Molecular modelers often face the challenge of managing and selecting specific residues in complex molecular structures. Whether you’re focusing on a particular chain, analyzing biophysical properties, or preparing data for workflows, accurate and synchronized selection across multiple views is crucial. Enter SAMSON’s Sequence View, an interactive feature designed to simplify your workflow by ensuring seamless connection between sequence, document, and 3D views.
What Is the Sequence View?
The Sequence View in SAMSON provides a synchronized, user-friendly interface where residues selected in the sequence are automatically selected in the 3D viewport and document view—and vice versa. This bi-directional linking makes it easy to analyze structures without constantly switching contexts.
For example, if you highlight a residue in the sequence, you can immediately visualize its position and neighbors in the 3D structure. Conversely, selecting an atom or residue in the 3D viewport highlights it in the sequence representation.
How to Access the Sequence View
There are two simple ways to access Sequence View in SAMSON:
- Use the View sequence command in the Home menu:
- Right-click directly on a structure in the context menu and navigate to Structural model > View sequence:
If you’re working with a structure composed of multiple chains, don’t worry—SAMSON provides a pop-up dialog where you can choose which chains you want to focus on in the Sequence View:
Powerful Biochemical Insights Through Colorization
The Sequence View isn’t just for residue selection; it’s a powerful visualization tool too. You can colorize residues in the sequence view by applying biophysical property-based schemes. These colors are then reflected in the 3D viewport, offering an intuitive way to analyze structural properties at a glance.
For instance, you can assign colors to residues based on charge, hydrophobicity, or other critical properties, helping you identify functionally important regions or patterns that might guide your next design step.
Why Is This Useful for Molecular Modelers?
Modelers often deal with tasks that require pinpoint accuracy from selection to visualization. With SAMSON’s Sequence View, you can:
- Effortlessly synchronize multiple representations of your structure.
- Make meaningful selections and track them across different views without losing context.
- Quickly identify structural motifs or analyze molecular properties using color-coded sequences.
By streamlining these basic, yet essential, steps in your workflow, SAMSON helps improve productivity and focus on what truly matters—molecular design and analysis.
To explore more about the Sequence View, visit the official documentation page: https://documentation.samson-connect.net/users/latest/sequence-view/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.