If you frequently work with complex molecular systems, you probably know how quickly things can get overwhelming. Multiple molecular models, imported data, annotations, and simulations — all layered into a single project. Navigating this spaghetti of atoms and information is one of the most common pain points for molecular modelers.
This post introduces a set of powerful but often overlooked tools in the SAMSON interface: the Document View, the History View, and the Inspector. Used together, they offer deep control and quick access to the internal structure and evolution of your molecular scenes.
1. Document View: See the Molecular Forest Through the Trees
The Document View displays the entire hierarchy of objects in your active SAMSON document — molecules, atoms, lights, simulations, annotations, and more. Think of it as a tree view of your molecular project.
You can:
- View and navigate the full hierarchy of your model
- Quickly select elements by name or ID
- Drag-and-drop nodes to reorganize your project
- Filter nodes using the Node Specification Language (NSL)
Need to isolate a specific molecule or residue? Just type part of its name or use NSL queries to filter the tree.
To open it: Interface > Document View or Ctrl+1 / Cmd+1.
2. History View: Go Back in Time (Safely)
Modelers often hesitate before making big changes, worried they might not be easily reversible. SAMSON’s History View addresses just that.
This panel tracks all undoable operations. You can click any point in your editing path to revert the document state instantly. It’s especially useful when iterating on structural modifications or testing different simulation setups.
To open it: Interface > History or Ctrl+3 / Cmd+3.
Note: not all operations are undoable, especially some simulation steps or geometry cleanups.
3. Inspector: Examine and Modify in One Place
Whether you’re debugging atom charges or adjusting a geometry, the Inspector gives detailed access to node properties: atom type, coordinates, display settings, and more.
With the Inspector, you can:
- Edit multiple selected elements simultaneously
- Use the filter bar to quickly locate specific attributes
- Preview trajectories and animations for selected nodes
To open it: Interface > Inspector or Ctrl+2 / Cmd+2.
Tip: Use Them Together
The Document View, History View, and Inspector become even more powerful when used together. Think of a workflow like this:
- Use the Document View to locate and select a molecular object
- Open it in the Inspector to modify or analyze its properties
- If needed, roll back changes or return to earlier states using the History View
This interconnected panel system is particularly helpful when working with large and heterogeneous molecular systems, like protein complexes with ligands, solvents, and visualization decorations.
To learn more about these interface tools and explore others, visit the SAMSON Interface documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.