Molecular modelers often juggle numerous molecules when working on simulations, analyses, or comparisons. Switching between them, copying structures, organizing data, and applying operations to specific groups without clutter can be a challenge. This is where Document View in SAMSON becomes especially useful.
Far from being just a file manager, SAMSON’s Document View interface is designed to help you manage, organize, and interact with complex systems of molecular structures with ease and efficiency.
Seeing the Bigger Picture
The Document View shows a hierarchical graph of all elements in the currently active document—molecules, atoms, residues, groups, cameras, folders, scripts, and more. This data graph allows you to:
- Browse and search molecular structures and associated data
- Show or hide nodes at different levels (e.g., molecules, atoms)
- Select nodes quickly using SAMSON’s powerful Node Specification Language (NSL)
- Change the document structure via drag-and-drop
- Access context-specific actions from the right-click menu
Managing Multiple Documents
You can open and manage several documents at the same time in SAMSON. However, only one document is active and shown in the Document View at any given time. This design allows users to work on different molecules or systems without merging unrelated data into a single workspace.
For example, you might be simulating ligand binding in one document and preparing protein visualization in another. With multiple documents open, copying and pasting structures or comparing different systems becomes easy.
To switch between documents, use the Documents list in the top-left corner of the main menu, or go to Home > Documents.
Creating and Navigating
Creating a new document is straightforward. Go to Home > File > New or use the shortcut Ctrl + N on Windows/Linux and Cmd + N on macOS.
To view a document:
- Enable the Document View window from Interface > Document view, or use the shortcut Ctrl + 1 / Cmd + 1.
A Modular Way to Work
The ability to embed folders, files, and scripts into documents makes SAMSON documents self-contained. This means you can:
- Send documents to collaborators without missing data
- Store simulations, visualizations, and related information together
- Use folders to apply actions to groups of elements (show/hide, group operations)
This flexibility adds depth to molecular modeling workflows without adding complexity to the user experience.
To learn more about Document View and document management in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.