Loading molecules

To load a molecule use Home > File > Open or the Ctrl+O shortcut (O as in Open) on Windows and Linux or Cmd+O on Mac. To open a recent file, follow Home > File > Recent, where you will find a list of the recently opened files.

SAMSON will use an appropriate importer to load a file based on its format. By default, SAMSON has importers and exporters for multiple file formats (see the list of supported formats). If you want to have more importers, follow to SAMSON Connect to the Marketplace section and check for other importers (see SAMSON Connect - Extensions section for more information on how to add extensions).

Depending on the importer and the file format you might need to specify additional parameters used by the importer as, for example, shown on the image below. The first time you use an importer its parameters are set by default, ones you modify them they will be saved for the next use.

Press OK or Enter and the file will be imported into SAMSON. You will see it in the Document view and in the viewport.

Molecular structures can also be downloaded with the help of specific Apps, like Fetch PDB (Home > File > Fetch), which allows you to download files (in PDB, mmCIF/PDBx, MMTF formats) from the RCSB Protein Data Bank.

Documents

Loaded or created molecules, files, and folders are added in the active document. You can see the document in the the Document view which you can open the Document view by clicking on Interface > Document view (1).

1. , : Ctrl+1, : Cmd+1

The Document view shows the data graph of the active document. Documents store all information about atoms, bonds, molecules, models, simulators, etc.

You can simultaneously have several Documents opened in SAMSON, however, only one document is active at any given time - the one you see in the Document view. Having several Documents is useful, for example, when you want to do different tasks with different molecules or copy structures from one document to another. To switch between Documents, click on the Documents list in the top-left corner of the menu, or Home > Documents (1). You can also see there the number of opened documents.

1. , : Ctrl+Tab and Ctrl+Shift+Tab
   : Cmd+Tab and Cmd+Shift+Tab

To create a new document, follow Home > File > New (1).

1. , : Ctrl+N, : Cmd+N

To open recently opened documents, use Home > File > Recent.

See Document view, document, and node types for more details.

Embedding files and folders

SAMSON Documents can contain not only molecular models, they enable Universal File Embedding and can embed Python scripts and any number of files and folders. This makes it possible to embed Python scripts and whole Python apps (e.g., machine learning apps), research papers, images, data, and so much more.

To embed files and folders within a document, drag-and-drop them in SAMSON and you will be asked whether your would like to embed them or use Home > Embed files or Home > Embed folders.

Folders and files are stored within the document, making the document self-contained, so you can transfer documents between computers and share documents.

Shared documents

SAMSON Connect provides the possibility to share Documents - see SAMSON Connect - Documents. You can also govern who can access your shared documents either when publishing them or in your account on SAMSON Connect.

Downloading shared documents

You can download Documents shared in SAMSON Connect - Documents by clicking Home > Download (1).

1. , : Ctrl+Alt+O, : Cmd+Alt+O

Sharing documents

You can also share your documents from SAMSON on SAMSON Connect by clicking Home > Publish (1).

1. , : Ctrl+Alt+S, : Cmd+Alt+S

In the dialog window, fill in the name of the document, its description, and choose the document visibility. For the document visibility you can choose one of the following options:

• Public - everyone can use this document, but editing requires an access right.
• Hidden - anyone with the link can use this document, but editing requires an access right.
• Restricted - using or editing this document requires an access right.

Then click Publish document and the document will be shared in SAMSON Connect - Documents and the link to it will be provided in the same window.

You can access and manage all your shared documents and the ones that have been shared with you in your account at SAMSON Connect - see Collaboration - Managing shared documents on SAMSON Connect.