For many molecular modelers, juggling multiple molecular systems during a modeling session is the norm, not the exception. Whether you’re comparing ligand binding modes, transferring fragments between structures, or running simulations on several conformations, managing multiple files effectively can be a challenge.
This is where the Document View in SAMSON really helps streamline workflows. Unlike platforms that force users to open one structure at a time, SAMSON allows you to load multiple documents simultaneously and switch between them on the fly — without losing track of structures or selections.
Work with Several Structures in Parallel
In SAMSON, each molecular system is organized into a Document. The Document View shows a hierarchical data graph of the currently active document — giving you full visibility into molecules, residues, atoms, and datasets related to the structure.
To switch between active documents in SAMSON:
- Click the Documents list in the top-left of the interface.
- Use Home > Documents.
- Or, try the keyboard shortcuts: Ctrl/Cmd + Tab and Ctrl/Cmd + Shift + Tab to cycle between opened documents.
What You Can Do in Document View
Beyond just toggling between molecular systems, the Document View helps you stay organized and control what you see on screen. For each document, you can:
- Show/hide specific nodes or whole molecular chains
- Select structures directly in the graph
- Filter nodes using name or Node Specification Language (useful for large systems)
- Drag and drop to change hierarchical structure
- Apply context-specific actions from the right-click menu
The real benefit: your selection context remains local to each document. You can work on modifying one protein structure while keeping another complex open as reference, or use one as the source for copy-pasting a ligand into another.
Why This Helps
Molecular modeling is rarely linear. You might fetch a predicted structure, identify a conflicting residue, switch to another document to verify a template alignment, and then go back to make adjustments. Multi-document navigation in SAMSON makes this nonlinear flow natural and efficient.
No more saving one file, closing it, opening another, and repeating. Instead, switch freely — like switching browser tabs — while SAMSON keeps track of where you are and what you were doing.
To discover more about the interface and how documents are managed, visit the SAMSON Interface documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.