When working with complex biomolecular systems, navigating 3D structures to select specific residues can be time-consuming and error-prone. Whether you’re preparing a simulation, designing a mutation, or analyzing a structural motif, efficient residue selection matters. Fortunately, SAMSON offers a synchronized Sequence View that streamlines this process by linking 1D sequence representations to 3D molecular models.
The Sequence View in SAMSON provides an interactive representation of a structure’s primary sequence. Here’s why it’s meaningful: it allows you to select residues directly from the sequence, which immediately highlights them in both the Document View and the 3D Viewport. This bidirectional synchronization—selecting in 1D highlights in 3D, and vice versa—saves time and reduces user error.
This is particularly helpful when you’re working with large proteins or assemblies where directly locating a residue in 3D could be tricky due to overlapping chains or regions with similar structures. You can also multi-select residues from the sequence to define regions of interest (e.g., binding sites, loops) and instantly manipulate or analyze them.
What else can you do in the Sequence View?
Besides selection, the Sequence View offers residue colorization based on biophysical properties. You can apply color schemes to highlight hydrophobic regions, charge distribution, or secondary structure elements. This colorization is also reflected in the 3D Viewport, helping you better understand the spatial arrangement of these features in your molecule.
How to access the Sequence View
SAMSON provides two ways to access the Sequence View:
- From the Home menu, click the View sequence button.
- Right-click directly on a structure and choose Structural model > View sequence in the context menu.
If your structure includes multiple chains, a pop-up lets you choose which sequences to display. This is especially useful when dealing with multimeric complexes or PDB files containing several distinct molecular entities.
In summary, the Sequence View in SAMSON provides a practical solution for more intuitive and efficient residue selection, reducing the need for manual, repetitive searching in 3D space. For modelers frequently working with large or complicated biomolecular assemblies, this can make a real difference in workflow speed and accuracy.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/sequence-view/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it at https://www.samson-connect.net.