For molecular modelers, one of the constant challenges is efficiently visualizing complex molecular systems. With the diverse structures and properties of molecules, traditional approaches often fall short, making it hard to intuitively grasp important details at a glance. Enter Visual Presets in SAMSON – a streamlined solution that combines multiple visual representations, color schemes, and features into a single, user-friendly feature.
The Power of Visual Presets
Visual Presets offer a quick and effective way to visualize molecular systems. They allow you to apply multiple representations and color schemes simultaneously with just a few clicks. Whether you’re analyzing proteins, ligands, or entire molecular complexes, this feature helps you see what matters most without wasting time on manual adjustments.
SAMSON provides a set of default visual presets for instant visualization, and the best part is that you can create and customize your own. Whether you prefer to tweak an existing preset or craft a completely new one from scratch, the possibilities are endless. Once created, these presets are saved and ready to use whenever you launch SAMSON.
Creating Custom Visual Presets
Building your own visual preset in SAMSON is a straightforward yet powerful process, thanks to the Visual Preset Editor. Rather than just accepting defaults, you can tailor presets to your specific modeling needs. Here’s how it works:
1. Navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create… to start creating a new preset.
2. Add a new step to your visual preset by clicking on the plus button: 
Add step.
3. For each step, define:
- Selection of nodes: Choose predefined options like “Receptor” or “Ligands” or create your own using the Node Specification Language.
- Optional actions: Apply actions such as hiding nodes, labeling atoms, or zooming on a selection for clear and precise visualization.
- Visual models: Specify how the selection is represented, whether using Van der Waals, Ribbons, or Licorice models, among others.
- Color schemes: Apply visual clarity with options like “Per chain” or “Constant color” to highlight specific molecular details.
4. Modify steps as needed, adjust their order, or remove steps selectively. Add multiple actions or customizations within each step for a more detailed approach.
Examples in Action
Let’s say you want to examine a protein-ligand interaction, such as PDB code 1AA1. The “Protein-ligand” visual preset streamlines the visualization to highlight key features of the interaction. Notice how the default preset brings clarity by applying specific colors and models:
With custom visual presets, you can further personalize these representations to suit your workflow.
Why Customization Matters
If your work involves recurring structures or properties, creating a reusable visual preset saves significant time. For instance, you might frequently work with water molecules but only want to focus on polar atoms. By fine-tuning steps within a preset, you’ll get consistent clarity every time – leaving you to spend more energy on actual analysis rather than visualization setup.
Save and Share Your Work
When you’re happy with your preset, simply hit “Save visual preset” to keep it for future sessions. If your custom preset has broader utility, you can even contact the SAMSON team to have it added to the list of default visual presets, making it accessible to all users.
Want to delve deeper? Check out the documentation page for detailed instructions and additional tips: https://documentation.samson-connect.net/users/latest/visual-presets/.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at https://www.samson-connect.net.