Molecular modelers often spend significant time adjusting visualization settings for complex systems. Whether it’s finding the right representation style or highlighting specific molecular regions, the process can be repetitive and time-consuming. What if you could simplify this workflow and apply multiple settings at once?
That’s where custom visual presets in SAMSON, the integrative molecular design platform, come to the rescue. Tailoring molecular visualizations becomes both faster and more versatile with the platform’s Visual Preset Editor. Let’s explore how you can save time and enhance your productivity by creating and using these presets effectively.
Why Create Custom Visual Presets?
Imagine a scenario where you need to regularly visualize protein-ligand complexes with specific color schemes and representations: ribbons for proteins and licorice for ligands. Every time a new dataset comes in, re-configuring the styles can feel like a bottleneck. With custom visual presets, these steps can be automated.
By crafting your own presets, you get:
- A personalized set of visualization settings that can be applied in a single click
- Flexibility to configure selection models, visual styles, color schemes, and even step sequences
- The ability to easily reuse and share preferred visualization workflows
How to Create a Visual Preset?
Creating or personalizing a visual preset in SAMSON is intuitive, thanks to the Visual Preset Editor. Follow these steps:
- Access the editor: Navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create… in the SAMSON interface.
- Add a step: Click the
button to insert a new step. Each step encompasses four configurable components: - A selection of nodes (e.g., proteins, ligands, water molecules)
- Actions to apply (e.g., label atoms, zoom on selection)
- A visual model for representation (e.g., ribbons, licorice, van der Waals)
- A color scheme for visual consistency (e.g., per element, per chain, or constant)
- Customize the settings: You can modify every aspect of a step. If an appropriate selection isn’t available, use the “More…” option to create one via SAMSON’s Node Specification Language. Actions and models can also be added or removed within seconds.
- Fine-tune colors: Selecting “constant color” or predefined schemes allows you to further adjust style. Double-click the palette to modify it if necessary.
- Save the preset: Once configured, click on “Save visual preset” to store your custom workflow. The next time you launch SAMSON, your presets will be ready for use!
Practical Examples
To better visualize what custom presets can do, consider the following:
- A protein-ligand complex where the receptor uses a “Ribbon” model with a “Per chain” color scheme, and ligands are presented in “Licorice” with a specific constant color.
- A visualization that highlights polar atoms, hiding water molecules and zooming in on the site of interest in one click.
The customization possibilities are endless, making visual presets an incredibly flexible tool for molecular modeling workflows.
Get More From SAMSON
Now that you know how to create and leverage visual presets, imagine the time you’ll save on routine visualization tasks. Whether you modify an existing preset or design one from scratch, the possibilities for personalization ensure that your molecular modeling workflows fit your unique needs.
To learn more about visual presets, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.