Color is more than aesthetics when it comes to molecular modeling—it’s a functional layer that reveals structural patterns, properties, and meanings at a glance. Whether you’re analyzing temperature factors, chain identities, or hydrophobic regions, having the right color scheme helps you quickly extract valuable insights from complex biomolecular structures.
In SAMSON, the integrative platform for molecular design, colorizing is handled through the application of materials, which are containers that define both color and other visual appearance options like metallicity and roughness. These materials can be applied to any node—atoms, residues, structural models—and automatically affect all of their descendants.
Common Molecular Modeling Pain: Visual Clarity in Complex Systems
It’s not uncommon to open a protein structure, only to be overwhelmed by a sea of indistinguishable atoms or residues. Finding meaningful patterns in such a visualization can be a challenge. Managing color schemes effectively allows you to highlight what matters: hydrophobic cores, charged residues, or even areas of structural flexibility using the temperature factor colorization.
What’s Included in SAMSON
SAMSON provides several built-in color schemes adapted to different modeling goals. These range from classic schemes like Per element (CPK) to illustrative versions inspired by the work of David S. Goodsell. You can also apply per-attribute schemes based on molecular properties:
- Temperature factor – visualize flexibility and uncertainty.
- Chain ID – differentiate distinct chains in multimeric proteins.
- Secondary structure – highlight helices, sheets, and coils.
- Residue type – show hydrophobic, polar, acidic, or basic residues.
- Side chain charge / polarity – useful for electrostatics and solubility analysis.
- Custom… – manually select an attribute and matching palette.
Each of these attributes is mapped to a default color palette, but users can freely swap them for alternatives chosen from diverse palette types, including HCL and HSV color spaces. For instance, you can use diverging HCL palettes to more clearly distinguish extremes in partial charge or hydrophobicity.
Working with Color Schemes
You can apply color schemes in multiple ways:
- Select a node, then use the context toolbar to pick a material or color scheme.
- Navigate to Visualization > Color to apply predefined schemes.
- Use the Inspector for deeper control—reset, modify ranges, or adjust palettes.
For example, choosing Residue hydrophobicity as the attribute allows you to visualize nonpolar cores in proteins. The Inspector also lets you tweak the minimum and maximum values of your attribute mapping—useful if you’re focusing on a particular temperature factor range or specific charge values.
Bonus: Accessibility Tools Built In
An often-overlooked aspect of molecular visualizations is accessibility. SAMSON includes a Color Vision Deficiency Emulator that previews how your color scheme appears to users with various color vision impairments. This is a great feature if you plan on sharing visuals with collaborators or in publications.
Tips for Best Results
- Use Auto update when previewing palettes to instantly see results.
- Reset colorization easily via the context toolbar or Inspector to return to default visuals.
- Don’t be afraid to create and save your own color palettes in HCL space for custom needs.
Summary
Effective color schemes can turn your molecular model from a chaotic jumble into a story-rich visualization. Whether you’re preparing figures for a paper or exploring structure-property relationships, investing a bit of time into mastering SAMSON’s color tools can pay off significantly.
To explore more details about color schemes and how to apply them in SAMSON, visit the official documentation: https://documentation.samson-connect.net/users/latest/colorizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.