A molecular modeling session can become difficult to manage long before the science does. Several molecules, intermediate structures, scripts, reference images, and documents may all be open at once. When the hierarchy is unclear—or important files are left outside the project—it takes extra effort to find the right object and share the work with someone else.
SAMSON documents offer a practical way to address both problems: organize the contents as a hierarchy, and embed supporting files so the document can travel as a self-contained project.
Start with the document hierarchy
A SAMSON document stores nodes in a hierarchy. Those nodes can include molecular structures such as molecules, residues, atoms, and groups, as well as cameras, folders, files, scripts, conformations, and paths. The Document view displays this structure, giving you a place to inspect and manage the contents of the active document.
Open it from Interface > Document view, or use Ctrl+1 on Windows or Linux and Cmd+1 on Mac. From there, you can inspect the structure, show or hide nodes, select nodes, filter by names or with Node Specification Language, and reorganize nodes by dragging and dropping. Context menus and the context toolbar provide actions for selected nodes.
A useful habit is to give related content an intentional place in the hierarchy instead of treating the document as an undifferentiated collection. For example, folders can group different types of nodes or sets of molecules. Once grouped, you can apply actions such as showing or hiding the group’s contents in one click. Create a folder from Edit > Folder.
This organization is especially helpful when returning to a project later: the hierarchy can make it easier to locate the relevant structures and understand how the document is arranged. You can also filter nodes when browsing the hierarchy becomes inconvenient.
Keep related documents separate, but accessible
Only one document is active at a time, but SAMSON can have several documents open simultaneously. This is useful when different tasks call for different molecules, or when you need to copy structures from one document to another. Switch documents using the Documents list in the top-left menu or Home > Documents. The list also indicates how many documents are open.
Keeping separate tasks in separate documents can help prevent unrelated structures from getting mixed into one working hierarchy. To start a fresh document, choose Home > File > New, or use Ctrl+N on Windows or Linux and Cmd+N on Mac. Recently opened documents are available from Home > File > Recent.
Make the project portable by embedding files
A project can be hard to hand off if its supporting material lives only in scattered locations on one computer. SAMSON lets you embed files and folders in a document. The documented examples include PDFs, images, data files, structure files, and scripts. Because embedded content is stored within the document, the document can be transferred between computers and shared with its supporting files included.
Think of this as a simple handoff check: before sharing, consider which reference material or files another person needs alongside the molecular structures. Embedding those items can make the document self-contained, rather than relying on the recipient to locate separate files. Folders can also be embedded, helping keep related material together.
For more detail about adding embedded content, see Embedding files and folders. To explore document hierarchies, folders, files, and related features, visit the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.