When working with complex molecular systems, visual clarity can be the difference between insight and confusion. Yet, customizing molecular representations for each project can become time-consuming — especially when switching between different systems or presentation styles.
This is where Visual Presets in SAMSON can save time and reduce repetitive tasks. With just a few clicks, you can apply rich, layered visual styles to highlight receptors, ligands, solvent molecules, and more — or build your own personalized presets tailored to your scientific needs.
Why custom visual presets matter
By default, SAMSON provides a curated set of visual presets. However, research needs are diverse. You might visualize protein-ligand complexes for docking studies one day, and examine hydration shells the next. With custom presets, you control exactly how these systems appear: from visualization styles like ribbons or van der Waals spheres to atom coloring schemes and automatic zooming or labeling of selections.
This workflow ensures consistency across visualizations and speeds up image creation for presentations or publications.
Getting started with the Visual Preset Editor
To begin creating your own preset:
- Go to
Home > Visual preset > Create...orVisualization > Visual preset > Create... - Click the plus icon to add a new preset:
- Add steps, each defining how a particular type of node should appear.
Each step includes:
- A selection of nodes (e.g., receptor, ligands, water molecules)
- Optional actions like hiding or zooming
- An optional visual model (e.g. ribbons, licorice, spheres)
- An optional color scheme (e.g. by chain, constant color, occupancy)
If the default selection list doesn’t match your use case, click on More… to define custom selections using the Node Specification Language.
Tips when building your preset
- Add multiple actions in a step: for instance, label ferrous atoms and zoom on the ligand.
- You can reorder steps to control how they apply.
- Want to adapt an existing style? Select a default preset, tweak it, and re-save.
- Customize color palettes by double-clicking on them and choosing or creating your own.
- Delete a step with the minus icon if you no longer need it.
Once saved, your presets are always ready
Your custom presets are available each time you open SAMSON. Whether you’re inspecting docking results or preparing figures, your visualization is just a click away.
If your preset might be useful to others, you can suggest adding it to the public list by clicking Send feedback in the interface.
To explore more about SAMSON’s visual preset system — including image examples of presets in action — visit the complete documentation page at:
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.