A familiar challenge in molecular modeling is keeping track of where a residue in a sequence sits in the structure. A sequence gives you a linear view; a 3D model gives you spatial context. Switching between them can make it harder to stay oriented, especially when you are inspecting a particular region or working with a structure that has several chains.
SAMSON’s Sequence View connects these perspectives. Residues selected in the sequence are also selected in the Document View and 3D Viewport, and selections made in the document or viewport are reflected in the Sequence View. That two-way connection makes it easier to move from “this position in the sequence” to “this part of the model” without treating them as separate tasks.
A practical way to inspect a region
When you want to examine a sequence region in its structural setting, open the Sequence View and select the residues you want to inspect. Their corresponding residues become selected in the 3D Viewport and Document View, helping you locate the region in the model. You can also begin in the structure: select residues there, then use the Sequence View to see where that selection falls along the sequence.
This is useful when a question starts in one representation but needs an answer in another. For example, you might notice a region in the model and want to understand its position in the chain, or start from a sequence position and locate its structural context. The synchronized selection provides a shared point of reference between those views.
Open the sequence for the structure you need
There are two documented ways to open a Sequence View. From the Home menu, choose View sequence. Alternatively, right-click a structure and choose Structural model > View sequence from the context menu.
If the structure contains multiple chains, SAMSON displays a pop-up so you can choose which sequence or sequences to view. This gives you an opportunity to focus on the chain relevant to your current inspection rather than treating a multi-chain structure as one undifferentiated sequence.
Use color to connect sequence properties to the model
Sequence Views can colorize residues based on biophysical properties, and those colors can be transferred to residues in the 3D Viewport. This offers another way to relate a sequence-level pattern to the shape of the structure: instead of relying only on a selection, you can view a property-based color pattern in both representations.
A simple workflow is to open the sequence for the structure, choose the relevant chain if prompted, and then use synchronized selection or colorization to move between sequence and 3D context. These are complementary ways to orient yourself: selection helps you focus on residues, while transferred colors let you inspect a property-based pattern across the structure.
For more details, see the Sequence View documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.