For molecular modelers, managing complex molecular structures and their associated data in an efficient way can often feel like a daunting task. This is where SAMSON’s document navigation and organization functionalities come to the rescue, allowing you to streamline your workflow and stay organized while working with molecular data.
In SAMSON, a document is essentially a hierarchy of nodes that stores all the information about molecular structures and other entities you work with. These nodes can include molecules, residues, atoms, cameras, Python scripts, and more.
Efficiently Navigating the Document View
The Document view offers a convenient way to visualize and manipulate the data graph (the hierarchical structure) of the active document. You can access the Document view in SAMSON via Interface > Document view or the shortcut Ctrl+1 on Windows/Linux and Cmd+1 on Mac.
From the Document view, you can:
- Explore the document’s structure to comprehend the hierarchy of nodes.
- Show or hide specific nodes to focus on what matters most to your task.
- Select nodes for applying operations using SAMSON’s selection tools.
- Filter nodes using the Node Specification Language (NSL) or by node names with the Filter nodes… tool.
- Reorganize the structure by drag-and-dropping nodes to new locations.
- Apply specialized actions to nodes using their context menu or context toolbar.
Working with Multiple Documents
In SAMSON, you can work on multiple documents at the same time. This feature can be invaluable for tackling different tasks on separate sets of molecules or copying structures between documents. However, only one document is active at any given moment — the active document is the one displayed in the Document view.
To switch between documents, click on the Documents list in the top-left corner of the menu or use the Home > Documents menu. You’ll also see the number of open documents here, making it easy to track your ongoing projects.
Creating or accessing documents is straightforward:
- Create a new document via Home > File > New.
- Reopen recently accessed documents through Home > File > Recent.
Organizing with Folders and Files
For better organization, SAMSON allows you to use folders within documents. You can group different types of nodes (e.g., molecule chains) to perform actions on them collectively, like showing, hiding, or repositioning. Folders can be created via the menu at Edit > Folder.
You can even embed folders with files in a SAMSON document. Files of various types — PDFs, images, scripts, and more — can be stored directly within documents, making them self-contained. This simplifies sharing documents and ensures all data is preserved when transferring documents between systems.
To read more about embedding files and folders, visit the documentation section about embedding files.
Conclusion
Whether you’re organizing complex molecular models or juggling multiple projects simultaneously, SAMSON’s document capabilities provide a robust framework to work efficiently and systematically. The Document view and related features make it simple to manage hierarchical data, apply operations, collaborate, and transfer structured information without hassle.
To learn more about SAMSON documents and all the features highlighted here, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.