples, visit the full documentation page: https://documentation.samson-connect.net/users/latest/visual-presets/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON on https://www.samson-connect.net.