A molecular project rarely consists of a structure alone. You may also need to keep track of related molecules, scripts, images, PDFs, conformations, and other data. When these pieces are scattered across folders or mixed together in one long list, it becomes harder to understand what belongs together—and easier to lose time searching.
In SAMSON, a document is a hierarchy of nodes. It can contain structural nodes such as molecules, residues, and atoms, as well as cameras, folders, files, Python scripts, conformations, paths, and other node types. Thinking of the document as a project workspace, rather than just a place to open a structure, can help make complex work easier to navigate and hand off.
Start by making the structure visible
The Document view displays the hierarchy of the active document. Open it through Interface > Document view, or use Ctrl+1 on Windows and Linux, or Cmd+1 on Mac. From this view, you can inspect the document’s structure, show or hide nodes, select nodes, and change the hierarchy by dragging and dropping nodes.
This view is useful when a scene has grown beyond a single molecule. Instead of relying on memory, you can inspect how its contents are arranged and use the node names and hierarchy to orient yourself.
Group related nodes with folders
Folders provide a simple way to group different types of nodes or sets of molecules. For example, you might organize items that you want to manage together, then use the folder structure to make those groups easier to locate. Folders can also help with operations on sets of molecules: the documentation gives hiding or showing a group in one click as an example.
Create a folder using Edit > Folder. Once you have a useful hierarchy, the Document view also lets you apply actions to nodes through their context menu and context toolbar. You can filter nodes by name or with Node Specification Language using Filter nodes…—a helpful option when navigating a larger document.
The goal is not to impose one universal folder scheme. A useful structure is one that makes the contents and relationships clear to you and to anyone who may open the document later.
Keep supporting files with the project
A common handoff problem is that the main structure arrives, but the supporting material does not. SAMSON lets you embed files—including PDFs, images, data files, structure files, and scripts—into a document. You can also embed folders containing files. The embedded folders and files are stored within the document, making it self-contained for transferring between computers and sharing.
This can make a project easier to pass along: instead of asking someone to locate every associated file separately, you can keep those materials together with the document. Before sharing, consider whether the contents are understandable to someone who did not build the project. Clear node names and a sensible folder hierarchy can provide useful context without requiring a separate explanation for every item.
Switch documents without losing track
You can have several documents open in SAMSON, but only one is active at a time. The active document is the one shown in the Document view. To switch, use the Documents list in the top-left corner of the menu, or choose Home > Documents. The list also shows how many documents are open.
Multiple open documents are useful when you are working on different molecules or need to copy structures from one document to another. To start a fresh workspace, choose Home > File > New; to revisit a recently opened document, choose Home > File > Recent.
A little organization can prevent a lot of avoidable searching. Use the hierarchy to understand what is in a document, folders to group related nodes, and embedded files to keep supporting material with the project. For details, see the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.