Visualizing complex molecular systems can often be daunting. As a molecular modeler, you may feel the need for specialized tools to streamline this process without spending countless hours fine-tuning representations and color schemes. Fortunately, SAMSON, the integrative molecular design platform, offers a fantastic feature to address this challenge: Visual Presets.
What Are Visual Presets?
Visual Presets allow you to enhance molecular systems’ visual representation effortlessly. They combine multiple visual representations and color schemes simultaneously in just a few clicks, delivering a clear and tailored visualization of your molecular models.
Whether you’re working on proteins, ligands, or complex biomolecular assemblies, the Visual Presets feature is designed to simplify how you analyze and present your systems. You can access these presets from the Visualization or Home menus, and they let you save time while maintaining accuracy and aesthetic clarity. SAMSON provides a series of built-in visual presets that you can use as-is, or customize further to meet your specific needs.
Here’s a quick example of the Protein-ligand preset applied to PDB code 1AA1:
How to Apply Visual Presets
Applying a visual preset is simple and intuitive. Follow these steps:
- Go to Home > Visual Preset or Visualization > Visual Preset from the main menu.
- Select the visual preset you want to apply from the list of existing options.
You can choose from predefined options like Protein-ligand visualizations, which showcase key structural elements with clarity. When applied, the preset generates a folder in your document containing visual models and node groups relevant to your selection or the entire document if no specific selection is made.
Here’s a view of how you can access the Visual Presets menu:
Customizing Your Visual Presets
What if the default presets don’t meet your exact needs? No problem! SAMSON allows you to create custom visual presets from scratch or modify the existing ones. By using the Visual Preset Editor, you can add, remove, or rearrange visualization steps to suit your requirements. Each step includes specific elements such as:
- A selection of nodes (e.g., receptor, ligands, water, etc.)
- Optional actions like “Hide,” “Label atoms,” or “Zoom on selection”
- A visual model (e.g., van der Waals, ribbons, licorice, etc.)
- An optional color scheme to enhance clarity
Want more customization? You can even define your own node selection criteria using the Node Specification Language (NSL), tailor color schemes to align with your style, and arrange steps in the most effective order for your specific visualization task.
Here’s what the Visual Preset Editor looks like:
Conclusion
By using SAMSON’s Visual Presets, molecular modelers can greatly reduce the time spent adjusting visualization settings. The ability to apply and customize presets simplifies workflows, whether you’re preparing a presentation, sharing data with collaborators, or analyzing molecular structures in detail. The flexibility and ease of use make this feature a go-to tool for productivity.
To learn more about Visual Presets, be sure to check out the official documentation page: https://documentation.samson-connect.net/users/latest/visual-presets/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON today!