Molecular modelers often need to create visually compelling and informative representations of complex molecular systems. This can involve customizing multiple parameters like visual representations and color schemes—a time-intensive process. Luckily, SAMSON offers a solution: Visual Presets. They allow users to apply a combination of visual representations, actions, and color schemes to molecular systems in just a few clicks, drastically simplifying and accelerating visualization workflows.
What Are Visual Presets?
Visual Presets are pre-configured settings available in SAMSON for quickly visualizing molecular systems. They enable you to apply multiple visual representations and color schemes simultaneously to different parts of a system. This feature is particularly useful for working with complex systems like protein-ligand interactions, where different components, such as receptors and ligands, can benefit from unique visual treatments.
These presets are accessible from the Visualization or Home menu. SAMSON comes with a set of default presets, and users can create their own by modifying existing ones or building from scratch.
How to Use Visual Presets
To apply a visual preset, simply go to Home > Visual preset or Visualization > Visual preset, and select one from the list. The preset will be applied to the selected nodes in your molecular system, or to the entire document if no selection is made.
For instance, applying the “Protein-ligand” preset to PDB code 1AA1 results in a clear visualization of the interaction. Here’s a snapshot of what the menu and result look like:
When you apply a preset, SAMSON automatically organizes the resulting visualization by creating a folder in the document. This folder contains visual models and node groups corresponding to your selections, ensuring that everything remains well-structured.
Customizing and Creating Visual Presets
One of the strengths of SAMSON is its flexibility in adjusting Visual Presets. Users can tweak existing presets or create new ones by leveraging the Visual Preset Editor. Each preset consists of a series of steps, and each step combines:
- A selection of nodes the step will apply to (e.g., “Receptor”, “Ligands”)
- Optional actions for the selection (e.g., “Label atoms”, “Zoom on selection”)
- Optional visual models to represent the selection (e.g., “Licorice”, “Van der Waals”)
- Optional color schemes applied to the visual model or nodes (e.g., “Per chain”, “Constant color”)
To create a new preset, navigate to Home > Visual preset > Create…. Use the Add step feature to add steps for specific actions, visual models, or color schemes as needed. You can preview your created presets and save them for future use. Customize freely to adapt the visual style to your specific requirements, whether for publication, analysis, or presentation.
When Should You Use Visual Presets?
Visual Presets in SAMSON are particularly valuable for:
- Rapid visualization during exploratory studies or structure validation
- Creating standardized visualizations for consistent presentations
- Highlighting specific features of molecular systems, such as binding sites or conformational changes
These presets save time, improve accuracy, and make modeling workflows more effortless.
To dive deeper into Visual Presets and learn how to create fully tailored visualizations, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.