Creating clean, expressive images of molecular systems often involves a lot of manual adjustments—choosing representations, applying colors, tweaking rendering settings. While this flexibility is essential, it can become tedious when you need consistent visuals or just want to focus on molecular science rather than presentation.
This is where visual presets in SAMSON can make a real difference.
What Are Visual Presets?
Visual presets are saved combinations of molecular representations and color schemes. In just a few clicks, you can transform a raw molecular file into a visually refined image that highlights the features you care about: chains, ligands, ions, or secondary structures.
Presets are applied based on selectors, which automatically identify molecular components—speeding up what would typically take several steps. Whether you’re preparing slides, creating animations, or just trying to better understand your system, these presets offer a fast-track to clarity.
Applying a Visual Preset
To apply a preset:
- Go to Visualization > Visual preset
- Select one of the available presets like “Protein-ligand”, “Illustrate…”, etc.
For instance, the Protein-ligand preset automatically highlights the ligand among the surrounding protein structure. Here’s what it looks like on the protein with PDB code 1AA1:
Making Your Own Presets
Not seeing exactly what you need? You can customize existing presets or create new ones based on your workflow. Go to create your own visual presets and experiment with different model types and color schemes. It’s a time-saver for repetitive tasks like preparing images for publications or teaching materials.
Illustrative Visualization Style
If you’re aiming for visuals that resemble David S. Goodsell’s illustrations in the Molecule of the Month series at RCSB PDB, SAMSON also offers a specialized preset for that:
- Apply the visual preset: Visualization > Visual preset > Illustrate…
- Then apply the rendering style: Visualization > Presets > Illustrative
This preset configures visual models using the van der Waals representation with custom cartoon coloring and applies soft lighting and shading effects for a more diagrammatic appearance.
Resetting the Style
Want to go back to basics? Just remove applied visual models in the Document view and select Visualization > Presets > Default or High quality.
Why Use Visual Presets?
Here’s when using them makes sense:
- Quick exploratory analysis: Apply a preset to immediately get a clean view of structural elements
- Routine visualization: Save time during recurring modeling tasks
- Teaching and outreach: Generate readable, educational figures more easily
- Collaborations and publications: Use consistent visual language across projects
To explore more about visual presets and related tools, visit the SAMSON Visualizing guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.