Visualizing complex molecular systems effectively and efficiently is a common challenge for molecular modelers. Whether you are working with proteins, ligands, or other molecular components, finding the right combination of representations, color schemes, and additional actions can be both time-consuming and daunting. SAMSON provides a streamlined solution to this challenge with its Visual Presets. These presets allow you to apply multiple visual representations and color schemes to your structures in just a few clicks, enabling clear and insightful visualizations.
What Are Visual Presets?
Visual presets in SAMSON are designed to provide a fast way to represent molecular systems. They bundle together visual models, selections, color schemes, and optional actions, so you can apply them to a molecular system swiftly. This means you no longer need to style individual components of your system manually, saving valuable time and reducing complexity.
You can access these visual presets via the Visualization menu or the Home menu. SAMSON includes several default visual presets to help you get started, and if needed, you can also create your own.
Applying Visual Presets
To apply a visual preset, simply navigate to Home > Visual preset or Visualization > Visual preset and select the desired preset. For example, the “Protein-ligand” preset applies an informative rendering style to protein-ligand complexes, as demonstrated in the image below:
When a visual preset is applied, SAMSON creates a corresponding folder in your document. This folder organizes visual models and groups selections automatically, ensuring that your workspace remains neatly structured.
Customizing and Creating Your Own Visual Presets
To address unique visualization needs, SAMSON offers a Visual Preset Editor that lets you tailor existing presets or create new ones from scratch. Each visual preset is composed of steps, and each step includes:
- A selection of nodes (e.g., “Receptor”, “Ligands”, “Water”).
- An optional set of actions (e.g., “Hide”, “Zoom on selection”).
- An optional visual model (e.g., “Van der Waals”, “Licorice”).
- An optional color scheme (e.g., “Per chain”, “Constant”).
Creating a new preset is simple. Go to Home > Visual preset > Create…, or Visualization > Visual preset > Create…. From there, you can modify existing presets or begin anew. For instance, you can add steps by clicking on the 
button. You can set specific actions, choose custom visual models and color schemes, or even define personalized node selections using SAMSON’s Node Specification Language.
The image below provides an example of the Visual Preset Editor in use:
With the flexibility to customize, save, and reuse visual presets, you can consistently produce the exact type of visualization you need with minimal effort.
Start Enhancing Your Molecular Visualizations
Visual presets in SAMSON are an excellent tool for anyone aiming to create high-quality and tailored molecular visualizations. Whether you’re a newcomer or an experienced user, these presets are sure to make your workflow more efficient. For further details and step-by-step guidance, check out the official SAMSON documentation on visual presets.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Start exploring by downloading SAMSON at SAMSON Connect.