One of the most time-consuming tasks in molecular modeling is consistently producing clear and accurate representations of complex molecular systems. Switching representations, tweaking visibility, adjusting colors, labeling atoms — these repetitive steps can quickly stack up, especially when working on large systems or preparing publication-quality visuals.
If you find yourself doing the same visualization steps repeatedly, SAMSON offers an efficient, customizable feature that may save you a great deal of time: Custom Visual Presets. These presets let you group together multiple visualization choices — selections, representations, color schemes, and even actions like zoom or hide — and apply them all at once with a click.
Create Once, Reuse Often
The Visual Preset Editor in SAMSON allows you to build visual presets one step at a time. Each step includes:
- A selection (e.g., “Ligands”, “Receptor”)
- Optional actions (e.g., Hide atoms, Zoom on selection)
- An optional visual model (e.g., Ribbons, Van der Waals)
- Optional color schemes (e.g., per chain, constant color)
You can add as many steps as needed to cover different parts or features of your molecular system. This modularity provides a lot of flexibility and helps you build a clear, comprehensive look for your models — and then reproduce it with a single command.
How to Create a Visual Preset
To build your own preset, go to Home > Visual preset > Create... or Visualization > Visual preset > Create.... To start from scratch, click the plus button next to the list of existing presets:
Add steps by clicking Add step. Each step lets you:
- Select specific groups of atoms or molecules. You can either choose from predefined options (like “Water” or “Heavy atoms in ligands”) or define your own with the Node Specification Language.
- Apply actions like hiding parts of the molecule or zooming in automatically.
- Add a visual model — for instance, show ligands in Licorice and proteins in Cartoon mode.
- Assign a color scheme, or let visual models use their default styles.
Here’s an example of step configuration:
Customize and Reorganize
After adding steps, you can easily adjust the order or remove individual steps. If you want to change colors, just double-click on the palette to edit it or revert to a default:
Once your visual preset is ready, click Save visual preset to store it — or simply click Apply and you’ll be prompted to save.
Why Use Custom Visual Presets?
Here are a few reasons molecular modelers choose to create their own visual presets:
- Consistency: Uniform visuals across different datasets or projects.
- Speed: From minutes of tweaking to one-click visualization.
- Reproducibility: Reuse the same settings when generating figures over time or sharing with collaborators.
If you have a preset that might benefit other users, you can even contact SAMSON to propose adding it to their default library.
To learn more about visual presets and how they fit into SAMSON’s visualization ecosystem, check the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.