One of the common challenges for molecular modelers is efficiently navigating and interacting with complex molecular structures. It’s easy to lose track of chains, residues, or areas of interest in large biomolecules, which can slow down workflows and create potential errors in structure manipulations. This is where the Sequence View in SAMSON shines, offering a synchronized and intuitive way to manage and analyze molecular sequences interactively.
What is Sequence View?
The Sequence View in SAMSON is a powerful feature designed to bridge your molecular sequences with 3D structure visualization. It ensures that when you select residues in the sequence, they are simultaneously highlighted in the 3D Viewport and vice versa. This seamless integration helps you focus directly on the parts of the molecule you care about, without manually searching for them in a crowded structural view.
Colorizing Residues
Through the Sequence View, you can also colorize residues based on their biophysical properties, enhancing your ability to interpret and analyze molecular features. For example, residues can be color-coded by hydrophobicity, charge, or other attributes, making it visually clear how biophysical properties are distributed along the sequence. What’s especially convenient is that these colorizations can be reflected on the corresponding residues in the 3D Viewport.
Accessing the Sequence View
Getting started with the Sequence View is simple. Within SAMSON, you can activate it through different methods:
- Click View sequence from the Home menu:
- Right-click on a structure and choose Structural model > View sequence within the Context menu for quick access:
If the structure you are working on contains multiple chains, SAMSON helps you avoid confusion by providing a pop-up dialog. This allows you to selectively view the sequences of specific chains, keeping your workspace organized and focused.
Why Use the Sequence View?
For molecular modelers, time and clarity are crucial. The Sequence View simplifies molecular selection and visualization, saving time and reducing the potential for errors. If you’re working on tasks like docking, dynamics, or structural analysis, being able to quickly navigate and characterize your molecule’s components can have a significant impact on productivity.
Learn More
If you’re ready to enhance your molecular modeling workflows with the Sequence View, check out the full documentation here: https://documentation.samson-connect.net/users/latest/sequence-view/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at https://www.samson-connect.net.