When a molecular modeling project grows, the structure itself is only part of the work. You may also be comparing several molecules, arranging related nodes, and keeping useful files close at hand. If those pieces are scattered across open documents and folders on your computer, it can become harder to see what belongs together—or to share the project with someone else.
SAMSON documents offer a way to bring these elements into one organized workspace. A document is a hierarchy of nodes: it can contain structural nodes such as molecules, residues, atoms, and groups, as well as cameras, folders, files, scripts, conformations, paths, and other node types. The Document view displays that hierarchy, giving you a place to inspect and manage the contents of the active document.
Use the hierarchy to make a project easier to navigate
A useful first step is to treat the Document view as more than a list of items. It represents the document’s data graph, so the way nodes are arranged can help you understand how the project is organized. You can select nodes, show or hide them, and change the document structure by dragging and dropping nodes. Context menus and the context toolbar provide actions for individual nodes.
For work involving several groups of molecules, folders can provide a simple organizational layer. Create one from Edit > Folder, then use folders to group different kinds of nodes. The documentation notes that folders can help you apply operations to sets of molecules—for example, hiding or showing a group in one action. That can make it easier to focus on one part of a scene without losing track of the rest.
Keep supporting files with the structure
A modeling project often depends on more than molecular structures. You might need to keep an image, a PDF, a data file, or a script alongside the nodes it supports. SAMSON documents can embed files and folders, including files of different types. Because embedded files and folders are stored within the document, the document can be self-contained and transferred between computers or shared without relying on a separate folder arrangement on the original machine.
This is especially useful when preparing a project for handoff: gather relevant supporting files into the document rather than assuming that another person has the same local paths. The documentation also describes embedding files and folders in its Embedding files and folders section.
Separate tasks without losing your place
You can have several documents open at once, but only one is active at a time. The active document is the one displayed in the Document view. Keeping separate documents for different tasks or molecules can reduce clutter, and multiple documents can also make it possible to copy structures from one document to another. Switch between them using the Documents list at the top-left of the menu, or through Home > Documents. The list also shows how many documents are open.
To start a clean workspace, use Home > File > New. To return to a recently opened project, use Home > File > Recent. If you need to locate a particular node in a large hierarchy, the Document view can filter nodes by name or with Node Specification Language using Filter nodes….
A small organization routine
- Create a separate document when you want to keep distinct modeling tasks apart.
- Use folders to group related nodes and make sets of molecules easier to manage.
- Embed relevant files and folders so supporting material travels with the document.
- Before switching documents, check which one is active in the Document view.
- Use filtering and node selection to find and focus on specific parts of a larger hierarchy.
These steps do not prescribe a particular project structure; they provide a practical starting point for making a document easier to inspect, work with, and share. For details about document contents, folders, files, and related workflows, see the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.