Communicating complex molecular systems often requires more than just structural accuracy—it demands clarity and readability. As a molecular modeler, you might spend valuable time adjusting colors, representations, and visual styles to produce a publication-ready image. What if you could do this in just a few clicks?
This is where Visual Presets in SAMSON come in. They’re a quick and consistent way to transform raw data into meaningful molecular illustrations—and they can save you serious time.
What Are Visual Presets?
Visual presets are pre-defined combinations of visual styles and color schemes that can be applied to molecular systems instantly. They’re especially helpful for representing complex systems such as protein-ligand interactions, nucleic acid structures, or macromolecular assemblies.
You can access them through Visualization > Visual preset in the top menu. SAMSON comes bundled with useful defaults such as the “Protein-ligand” preset, which applies specific models and coloring tailored for clarity and visual appeal.
Example: Applying the “Protein-ligand” Visual Preset
Let’s say you’ve opened the PDB structure 1AA1. To apply a preset designed for this type of system, simply go to Visualization > Visual preset and select “Protein-ligand”. The scene is instantly updated with ribbon models, color schemes per chain, and atomic ball-and-stick representations for small molecules.
Illustrative Style: Think RCSB PDB “Molecule of the Month”
If you’re aiming for an illustration-style figure similar to those created by David S. Goodsell, SAMSON includes presets for that too.
- Use Visualization > Visual preset and choose Illustrate to switch the visual model to van der Waals spheres colored by chain ID.
- Then switch the rendering style via Visualization > Presets > Illustrative, which activates soft lighting and cartoon-like shading.
Make It Your Own
Beyond the defaults, you can create your own visual presets. Start from a default, tweak the models, colors, and rendering effects to match your preferences, and save it for future use. This is especially useful when working across multiple similar systems where visual consistency is important—such as across different variants of a protein.
Why It Matters
Whether you’re preparing a figure for publication, teaching students, or documenting your research, visual clarity impacts how your molecular message is perceived. Visual presets streamline this process without sacrificing flexibility or quality, giving you more time to focus on analysis and interpretation.
If you’re regularly spending 30 minutes adjusting visual settings before capturing a screenshot, try presets—you may reduce that time to seconds.
Explore more about visual presets and how to apply and customize them in the full documentation: https://documentation.samson-connect.net/users/latest/visualizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.