For molecular modelers, managing large and complex molecular structures can often feel overwhelming. Whether identifying specific residues, highlighting biophysical properties, or switching between structural chains, the process can be tedious and time-consuming. SAMSON’s Sequence View offers an interactive and intuitive solution, redefining the way you interact with molecular data while synchronizing seamlessly with the platform’s core views – the Document View and the 3D Viewport.
What is the Sequence View?
The Sequence View in SAMSON allows you to explore and visually manipulate molecular sequences directly within your project. Residues highlighted in the Sequence View synchronize with the Document View and the 3D Viewport, and vice versa. This ensures that any selections you make across SAMSON’s interface are consistent, making your workflow more efficient.
Notably, Sequence Views also facilitate the colorization of residues based on their biophysical properties. These colorizations can be applied to 3D molecular models, enriching your visual exploration and analysis of molecular structures. For instance, you can quickly color residues based on hydrophobicity, polarity, or secondary structure to better discern structural details in your modeling.
Using the Sequence View
Accessing Sequence Views is user-friendly. You have two convenient options:
- From the Home menu, click on the View sequence command. A single click brings you directly to the Sequence View.
- Right-clicking on a structure opens a Context Menu. From there, navigate to Structural model > View sequence to activate the Sequence View for the selected structure.
Exploring Structures with Multiple Chains
If your structure contains multiple chains, SAMSON ensures you have full control. When you initiate a Sequence View in such cases, a pop-up dialog appears, allowing you to select which chains you want to visualize. This targeted approach helps narrow down your focus and supports you in analyzing specific sequences or chains.
Maximizing the Colorization Options
One of the most powerful features of the Sequence View is its ability to color residues based on biophysical properties such as hydrophobicity, charge, or secondary structure. Not only is this color-coded information visible within the Sequence View itself, but SAMSON allows you to transfer these colors into the 3D Viewport. This lets you instantly map biophysical properties onto the structure you are modeling, facilitating easier spatial interpretation and communication of results.
Conclusion
The Sequence View is designed to make molecular modeling more intuitive, interactive, and visually engaging. From selecting residues to defining colors that reflect biophysical insights, the tool bridges the gap between sequence analysis and 3D modeling. To learn more about this feature, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download the platform at https://www.samson-connect.net.