One of the most common challenges molecular modelers face is making complex molecular structures easy to interpret and visually insightful. Whether it’s distinguishing between chains, mapping specific properties like temperature factors, or customizing visuals for specific workflows, colors play a significant role. Luckily, SAMSON makes this process smooth by providing powerful tools for applying and customizing color palettes.
In this guide, we’ll focus on custom color palettes, which let you represent information in ways that are not only scientifically meaningful but also optimized for human perception and even consideration of color vision deficiencies.
Why Use Custom Color Palettes?
Default color palettes in SAMSON are already tailored to many scientific needs, but every modeling problem is unique. Custom color palettes allow you to:
- Customize the representation of specific molecular properties (e.g., atomic charges, hydrophobicity).
- Switch between vibrant, qualitative palettes and sequential or diverging color scales tuned for continuous data.
- Ensure accessibility for users with specific color vision deficiencies.
This flexibility is particularly helpful for research collaboration, teaching molecular design, or presenting results to diverse audiences.
How to Customize a Color Palette in SAMSON
SAMSON offers multiple preset color palettes in HCL (Hue-Chroma-Luminance) and HSV (Hue-Saturation-Value) spaces, with support for sequential, diverging, and qualitative designs. To create your custom palette:
- Open the Visualization > Color > Custom… menu.
- In the dialog window, select a starting palette. The interface allows you to preview changes in near-real time with the Auto update option.
- Customize the range and transition of colors by adjusting the Hue, Chroma, and Luminance parameters.
- Optionally, reverse the left and right arms of the palette for diverging scales.
- Click Save to store your custom palette locally for reuse across projects.
Here’s how it looks when you’re creating a custom color palette:
Support for Color Vision Deficiency
Beyond utility, SAMSON includes a Color Vision Deficiency Emulator, which enhances inclusiveness in your visualizations. Found at the bottom of the color palette dialog, it enables you to test your visuals as they would appear to individuals with common color blindness types. This feature ensures your materials communicate effectively to all collaborators or students.
Practical Tips for Effective Coloring
- For continuous data like temperature factors, use sequential or diverging palettes for better granularity and contrast.
- Always preview how the palette interacts with the structure to ensure it highlights the properties you want to showcase.
- If your collaborators have specific needs, export a sample image of your model using their preferred palette to get early feedback.
Customizing your visualization workflow is a game-changer for communicating molecular insights effectively. Experiment with custom palettes to find what works best for your specific model and audience.
To learn more, visit the original documentation at https://documentation.samson-connect.net/users/latest/colorizing/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.