For molecular modelers, one of the most time-consuming aspects of their work is achieving a clear, visually informative representation of complex molecular systems. Manually configuring visual representations and applying color schemes to large protein-ligand structures can be tedious and error-prone. This is where SAMSON’s Visual Presets come to the rescue, offering an efficient way to enhance molecular system visualization.
What Are Visual Presets?
Visual Presets in SAMSON allow users to simultaneously apply multiple visual representations and color schemes to a molecular system with just a few clicks. Whether you’re working with proteins, ligands, water molecules, or any other structures, these presets simplify the visualization process, saving you time and effort.
Visual Presets are easily accessible from the Visualization menu and the Home menu, making them convenient for users at any stage of their workflow. SAMSON even provides a set of default presets, which can be modified or extended to suit your specific needs.
How to Apply Visual Presets
Applying a visual preset is simple:
- Click on Home > Visual preset or Visualization > Visual preset.
- Choose a preset from the list of pre-defined or custom visual presets.
For example, here’s how the “Protein-ligand” preset visualization looks on PDB code 1AA1:
When a visual preset is applied, it creates a dedicated folder in the document structure, enabling better organization. This folder contains visual models and node groups that correspond to selections made during visualization, ensuring your project remains tidy and structured.
Create Your Own Visual Presets
If the default presets don’t fully meet your needs, SAMSON allows you to easily create your own. Using the Visual Preset Editor, you can customize visualization steps to highlight specific aspects of your molecular systems. For instance, you can:
- Select specific types of nodes like receptors, ligands, or water molecules.
- Apply actions such as hiding nodes, labeling atoms, or zooming in on selections.
- Choose a visual model (e.g., Van der Waals, ribbons, or licorice).
- Apply color schemes, whether constant colors, element-based schemes, or chain-specific colors.
This level of customization allows you to adapt SAMSON visualizations precisely to your research objectives, making it much easier to present molecular data clearly and effectively to colleagues or in publications.
Here’s a glimpse of the Visual Preset creation window:
To create a new preset from scratch, navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create…. If you wish to build from an existing preset, simply select it, modify the steps, and save your adjustments. This flexibility ensures you can capture novel insights and tailor visualizations to changing research goals.
Conclusion
SAMSON’s Visual Presets make molecular visualization more efficient, accurate, and customizable. Whether you’re streamlining your workflow, organizing large data sets, or creating publication-ready visuals, these tools are designed with molecular modelers’ pain points in mind.
Learn more on the official documentation page: https://documentation.samson-connect.net/users/latest/visual-presets/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.