For molecular modelers, organization is key. When managing complex molecular data, having an intuitive and robust structure can significantly improve productivity. In SAMSON, the integrative molecular design platform, Documents provide a powerful hierarchical framework to store and manage your molecular models, scripts, and data files. This post introduces you to the basics of SAMSON Documents and how to harness their full potential.
What Are SAMSON Documents?
SAMSON Documents are hierarchical structures that store all information on nodes. These nodes may represent structural elements such as molecules, residues, atoms, groups, folders, Python scripts, conformations, or even specialized tools such as cameras and paths. Thanks to this organization, you can group, sort, and manipulate your molecular data efficiently.
Visualizing and Managing Documents in SAMSON
The Document view in SAMSON allows you to interact with your document’s hierarchical structure. You can open the Document view by navigating to Interface > Document view or using the shortcut Ctrl+1 (Windows/Linux) or Cmd+1 (Mac).
From the Document view, users can:
- Inspect the structure of the active document
- Show or hide nodes
- Select specific nodes
- Filter nodes using the Node Specification Language or node names via the Filter nodes… field
- Rearrange structures by drag-and-dropping nodes
- Apply actions to nodes through their context menu or toolbar
Working with Folders and Files
Managing multiple nodes? Group them into folders! SAMSON supports folders, which let you organize various node types and perform batch operations, such as hiding or showing groups of molecules. To create a folder, follow Edit > Folder.
Folders and files embedded in a document are stored within the document itself, which makes sharing and transferring your data effortless. This includes PDFs, structure files, images, scripts, and other valuable resources. Learn more about embedded files and folders by visiting the Embedding files and folders section.
Switching and Managing Multiple Documents
Did you know that you can have several documents open at once in SAMSON? Even though only one document is active at a time, this feature is incredibly useful for tasks like copying molecules between documents or maintaining separate projects. To switch between open documents, use the Documents list in the top-left corner of the menu (Home > Documents).
Creating and Accessing Documents
Need to start from scratch? Create a new document via Home > File > New. To access recently used documents, navigate to Home > File > Recent. These straightforward options ensure you’re always ready to organize and analyze molecular data effectively.
Conclusion
Efficiently managing molecular models and supporting files is crucial for molecular modelers. SAMSON’s document hierarchy and advanced tools like the Document view, folder organization, and embedded file support make it easier to maintain order and productivity in complex projects. To dive deeper into SAMSON’s document management capabilities, visit the original documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at https://www.samson-connect.net.