A molecular project can be difficult to hand off even when the structure itself is easy to open. The modeler receiving it may also need to understand how its nodes are organized, find supporting files, or tell which of several open documents is the one to work on. A little organization inside the SAMSON document can make that handoff clearer—and reduce the chance that useful context gets left behind.
SAMSON documents are hierarchies of nodes. Alongside structural nodes such as molecules, residues, atoms, and groups, a document can contain folders, files, Python scripts, conformations, paths, and other nodes. The Document view displays this hierarchy, giving you a place to inspect and organize what belongs to the active document.
Start by checking what is actually in the document
Before sharing or moving a project, open the Document view using Interface > Document view, or use Ctrl+1 on Windows and Linux or Cmd+1 on Mac. Take a moment to review the data graph. This is useful when a document has accumulated structures or other nodes during a session: the hierarchy gives you a way to see what is included, select nodes, and show or hide them.
The view also supports filtering nodes by name or with Node Specification Language. When you are dealing with a crowded document, filtering can help you locate a particular node without relying on memory or repeatedly scanning the whole hierarchy. You can change the document structure by dragging and dropping nodes, and access node-specific actions from context menus and the context toolbar.
Use folders to make groups understandable
Folders are useful when a document contains different kinds of nodes or sets of molecules that you want to manage together. Create one through Edit > Folder, then use folders to give the hierarchy a more intentional shape. For example, you might group related nodes by the role they play in your work, rather than leaving everything at the same level. The exact organization depends on the project; the goal is to make it easier for you—or a collaborator—to find the relevant group.
Grouping can also make routine visibility changes simpler. SAMSON lets you show or hide nodes, and folders can help you apply such operations to sets of molecules in one click. A folder is therefore not just a label for tidiness: it can make common interactions with related nodes more convenient.
Keep supporting files with the project
A structure file may not be the only thing someone needs. A project may also rely on a PDF, an image, a data file, or a script. SAMSON can embed files and folders in a document; embedded items are stored within it, making the document self-contained and allowing it to be transferred between computers and shared.
That makes embedding worth considering before you send a document to someone else. Check whether the files that provide useful context are included in the document, rather than assuming that a recipient has the same files on their computer. SAMSON supports embedding many kinds of files, including PDFs, images, data files, structure files, and scripts. The documentation’s Embedding files and folders section explains this related workflow.
Keep multiple open documents straight
You can have several documents open at once, but only one is active at a time. The active document is the one shown in the Document view. If you are comparing molecules or copying structures between documents, check which document is active before making changes. Switch documents from the Documents list in the top-left menu or through Home > Documents. To start a separate document, use Home > File > New; recently opened documents are available under Home > File > Recent.
A practical handoff check is simple: review the document hierarchy, group related nodes where useful, and embed the supporting files that should travel with the project. Then confirm that you are looking at the intended active document. These steps do not replace scientific documentation, but they can make the working material easier to navigate and share.
For details, see the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.