See First look: the interface for the general description of the SAMSON interface.
Menu
The menu bar, located at the top of the interface, is composed of 8 menus: Home, Edit, Visualization, Biology, Apps, Editors, Interface, and Help. Note: The menu may slightly differ on Windows, Linux, and Mac.
Home
The Home menu is used to manage Documents, access the default editors, manage simulators, and access favorite commands (including Apps):
Group Documents:
- New...: creates a new document with a user-defined name.
- Download: downloads a document shared with you using document's identifier or a shareable link.
- Open...: shows a modal dialog to open a document. Files with extensions .sam or .samx correspond to entire SAMSON documents, whereas files with other extensions are imported into the current document.
- Recent: shows the list of recently opened files.
- Share: shares a document on SAMSON Connect and provides you with a shareable link which you can share with others.
- Save: shows a modal dialog to save data to a file. Selecting files with extensions .sam or .samx saves the entire active document to the file, whereas selecting a file with another extension saves the current selection to the file, or the entire document if nothing is selected.
- Save as...: same as save, but with the possibility of saving to a different file, even if the document has already been saved.
- Documents: switch between the opened Documents, the number indicates the number of opened Documents.
- Close: closes the active document.
Group Select:
- Select: an editor for selecting nodes in the viewport using the Rectangle selection editor.
- Select all: selects all selectable nodes in the active Document.
- Deselect all: deselects all selectable nodes in the active Document.
- Group: creates a group out of selected nodes.
- Export: saves the selected part in a file.
- Find: opens a find window which allows you to do complex searches in the active Document.
Group Edit: default Editors
- Move: a group of different move editors to translate and rotate atoms and other structural nodes.
- Add: add atoms, fragments, connect atoms with bonds.
- Erase: erase the selected nodes in the viewport.
- Label: add labels to atoms, bonds, residues and other nodes depending on the Selection filter.
- Measure: measure distances and angles between atoms.
Group Simulate:
- Minimize: run an interactive minimization.
- Store: stores a conformation of selected nodes.
- Add simulator...: add a Simulators simulator. Opens a window where you can set up a simulator - choose an interaction model and state updater.
- Start: starts a simulation or shows that a simulation is already running.
- Stop: stops a simulation or shows that a simulation is already stopped (there is no running simulation).
Group Favorites: favorite commands including Editors and Apps.
Group News: check out News from SAMSON Connect.
Edit
The Edit menu is used to edit Documents:
- Undo: undo an operation.
- Redo: redo an operation.
Group Clipboard:
- Cut: cut the selected part.
- Copy: copy the selected part to the clipboard.
- Paste: paste from the clipboard.
Group Edit: A set of default editors: select, move, add, erase, edit bonds order, edit formal charges.
Group Snapping: The snapping settings for move editors.
Group Add:
- Add folder...: add a folder to the active Document.
- The quick access to add common atoms.
- Add rings.
- Periodic table: add atoms from the periodic table.
- Assets: add fragments from asset libraries.
Group Adjust:
- Add hydrogens: adjust hydrogens in the selection.
- Remove hydrogens: remove hydrogens from the selection.
Group Conformations:
- Store conformation: stores a conformation of selected nodes.
Visualization
The Visualization menu is used to access visualization actions:
- Save image: captures the viewport (the settings can be changed in the Preferences).
Group Visualize:
- Visual model: adds a Visual model for the selection.
- Licorice: adds the Licorice Visual model for the selection.
- Ball and stick: adds the Ball and stick Visual model for the selection.
- Van der Waals: adds the Van der Waals Visual model for the selection.
Group Colorize: A quick access to some colors and to color selection for colorization.
Group Visualize:
- Background: changes the background.
- Blur: switches on/off the depth-of-field rendering.
- Fog: switches on/off the fog rendering.
- Occlusion: switches on/off the screen-space ambient occlusion rendering.
- Shadows: switches on/off the shadows rendering.
- Silhouettes: switches on/off the silhouettes rendering.
Group Viewport:
- Compass: toggles showing of the compass (camera controller) in the viewport.
- Scale: toggles showing of the scale in the viewport.
- Grid: toggles showing of the grid in the viewport.
Group Cameras:
- Add camera: adds a camera to the active document.
