Molecular modeling often requires combining clarity with aesthetic quality. When working with complex biomolecular systems, it can be time-consuming to apply multiple visual layers manually — ribbons for secondary structures, sticks for ligands, van der Waals spheres for ions, color schemes, rendering styles, and so on.
If you frequently prepare molecular systems for analysis or presentations, there’s a good chance that you’re spending a lot of time repeating visualization steps. But there’s a faster way: Visual Presets in SAMSON.
What are Visual Presets?
Visual presets in SAMSON are collections of visual representations and color schemes applied simultaneously to a molecular system. They allow you to apply aesthetically beneficial and informative representation styles with just a few clicks. They also save time and help maintain visual consistency across projects.
For example, instead of separately selecting atoms, applying ribbon representations, colorizing chains, adjusting rendering settings, and hiding irrelevant elements, visual presets let you bundle all of these operations into a single step. SAMSON includes several built-in presets, and you can also save your own.
How to Use Visual Presets
To apply a visual preset:
- Go to Visualization > Visual preset.
- Select a preset such as Protein-ligand, Illustrate…, or others.
For instance, the Protein-ligand preset automatically applies protein and ligand-friendly representations and color schemes for a well-defined analysis and presentation layout. Here’s an example of how it looks applied to the PDB structure 1AA1:
Creating Custom Presets
Custom presets are particularly useful when you have specific representation preferences across multiple projects. To create your own:
- Modify an existing visual preset’s settings (color schemes, representation types, etc.).
- Go to Visualization > Visual preset and select Create….
- Save the new preset for future use.
Custom presets are especially valuable for labs or teams to maintain uniformity in the visual appearance of shared data.
Illustrative Visuals in a Click
If you admire the style used in the RCSB PDB Molecule of the Month, created by David S. Goodsell, you’ll find the Illustrate… preset especially handy. This preset applies soft, pastel-like coloring and appropriate surface models to mimic that distinctive illustrative style.
Switching to this style takes only seconds and is perfect for creating publication-ready graphics or educational material without needing graphic design tools.
Final Thoughts
Using visual presets can dramatically reduce the time needed to prepare molecular systems for publications, presentations, or classroom demonstrations. They offer a consistent, repeatable, and efficient way to create clear and beautiful molecular visuals.
Learn more in the full visualization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.