Anyone working regularly in molecular modeling knows how repetitive and time-consuming setting up a clean, clear visualization can be. You may spend several minutes choosing representations, hiding solvent atoms, coloring chains, creating attractive figures—only to repeat the same steps a few hours later on another system. 🌀 What if your work style could be captured, re-applied, and even shared in just a few clicks?
SAMSON, the integrative platform for molecular design, includes a feature called Visual Presets that addresses this common pain point. In this blog post, we’ll explore how you can create your own custom visual presets in SAMSON to speed up your workflow and ensure consistent, reproducible, and personalized visual representations.
Why create custom visual presets?
Think of visual presets as layered instructions for visualization. Each preset includes steps like:
- What to apply the visualization to (e.g., ligands, solvent, backbone atoms).
- Actions to perform (e.g., hide atoms, label residues, zoom in).
- How to display the selection (e.g., Licorice, Van der Waals, Ribbons).
- Which coloring scheme to use (e.g., per occupancy, constant, per chain).
Once you’ve configured a preset to your taste, you can save it and apply it to any molecular structure in the future with a single click. No more starting from scratch every time. 🎯
How to create your first custom preset
Let’s walk through the process. First, go to:
- Home > Visual preset > Create… or
- Visualization > Visual preset > Create…
To define what the preset should do, click on the Add step button. Each step gives you control over a particular part of the system. For instance, you might create a step that:
- Selects ligand atoms
- Labels the polar atoms
- Displays them using the Van der Waals representation
- Uses a per-element color scheme
Need more customization? Create your own selection using the Node Specification Language by choosing More… in the selection options. This allows you to define highly specific criteria for atom, residue, or group selection.
Customize further by adding actions like zooming in on the region or hiding surrounding atoms. You can even personalize the color palette by double-clicking on it to adjust or reset it.
Once your preset is ready, save it by clicking on Save visual preset. You can apply it immediately or access it later from the Visual preset menu. If you’re refining an existing preset, you can modify steps or change their order with the Move up and Move down controls.
Sharing your style
Sharing consistent visuals across teams can be difficult. With visual presets, you can develop a shared style guide for molecular representations—especially useful when preparing figures for publications or giving presentations. While the documentation doesn’t mention export/import, if you’re interested in adding your custom presets to SAMSON’s default list, reach out using the in-app Send feedback feature.
Final thoughts
Visual presets help reduce repetitive work, promote visual clarity, and give you control over how you see and present molecular systems. Whether you’re analyzing structure-function relationships or preparing figures for a paper, visual presets let you spend less time adjusting views and more time making discoveries.
To learn more, visit the official documentation: https://documentation.samson-connect.net/users/latest/visual-presets/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.