Effective molecular visualizations can sometimes feel like an insurmountable challenge for researchers and modelers. If you’ve ever struggled to clearly communicate attributes like chain ID, temperature factor, or residue polarity in a visually compelling way, SAMSON has a solution that might simplify your work: color schemes. This blog post will walk you through the basics of applying SAMSON’s powerful color schemes to enhance your molecular modeling workflows.
Why use SAMSON’s color schemes?
Color schemes in SAMSON allow you to quickly and intuitively visualize structural attributes in molecular models. Whether you’re colorizing nodes such as atoms and residues by their formal charge or highlighting hydrophobic versus hydrophilic regions in proteins, SAMSON provides a range of default color schemes to suit your needs. These tools are ideal for making structural patterns easier to discern, improving communication in collaborative settings, and creating impactful visuals for presentations and publications.
How to apply color schemes to nodes
Applying color schemes in SAMSON is straightforward and can be done in multiple ways:
- From the context toolbar menu: Select the desired node in your model, then click on the material option in the context toolbar.
- Using the menu: Select your node and navigate to Visualization > Color, where you can pick a specific color scheme.
- Via the Inspector: Use the Inspector to modify or apply materials directly, accessing advanced options like custom color palettes.
For example, let’s explore how to colorize a model based on its hydrophobicity. You can select a structural model in the Document view, then navigate to Visualization > Color > Per attribute > Residue hydrophobicity. Check out the example below:
The residues will now be colorized according to their hydrophobicity, as shown here:
Fine-tuning colors with palettes
Each color scheme uses a default color palette for its assignment, but customization possibilities exist. For instance, you can:
- Modify the color palette for a given scheme through the Inspector.
- Select Color > Custom… from the menu to open a dialog where you can manually adjust the palette.
Custom color palettes enable precise control over value ranges, diversifying the data visualization styles you can achieve. Additionally, SAMSON includes palettes designed for flexible diverging and sequential color spaces, better suited for human perception. This is demonstrated clearly in the Color Vision Deficiency Emulator:
Tip: You can also create your own palettes by modifying existing ones, giving you the flexibility to adapt your visualizations to any specific needs.
Experimenting with materials in the Inspector
SAMSON’s Inspector offers advanced material manipulation for users who want to further customize appearance. Once a material is applied, you can:
- Adjust color schemes.
- Change color palettes for “per attribute” schemes.
- Reset min-max ranges of attributes like temperature factors.
Here’s how you can manage materials more effectively:
Getting Started
To see these features in action, try fetching a structural model from RCSB (via Home > Fetch), apply a constant or per attribute color scheme, and explore the visualization results directly in your SAMSON workspace.
For a step-by-step breakdown of everything shared here, be sure to delve into SAMSON’s complete colorizing documentation at this link.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.