Molecular modeling can be a visually complex task. To make sense of molecular structures and their properties, using color schemes effectively is paramount. This post will guide you through applying color schemes in SAMSON, the integrative molecular design platform, enabling you to better visualize and interpret your models.
Color schemes in SAMSON allow you to customize the appearance of molecular models at various levels, from individual nodes such as atoms or residues to entire structural models. For example, with color schemes, you can assign specific colors to atoms of certain elements, highlight residues by hydrophobicity, or even adopt styles inspired by David S. Goodsell.
How to Apply Color Schemes
Applying color schemes to your model is straightforward. Here’s how you can do it step by step:
- Using the Context Toolbar: Select a structural node or model in the Document view, and click on the material in the context toolbar to choose a color scheme. For example, you can apply a constant color scheme as shown in this image:
- Through the Visualization Menu: Use the menu path Visualization > Color to access various options. Options include constant color schemes as well as per-attribute schemes such as “Residue hydrophobicity.”
- Via the Inspector: Open the Inspector to view and modify materials applied to nodes. You can add, reset, or replace color schemes right from there:
Notably, when you apply a material (which includes a color scheme), all the descendants of the selected node inherit the appearance changes.
Visualizing Specific Attributes
SAMSON lets you colorize based on a broad array of attributes. For example, you can easily set colors by chain, residue type, or even properties like temperature factor. The “Residue hydrophobicity” color scheme is especially useful for representing proteins. Here’s how this appears:
Colorized models like this allow you to quickly spot patterns or regions of interest in molecules that would otherwise be harder to discern.
Customizing Your Palette
Each color scheme comes with a default palette, but SAMSON gives you the ability to change it. For example, when coloring per attribute, you can:
- Modify the palette using the Inspector by clicking on the color bar.
- Select “Color > Custom…” to open a dialog where you can choose a palette and see live updates by enabling the “Auto update” option.
You can also create your own palettes for specific visualization needs and save them for future workflows.
Reverting to Default Visualization
If you need to reset the applied color scheme, SAMSON provides a simple way. In the context toolbar or the Visualization menu, choose Color > Reset color:
This is particularly helpful if you want to return to unbiased views after experimenting with color schemes.
Get Started with SAMSON
Now that you know how to use color schemes in SAMSON, you can add clarity and precision to your molecular models, whether you’re studying protein structures, small molecules, or large complexes. To dive deeper into the topic, check out the full guide at the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at SAMSON Connect.