For molecular modelers, juggling between multiple views of a structure can be a daunting task. Connecting what you see in a sequence, a structural model, and a 3D view often feels like navigating through a maze. This challenge is especially prevalent when trying to ensure selections and annotations are consistent between these representations. Fortunately, SAMSON alleviates this pain with its Sequence View, a versatile feature designed to keep everything interconnected and visually coherent.
What is Sequence View?
The Sequence View in SAMSON is an interactive interface that synchronizes seamlessly with both the Document View and the 3D Viewport. When a residue is selected in the Sequence View, it instantly becomes selected in the 3D Viewport and Document View, and the reverse is also true. This interconnected nature significantly reduces the hassle of tracking and manipulating molecular structures in different contexts.
Adding Visual Depth
A key feature of the Sequence View is the ability to colorize residues based on biophysical properties. This visual enhancement allows users to analyze molecular structures in a more meaningful way. For instance, if you colorize residues to represent hydrophobicity, these colors can be directly transferred to the 3D model. This makes it much easier to identify regions of interest, such as hydrophobic cores or interaction hotspots.
How to Access Sequence View
Accessing the Sequence View is straightforward and can be done in multiple ways. From the Home menu, simply click the View sequence command:
Alternatively, you can right-click directly on a structure in the 3D Viewport and navigate to Structural model >> View sequence in the Context menu:
If your structure contains multiple chains, SAMSON provides a pop-up selection dialog to let you choose which specific sequence(s) to visualize. This comes in handy when working with complex assemblies.
Why Sequence View Makes a Difference
The synchronization between different representations is a game-changer for molecular modelers. By selecting or highlighting residues in the Sequence View, you effectively gain control and context in multiple views simultaneously. Pair this with the colorization feature, and you have a robust tool for visually insightful molecular modeling. Whether you are analyzing protein-ligand interactions or exploring the structural implications of mutations, the Sequence View makes the workflow smoother and more intuitive.
Learn More
The Sequence View is just one of the many features that make SAMSON an integrative molecular design platform. To explore this feature in detail, visit the original documentation page: https://documentation.samson-connect.net/users/latest/sequence-view/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.