When working on complex molecular modeling projects, it’s easy to get lost in a sea of nodes, structures, ligands, ions, and metadata. You might load a protein structure or build a molecular system, only to quickly find that navigating and managing its components becomes tedious. Manually toggling visibility, hunting for specific chains, or understanding what residue lies where can drastically slow down your workflow.
This is where SAMSON’s Document View offers a practical and efficient solution. Designed to help you organize and interact with your molecular system, the Document View offers a clear, hierarchical representation of your entire molecular model within SAMSON. Think of it as a tree-like structure that gives you a bird’s-eye view without losing detail.
Understanding the Document View
Accessing the Document View is straightforward: Go to Interface > Document view, or use the keyboard shortcut Ctrl+1 (on Windows/Linux) or Cmd+1 (on Mac). This opens a panel displaying a hierarchy of all the elements included in your current molecular document.
Why Use the Document View?
The Document View supports several useful features that can significantly ease the pain points of molecular modelers:
- Hierarchy Navigation: View parent-child relationships between atoms, residues, molecules, and groups.
- Visibility Management: Toggle visibility of specific nodes such as ligands, ions, or water with just a click.
- Search and Filter: Quickly find nodes by name or using the Node Specification Language (NSL). This is extremely helpful when working with large systems.
- Reordering and Structuring: Rearrange nodes by dragging and dropping. This is handy if, for example, you want to regroup parts of a system under a new category.
- Access to Contextual Actions: Right-clicking on nodes reveals context menus with useful actions (e.g., renaming, deleting, measuring, etc.).
Here’s a handy gif showing how selection works directly through the Document View:
Use Cases
Imagine you’re preparing a molecular dynamics simulation. You need to:
- Check if water molecules are present
- Remove all heteroatoms except for your ligand
- Rename chains for consistency
All of this becomes simpler inside the Document View. You can quickly locate water molecules, visually confirm the ligand position, and right-click nodes to perform actions — no command-line scripting necessary (though you can script in SAMSON too).
Working with Multiple Documents
SAMSON also supports multi-document workflows. If you’re comparing different protein structures, or examining conformers side-by-side, the Document View helps you switch between open documents from the ‘Documents’ list or via shortcut (Ctrl+Tab or Cmd+Tab).
A Helpful Tool to Make Your Modeling Smoother
The Document View doesn’t do modeling for you — but it removes the friction of navigating and managing your molecular systems. Whether you’re organizing a protein-ligand complex, validating mutation impacts, or just making sure your structural data is clean, it’s worth getting familiar with this part of the SAMSON interface.
To learn more, check out the original documentation page here: https://documentation.samson-connect.net/users/latest/interface/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.