When working with molecular systems, visualization can be a time-consuming process, especially when dealing with complex systems like protein-ligand interactions or polymers. Is there a way to simplify this? Yes! Visual presets in the SAMSON molecular design platform are a game-changer for rendering molecular models aesthetically and functionally valuable in just a few clicks.
The Problem: Simplifying Molecular System Visualization
For molecular modelers, visualizing structures effectively is crucial for understanding interactions, forming hypotheses, and presenting data. Instead of manually applying multiple visual representations and color schemes, visual presets enable users to select predefined setups that combine these elements for diverse structural contexts. This saves massive time and maintains consistency in visual presentations.
What Are Visual Presets?
Visual presets allow users to apply a combination of visual styles (e.g., ribbons, spheres, or licorice) and color schemes (e.g., per chain or occupancy-based colorization) to molecular parts systematically. Accessible from the Home or Visualization menus, this feature reduces the complexity of navigating different visual tools for large biomolecular structures.
For example, applying the “Protein-ligand” visual preset to the PDB code 1AA1 delivers a clear representation of both the protein backbone and its ligand within moments:
In just a few clicks, your visualization becomes complete and presentation-ready!
How to Apply a Visual Preset
Here’s how simple it is to transform your molecular system using SAMSON:
- Go to either Home > Visual preset or Visualization > Visual preset.
- Select a desired preset from the list.
Once the preset is applied, SAMSON organizes your molecular system automatically. It creates a folder in your document, storing the visual components and related groups within the document’s hierarchy. This keeps your workspace structured and allows you to tweak individual components if needed later on.
Customizing and Creating Your Own Visual Presets
Don’t see a visual preset that meets your needs? SAMSON’s Visual Preset Editor lets you create custom visualizations to fit specific use cases. Here’s how you can get started:
- Create from scratch: Use the
button to add steps to your visual preset, specifying selections, actions, visual models, and color schemes. - Base it on an existing preset: Choose an existing preset and modify its steps, colorizations, and presentations to suit your needs.
Here’s the interface to add new steps to your visual preset:
Your saved visual presets will load automatically whenever you launch SAMSON, ensuring your preferred styles are always ready to go.
Applications Beyond Visualization
Visual presets aren’t just about aesthetics. With predefined steps such as zooming on selections, hiding specific elements, or labeling atoms, these tools are invaluable for:
- Preparing high-quality visualizations for presentations and publications
- Exploring specific molecular interactions, like the binding between ligands and proteins
- Creating animations that narrate interactions within molecular systems
Learn More
For a deep dive into how visual presets work and guidance on building your own, visit the full documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.