Visualizing molecular systems effectively can be a challenging task. Molecular modelers often face the pain of merging different visual representations and color schemes to analyze complex systems cohesively. This process can be time-consuming and frustrating, often requiring multiple steps to achieve the desired view. But what if you could simplify and speed up this process, combining all elements with just a few clicks?
Introducing Visual Presets in SAMSON
With SAMSON’s Visual Presets, you can simplify the visualization process by applying predefined styles to molecular systems. Visual Presets allow you to orchestrate multiple visual representations and color schemes, enabling users to create consistent, informative, and visually appealing models effortlessly. These presets are accessible from the Home or Visualization menus in SAMSON.
For example, let’s take the Protein-ligand preset and apply it to a specific molecular system such as PDB code 1AA1. This preset integrates ribbon and licorice visual models and applies different coloring for better structural insights in an instant. Below is how the Protein-ligand preset appears when applied:
How to Apply Visual Presets
To apply an existing visual preset, navigate to the Home > Visual Preset or Visualization > Visual Preset menu. Choose one of the available presets that best fits your needs. These presets can be applied to specific selections within your molecular system or to the entire system if no selection is made.
Note: When a visual preset is applied, a dedicated folder is created in your document, housing node groups and visual models generated by the preset. This structured approach ensures easy organization and retrieval of applied visual styles.
Creating Custom Visual Presets
Do you often repeat specific steps for your visualizations? SAMSON provides the flexibility to create and save your own visual presets, reducing repetitive tasks. By using the Visual Preset Editor, you can craft custom presets from scratch or modify existing ones. Each custom preset comprises a series of steps, and each step includes:
- A selection of nodes to apply the step (e.g., “Ligands,” “Receptor,” or “Water” molecules).
- Optional actions such as “Hide,” “Label atoms,” or “Zoom on selection.”
- Optional visual models like “Ribbons,” “Licorice,” or “Van der Waals.”
- Optional color schemes (e.g., “Per chain” or “Per occupancy”).
Here’s a quick visual example of setting up a custom visual preset step:
Want to make finer adjustments? You can even create custom node selections using the Node Specification Language—ideal for advanced users who need detailed flexibility.
Once you have customized or created your preset, don’t forget to save it! The saved presets load automatically when you launch SAMSON, enabling instant access and quicker workflows.
Why Visual Presets Add Value
Visual Presets offer molecular modelers a streamlined approach to visualizing systems with enhanced clarity. By combining styles in seconds rather than minutes, they tackle a significant pain point for researchers and educators alike. Additionally, they provide versatility for crafting presentations, animations, or conducting detailed inspections.
Want to dive deeper into the possibilities? Explore the full documentation on visual presets here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get started by downloading SAMSON at this link.