Creating clear and informative molecular visualizations can quickly become time-consuming—especially when dealing with complex systems like protein-ligand complexes, membrane assemblies, or large macromolecular structures. If you’ve ever found yourself spending more time setting up your visual representations than analyzing your data, there’s a good chance Visual Presets in SAMSON can help streamline your workflow.
Visual Presets allow you to apply a series of visual representations, selections, and color schemes all at once, without having to tweak every visual model manually. Whether you’re preparing figures for publication 📄, making educational content 🎓, or just trying to locate key components in a large molecular assembly, visual presets can be a huge time-saver.
Why Visual Presets Matter
Let’s say you’re analyzing a protein-ligand binding structure. You probably want to:
- Show the protein backbone as ribbons
- Display ligands in a licorice or ball-and-stick model
- Color residues by chain or element
- Hide water molecules
Doing this manually for each new file can take minutes you don’t have. With SAMSON’s visual presets, all of this can be done in two clicks.
How to Apply a Visual Preset
Click on Home > Visual preset or Visualization > Visual preset in SAMSON to access the list of default visual presets. Choose the one that matches your needs (e.g., “Protein-ligand”) and it will instantly configure multiple visual settings across your structure.
For example, here’s how the Protein-ligand preset renders PDB code 1AA1:
How It Works
When applied, a visual preset creates a folder in your document. This folder contains both the visual models and the groups of nodes they were applied to. This helps maintain a clean and organized structure in your workspace, especially when working with multiple layers of data.
If nothing is selected, the preset is applied to the whole document. But if you’ve selected specific atoms or residues, the preset will target only those nodes. This is great for zooming in on a binding pocket or emphasizing a drug molecule 🌟.
Customizing Your Workflow
Want a unique look or working style? You can customize an existing visual preset or create your own from scratch. Whether you prefer a muted color scheme or want to differentiate ligands by occupancy, you can define exactly how things should look and save it for future use. Every time you launch SAMSON, your custom presets will be available alongside the defaults.
This flexibility makes it easy to maintain consistency across your visualizations, which is particularly important when collaborating or publishing results.
A Quick Recap
- Visual presets allow you to instantly apply multiple visualization steps
- Access presets via Home > Visual preset or Visualization > Visual preset
- You can create or modify presets to suit your specific needs
- Presets save time, improve clarity, and help maintain consistency
To learn more about using and creating visual presets in SAMSON, visit the original documentation page here: https://documentation.samson-connect.net/users/latest/visual-presets/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.