Molecular modeling often involves the challenge of visualizing complex molecular systems in a clear and aesthetically pleasing way. For many researchers and scientists, this can be a time-consuming task, requiring multiple adjustments to colors, representations, and selections. This is where SAMSON‘s Visual Presets can be a game-changer. Let’s delve into how these presets can simplify and enhance your visualization workflows.
What Are Visual Presets?
Visual presets in SAMSON allow you to apply multiple visual representations and color schemes to a molecular system in just a few clicks. Rather than configuring every aspect manually, you can choose from a range of pre-configured templates that transform molecular systems into scientifically insightful and visually appealing renditions. These presets are accessible from both the Home and Visualization menus in SAMSON.
For instance, the Protein-ligand preset can instantly adjust the visualization of a protein-ligand complex into a polished representation, applying unique colors to chains, showing molecular interactions clearly, and much more. Here is an example of how this preset looks on the PDB entry 1AA1:
Applying Visual Presets
Saving time with visual presets is simple:
- Open the Home or Visualization menu.
- Select the Visual preset option.
- Choose a pre-configured preset from the menu to apply it to your molecular system.
Note that, when no specific nodes are selected, the preset is applied to the entire molecular document. When applied, the preset creates a dedicated folder in the document containing visual models and node groups that correspond to the applied settings. This intuitive organization ensures that your adjustments are both traceable and manageable.
Customizing and Creating Presets
While default presets add convenience, there may be scenarios where you want to tailor them to better suit your needs—or even create entirely new ones from scratch. This is achievable through the Visual Preset Editor. To access it, navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create….
Each visual preset consists of customizable steps that allow fine-tuning at multiple levels. In a single step, you can:
- Select specific nodes to which the step will apply.
- Define actions like hiding atoms, labeling specific components, or zooming into a region of interest.
- Choose a visual model (e.g., “ribbons,” “licorice,” or “Van der Waals”).
- Apply a color scheme, from constant colors to attribute-based schemes like “per chain” or “per occupancy.”
Here’s how you can add a new step to your custom preset:
You can even assign custom selections using the Node Specification Language, add or remove actions, modify existing visualization models, and fine-tune color schemes. Once done, simply save your newly created visual preset, and it will be available for future use whenever you launch SAMSON.
Conclusion
Visual presets in SAMSON are a powerful tool to simplify the visualization of molecular systems, enhance clarity, and ultimately save time for molecular modelers. Whether you use default presets or create personalized ones, this feature brings incredible flexibility. For more details, check out the original documentation page at SAMSON Documentation: Visual Presets.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at SAMSON Connect.