For molecular modelers, managing and visualizing structures effectively can be a significant challenge, especially when working with complex biomolecular models. One particularly useful feature of SAMSON is the Sequence View tool, which bridges the gap between sequence and spatial representation, helping you streamline your modeling workflows. Let’s explore how Sequence Views can help you interact with your molecular models more intuitively.
What Is the Sequence View?
In SAMSON, the Sequence View offers an interactive representation of the molecular sequence. Not only is it in sync with the 3D Viewport and the Document View, but it also allows you to perform powerful operations, such as selecting residues across these contexts. Whether you’re working on nucleotide sequences or protein chains, interactions in one view (such as selecting residues) reflect automatically in the others, making it easier to analyze and refine your structures.
Why Use the Sequence View?
Molecular modeling often involves exploring properties like colorization of specific residues or navigating complex molecular structures. Sequence View makes it significantly easier to:
- Colorize Residues: Apply biophysical color schemes to residues in the sequence, and automatically see these updates in the 3D Viewport. This feature is invaluable for identifying and analyzing specific molecular regions based on their properties.
- Work on Selected Residues: Seamlessly select residues in the sequence and apply downstream workflows like structural analysis or presentation customization with precision.
Accessing the Sequence View
You can open the Sequence View with ease from either of the following methods:
- Home Menu: Click the “View sequence” command under the Home menu. This is ideal for accessing the sequence globally.
- Context Menu: Right-click on a structure, then select Structural model > View sequence. This method allows you to focus on specific sequences when working with multi-chain structures.
If a structure includes multiple chains, SAMSON provides a pop-up dialog to let you choose which chains or sequences to view. This ensures you can focus on the sequences you’re interested in and avoid unnecessary data clutter.
Make It a Regular Part of Your Workflow
Using the Sequence View streamlines your interaction with both molecular sequences and 3D models. By coupling the spatial and sequence representations, SAMSON ensures molecular modelers have a more intuitive toolset to perform their visualizations, analyses, and presentations. From precise selection to colorization, Sequence Views are a critical asset for both beginners and seasoned professionals.
Learn more about Sequence Views by visiting the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.