Molecular modelers often face the challenge of efficiently visualizing complex molecular systems. Adjusting individual representations and color schemes can quickly become a tedious and time-consuming task, especially when working with intricate structures like proteins, ligands, and other biomolecules. This is where SAMSON’s Visual Presets come in, offering a comprehensive solution to streamline this process.
The Power of Visual Presets
SAMSON’s Visual Presets provide a fast and effective way to manage molecular visualizations. With just a few clicks, you can apply multiple visual representations and color schemes simultaneously. Whether you need a clear view of ligands binding to a receptor, want to differentiate atoms based on their properties, or create a visually engaging depiction for a presentation, Visual Presets let you do it all in record time.
From the Visualization or Home menu in SAMSON, you can access a range of predefined visual presets. These presets allow you to instantly switch between visualization styles tailored to specific needs. For instance, the “Protein-ligand” preset is particularly useful for analyzing interactions within protein-ligand binding complexes.
Applying a Visual Preset
Using these presets is straightforward:
- Navigate to Home > Visual Preset or Visualization > Visual Preset.
- Select your desired visual preset from the list.
You can apply presets to specific parts of your molecular system by selecting nodes, or to the entire molecular document if nothing is selected. When you apply a preset, a dedicated folder containing visualization elements and node groupings will appear in your molecular document, keeping your workflow organized.
Here’s an example of how the “Protein-ligand” preset looks when applied to PDB code 1AA1:
Customizing and Creating Visual Presets
Sometimes, the predefined visual presets might not cover your specific needs. SAMSON makes it easy to modify existing presets or create your own from scratch. Here’s how:
To create a new visual preset:
- Go to Home > Visual Preset > Create… or Visualization > Visual Preset > Create….
- Use the Visual Preset Editor to build a series of steps. Each step allows you to:
- Select nodes (e.g., “Receptor”, “Ligands”, “Heavy atoms”).
- Apply actions like “Hide”, “Zoom”, or “Label atoms”.
- Choose a visual model (e.g., “Van der Waals”, “Ribbons”).
- Set a color scheme (e.g., “Per chain”, “Constant”).
If you want to base your preset on an existing one, simply select it, then customize its steps as needed. Alternatively, you can start entirely from scratch, adding your own steps with the 
button to build the preset from the ground up.
For example, here’s how you can choose a set of nodes for a step:
Each step can also include actions and colorization to customize visualizations to your liking:
- Add multiple actions in one step—simply click in the “Apply actions” row.
- Pick a specific color palette or customize one to better fit your visualization needs.
After you’ve built your perfect preset, click “Save visual preset” to store it. It will be available every time you launch SAMSON, ensuring that you can create the visualizations you need with remarkable speed and efficiency.
Conclusion
With SAMSON’s Visual Presets, molecular visualization becomes both intuitive and highly customizable. Whether you’re working on a publication, preparing a presentation, or simply exploring molecular structures, Visual Presets can help you focus on what truly matters: understanding your molecular system.
To explore these features further and see how Visual Presets can enhance your molecular modeling workflows, visit the official documentation page at https://documentation.samson-connect.net/users/latest/visual-presets/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.