- Projection: toggles the orthographic projection mode for the active camera.
Group Stereo:
- Stereo on/off: switches on/off stereo.
- Flip eyes: flips eyes in stereo.
Biology
A menu with the quick access to commonly used commands.
Apps
The Apps menu shows all the Apps installed in your SAMSON, subdivided into categories. It also gives you a fast access to your favorite apps. You can add more apps from SAMSON Connect - Extensions.
Editors
The Editors menu shows all the Editors installed in your SAMSON, subdivided into categories. It also gives you a fast access to your favorite editors. You can add more editors from SAMSON Connect - Extensions.
Interface
The Interface menu is used to manage SAMSON interface, update SAMSON, Preferences, and access logs:
Group Information:
- Node details: toggle showing of a node detail information in the viewport when hovering above nodes. The node information depends on the current Selection filter.
- Tips: toggle showing tips.
Group Select:
- Document view: shows/hides the document view.
- Inspector: shows/hides the Inspector.
- History: shows/hides the history view.
- Assets: shows/hides the asset libraries window.
- Periodic table: shows/hides the periodic table.
Group Arrange:
- Hide interface: hides the SAMSON interface.
- Full screen: goes in the fullscreen mode.
Group Control:
- Show log: shows the SAMSON log.
- Preferences: opens the preferences window.
Group Extend:
- Get assets: opens SAMSON Connect - Assets web-page.
- Add elements: opens SAMSON Connect - Extensions web-page.
Group Update:
- Update SAMSON: checks for SAMSON updates.
Help
The Help menu allows you to access various documentation, tutorials, and the forum.
Viewport menu
The menu in the viewport provides a quick access to the viewport associated commands, selection associated commands, favorite apps and editors, and quick actions associated to the active editor.
The menu in the top-left corner of the viewport has commands associated to selection:
- Selection filter: allows you to specify types of nodes to which the selection should be applied.
- Select all: selects all selectable nodes in the active Document.
- Deselect all: deselects all selectable nodes in the active Document.
- Group: creates a group out of selected nodes.
- Find: opens a find window which allows you to do complex searches in the active Document.
The menu in the bottom of the viewport has commands associated to the view, rendering, and the viewport.
The menu on the left side of the viewport provides a quick access to the favorite apps.
The menu on the right side of the viewport provides a quick access to the favorite editors.
The menu in the top-right corner of the viewport provides a quick access commands for the active editor.
Find commands
The Find commands search box placed in the in the top-right corner allows you to easily find commands, apps, and editors and get help on them. It searches in names, tooltips, and shortcuts of commands, apps, and editors.
Viewport
The viewport is dedicated to showing the visual representation of molecules.
Document view
The Document view can be opened by clicking on Document view in the Interface menu or via shortcut Ctrl + 1 on Windows and Linux or Cmd⌘ + 1 on Mac.
The document view shows the data graph of an active Document. You can filter the nodes using Node Specification Language and names of the nodes. See node types for more details on types of nodes in the SAMSON document.
SAMSON documents store all information about atoms, bonds, molecules, models, simulators, etc. The document view shows the document structure:
Multiple documents may be opened simultaneously in SAMSON. Use the Home menu to switch documents, or the Ctrl/ Cmd⌘ + Tab and Ctrl/ Cmd⌘ + Shift + Tab shortcuts.
History
The History can be opened by clicking on History in the Interface menu or via shortcut Ctrl + 3 on Windows and Linux or Cmd⌘ + 3 on Mac.
The History shows a history of undoable operations, by clicking on any of them you may return to the associated state in the history.
Important: Not all the operations are undoable, if in between of undoable operations you did operations which are not undoable it might not be possible for SAMSON to properly undo operations, which may result in a loss of data.
Inspector
The Inspector can be opened by clicking on Inspector in the Interface menu or via shortcut Ctrl + 2 on Windows and Linux or Cmd⌘ + 2 on Mac.
The Inspector provides a possibility to view and edit the properties of the selected nodes.
The Inspector has controls that allows you to choose a) whether you inspect the descendants of the selected nodes as well, and b) whether you edit all selected nodes or only the last selected node. You can use the filter to see matching attributes only.
Status bar
The status bar is dedicated to showing status messages from SAMSON and SAMSON Extensions.