Creating clear and expressive molecular visualizations can be a time-consuming task. Whether you’re working on a presentation, preparing figures for publications, or simply exploring a structure, it often involves repetitive steps: selecting atoms, applying representations, choosing color schemes, adjusting views, and more. Repeating these steps manually every session can quickly become a burden.
That’s where custom visual presets in SAMSON can make a significant difference. SAMSON’s visual presets let you apply complex combinations of visual models, selections, color schemes, and actions in just a few clicks. Better yet, you can create your own presets tailored to your workflow.
Why create your own visual presets?
If you often visualize similar types of molecular systems (e.g., protein-ligand complexes, nucleic acid structures, small molecule assemblies), a personalized visual preset can automate your routine. This reduces human error, speeds up your work, and ensures consistent visuals across projects.
Building a visual preset in SAMSON
To create a new visual preset from scratch in SAMSON:
- Go to Home > Visual preset > Create… or Visualization > Visual preset > Create…
- Click the
icon next to the list to add a new preset
Each preset is made of steps, and each step includes:
- Selection: choose nodes like “Ligands” or “Receptor”. If you don’t find what you need, click More… to use the Node Specification Language.
- Actions: apply operations such as Label atoms or Zoom on selection.
- Visual model: apply models like Ribbons, Licorice, or Van der Waals.
- Color scheme: choose from per chain, constant color, or attribute-based schemes.
Steps can be reordered or removed as needed. When you apply the preset, the changes are applied either to the selected nodes or to the entire molecular document if nothing is selected. Your visual models and node groups will be organized in a dedicated folder in the document.
Double-click on the color palette to select or edit it:
Good use cases for custom presets
- Coloring ligands by occupancy while hiding water and highlighting polar contacts.
- Automatically zooming and labeling residues around a binding pocket.
- Applying consistent styles across different protein systems for publication figures.
You can apply your custom preset anytime by selecting it from the Visual preset menu. To make it available for future use, be sure to click Save visual preset.
Want to see your preset added as a default in SAMSON? You can suggest it using the Send feedback button within the platform.
To learn more about visual presets and get an overview of all related features, visit the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.