One of the common challenges molecular modelers face is efficiently visualizing complex molecular systems. Whether you’re working on a protein-ligand interaction, a nucleic acid structure, or simulating a complex, understanding the molecular arrangement visually is crucial. However, setting up multiple visual representations and color schemes for large systems can be time-consuming and prone to errors.
Fortunately, SAMSON simplifies this process with its powerful Visual Presets, allowing users to effortlessly apply predefined or customizable visualization templates in just a few clicks. Imagine saving valuable time while achieving visually compelling molecular presentations. Here’s how SAMSON’s visual presets can make your work more efficient:
What Are Visual Presets?
Visual presets are predefined visualization configurations in SAMSON. They enable you to simultaneously apply multiple representations (e.g., ribbons, licorice, Van der Waals) and color schemes to selected parts of a molecular system or the entire structure.
Where to find them: Access visual presets from the Home > Visual preset or Visualization > Visual preset menus in SAMSON.
How to Apply Visual Presets
Applying visual presets is straightforward. Follow these steps:
- Navigate to Home > Visual preset or Visualization > Visual preset.
- Choose one of the predefined visual presets from the menu.
- If nothing is selected, the preset applies to the entire molecular document. Otherwise, it focuses on the selected regions.
For instance, here’s how the Protein-ligand preset beautifully visualizes the protein-ligand interaction of PDB code 1AA1:
Want to Tailor Your Visualization?
While the default presets cover various needs, custom visual presets offer molecular modelers the ultimate flexibility. Using the Visual Preset Editor, you can easily:
- Adjust node selections for specific steps (e.g., receptors, ligands, heavy atoms).
- Add or remove actions like zooming, hiding, or labeling atoms.
- Apply specific representations (e.g., ribbons for the protein backbone).
- Select custom color schemes to bring out the clarity in your molecular system.
For instance, adding or removing steps to a visual preset is as simple as clicking on the 
add step or 
delete step buttons.
Each step can be customized to define which nodes the step applies to, specify optional actions, include detailed visual representations, and refine color settings. You can even compose your node selection using SAMSON’s Node Specification Language.
Boost Creativity in Molecular Presentations
Custom visual presets particularly shine when preparing molecular presentations and animations. By saving visual presets, you ensure consistent styles across different projects and presentations while simplifying repetitive workflows.
Would you like your custom-made visual preset to be added to SAMSON’s default list of presets? The team at SAMSON welcomes your contributions! You can send feedback directly through the platform.
To dive deeper into the nitty-gritty of visual presets, or for step-by-step guidance, explore the documentation page on visual presets.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started by downloading SAMSON at this link.