For molecular modelers, the challenge of effectively visualizing complex molecular systems is all too familiar. Whether you’re working with protein-ligand interactions or full macromolecular assemblies, the time spent setting up visual representations and color schemes can hinder productivity. This is where SAMSON’s Visual Presets can transform your workflow by enabling you to apply tailored visual setups in just a few clicks.
The Visual Presets feature simplifies molecular visualization by allowing users to predefine combinations of visual representations, color schemes, and structural actions. Let’s dive into how you can create, save, and utilize custom visual presets to streamline your molecular modeling tasks.
Why Use Visual Presets?
Visual presets provide an integrated approach to rendering molecular systems. Instead of setting up individual visual components like ribbons, licorice-style atoms, or specific color schemes manually, you can automate the entire process. Pre-configured or customized visual presets ensure consistency in your visualizations and save valuable time.
For example, you could create a single preset to display protein regions with ribbons while highlighting ligands and water molecules in distinct styles, all in one step. This level of customization makes it easier to communicate findings, analyze structures, or generate publication-ready images.
How to Create Custom Visual Presets
Creating or modifying visual presets is straightforward in SAMSON. Here’s a step-by-step guide:
1. Start Creating:
Navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create…. To start from scratch, click on the 
Add New button next to the list of visual presets.
2. Add Steps to Define Your Visualization:
A visual preset consists of sequential steps. Click Add step to define a new step. For each step, you choose:
- A selection of nodes for the step (e.g., “Receptor”, “Ligands”, or “Water”). If no default options suit your needs, click More… to specify a custom selection using SAMSON’s flexible Node Specification Language.
- Structural actions like “Hide”, “Zoom on selection”, or “Label atoms,” which are applied to the selected nodes.
- An optional visual model for rendering (e.g., ribbons or van der Waals spheres).
- An optional color scheme (e.g., “Per chain”, “Per occupancy”, or a custom color palette).
3. Fine-Tune Step Details:
You can apply multiple actions in a single step and reorder them for precise control. To remove an action or step, simply click the corresponding delete button.
4. Save and Reuse:
Once your visual preset is ready, click Save visual preset for future use. Alternatively, clicking Apply lets you use the preset immediately, with an option to save it as well.
Modify or Start Fresh
If you prefer to base your visual preset on an existing one, SAMSON lets you make edits by altering steps, adding new ones, or changing color schemes and visual models. Alternatively, you can start fresh and craft a preset tailored to your specific needs.
Adding color schemes and palettes is especially handy when style consistency is crucial. Whether you’re visualizing hydrophobic pockets or charged residues, SAMSON’s palette options ensure customization stays both precise and visually effective.
Empower Your Molecular Modeling
Once built, your custom visual presets will become invaluable assets for molecular exploration, ensuring you can focus on science rather than setup. And if you’re particularly proud of your creation, you can even share feedback with the SAMSON team to include your preset in the default library.
Learn more about visual presets and how they can simplify your workflow by visiting the complete documentation at SAMSON Visual Presets Guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON at https://www.samson-connect.net.