When working on molecular modeling projects, things can get complex very quickly. Trying to manage multiple molecules, simulation settings, scripts, and custom data often leads to workflows spread across different tools, folders, or even computers. This fragmentation can cause confusion and introduce errors, especially in collaborative or long-term projects.
SAMSON addresses this common pain with an elegant solution: the concept of a document as a self-contained data graph—what they call the Document View. Understanding and utilizing this feature can simplify how you organize your research.
What Is a SAMSON Document?
A SAMSON document is more than a file—it’s a hierarchical structure containing everything related to your project: molecules, atoms, simulation parameters, scripts, cameras, files, and folders. Each item is a node, and documents are built as trees of such nodes.
Navigating the Document View
The Document View graphically displays this structure and helps you interact with it. You can access it via Interface > Document view or the shortcut:
Ctrl + 1(Windows/Linux)Cmd + 1(Mac)
This view allows you to:
- Understand the full hierarchy of your project
- Select, show, or hide specific nodes
- Filter nodes using names or the Node Specification Language (NSL)
- Organize items via drag-and-drop
- Access useful actions through context menus
Working with Multiple Documents
SAMSON also lets you work with multiple documents simultaneously. This is useful when comparing structures, copying parts from one molecule to another, or running different workflows in parallel. Only one document is considered active at a time—the one shown in the Document View—and you can switch between them from the top-left menu or via Home > Documents.
Organizing with Folders
Use folders in a document to group nodes logically. For example, group all ligands, residues involved in binding, or simulation outputs. Once grouped, you can hide/show them in one click, or apply bulk operations. Create a folder from Edit > Folder.
This layered approach makes your projects easier to read, navigate, and share. Everything stays within the document, and you don’t have to worry about missing files when transferring or collaborating.
Self-Contained by Design
You can even embed files inside a document: PDFs, images, scripts, or structure files. This turns your document into a self-contained archive. Open it anywhere with SAMSON, and the structure, data, and user interface behave identically.
A typical workflow might include generating different conformations in separate documents, organizing them in folders by type, and saving custom scripts or analysis reports—all within the document structure. This workflow remains reproducible and shareable without extra setup on another system.
To learn more about document structure in SAMSON, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.