Molecular modelers often face the challenge of effectively visualizing complex molecular systems. Whether it’s a protein-ligand complex or a vast molecular structure, presenting clear, insightful visuals takes time and effort. The Visual Presets feature in SAMSON is designed to make this easier by applying multiple visual representations and color schemes to molecular systems with just a few clicks. But did you know you can also customize visual presets to tailor them to your specific needs?
What Are Visual Presets?
At its core, a visual preset is a tool that helps molecular modelers apply predefined visualizations and color schemes to molecular systems. By default, SAMSON provides several presets accessible from the Visualization and Home menus. These presets can save time and effort when analyzing molecular data. However, if the default options do not perfectly match your needs, you can create and save your own custom visual presets.
How to Create Custom Visual Presets
The Visual Preset Editor in SAMSON enables you to build a completely personalized visualization setup. Each visual preset is composed of multiple steps, and each step allows you to define:
- A selection of nodes to apply changes to (e.g., “Ligands” or “Heavy atoms”).
- An optional set of actions, such as labeling atoms or zooming in on a selection.
- An optional visual model to change appearance (e.g., “Licorice” or “Van der Waals”).
- An optional color scheme for further customization (e.g., “Per chain” or “Constant”).
Step-by-Step Guide to Creating Presets
- Navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create….
- Add a new step by clicking the
Add step button. - Choose the type of nodes the step should target (e.g., “Receptor”, “Water”). If no suitable option exists, create a custom one using the Find window.
- Add actions to the nodes by selecting them in the Apply actions row. You can freely add, rearrange, or remove actions as needed.
- Select a visual model and/or color scheme to enhance the appearance of your selection.
To save your new preset, click Save visual preset. If desired, you can modify existing presets by adding or removing steps, changing nodes, or adjusting color schemes. Your custom presets will load every time you launch SAMSON, ensuring your workflow remains efficient.
Practical Example of Editing a Visual Preset
Suppose you’re working on a protein-ligand system and prefer specific colors and visual models for distinct parts of the structure. By creating a visual preset, you can:
- Highlight the receptor with a “Ribbons” model and apply a “Per chain” color scheme.
- Use a “Van der Waals” model for ligands with vibrant constant colors.
- Zoom on the binding site to focus on key interactions.
These tailored visual elements help you present data clearly and consistently without manual adjustments each time.
Streamline Your Visualization Workflow
Whether you’re a student, researcher, or professional molecular modeler, creating and saving custom visual presets in SAMSON can make your visualizations more effective. To dive deeper into visual presets, including tips on optimizing them for your projects, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at SAMSON Connect.