When working with complex molecular assemblies—especially during collaborative projects or presentations—ensuring that your visualizations are both clear and consistent can be surprisingly tricky. Different color schemes, inconsistent representations, and scattered visibility settings can all make it difficult for collaborators to interpret models quickly, especially when switching between representations of proteins, ligands, and solvents.
SAMSON offers a useful solution to this problem: Visual Presets. These allow you to apply a predefined set of styles, representations, and color schemes to molecular systems in just a few clicks, ensuring your structures always look how you need them to.
Why Use Visual Presets?
You might be in one of the following situations:
- You’re preparing publication figures and want uniformity across all molecular views.
- You need to rapidly evaluate different aspects of a structure (e.g. seeing hydrogen bonds or highlighting ligands).
- You frequently repeat the same color and model choices when loading structural files like .pdbs.
Rather than manually applying styles each time, visual presets streamline this process, allowing batch-like behavior visually without any scripting.
How to Apply a Visual Preset
Once your molecular system is loaded, you can go to:
- Home > Visual preset, or
- Visualization > Visual preset
Choose a preset from the list. Presets like Protein-ligand will automatically apply multi-step renderings that combine ribbons, licorice, and various color schemes relevant to molecular components.
Presets can apply to the whole file (document) or to selected parts (nodes), and they generate a dedicated folder in your Document with structured visual model outputs.
Creating Custom Visual Presets
If you often use a specific style not covered by existing presets, SAMSON lets you make and save your own:
- Go to Home > Visual preset > Create…
- Use the Visual Preset Editor to add one or more steps
- For each step, define a selection (e.g., ligands), assign actions (hide, zoom), apply a visual model (e.g., Van der Waals), and select a color scheme (e.g., per element)
What makes this especially flexible is the ability to define your own node selections, create combinations of visual styles, and re-use your setups for other systems.
When Custom Presets Save Time
Do you frequently want to:
- Zoom automatically to selected ligands upon loading?
- Apply a specific highlight color to metal ions?
- Hide water molecules by default?
These preferences can be encoded into your own visual preset once, and then reused indefinitely, making repetitive style application obsolete.
Final Thoughts
Standardizing visualization is about more than making things look nice—it’s about clarity and efficiency. Visual presets in SAMSON help ensure others can follow your work without confusion, and they let you focus on chemistry rather than software clicks.
To learn more and explore other visualization features in SAMSON, visit the official documentation page on visual presets.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.