SAMSON Interface

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, Animation, 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):

MenuHome.png
The Home menu

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.
  • Connected: select atoms and bonds within the same connected components as the currently selected atoms.
  • Similar: selects structures similar to the currently selected ones based on names and/or hierarchy.
  • 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 Annotate:

  • Add note: adds a note to the document. You can put in a note any plain text or html information to store it with the document.

Group News: check out News from SAMSON Connect.

Group Favorites: favorite commands including Editors and Apps.

Edit

The Edit menu is used to edit Documents:

MenuEdit.png
The Edit menu
Group History:

  • 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.

MenuEdit.gif
The Edit menu: a usage example

Select

The Select menu is used to perform various selections in Documents:

MenuSelect.png
The Select menu

Visualization

The Visualization menu is used to access visualization actions:

MenuVisualization.png
The Visualization menu
Group Capture:

  • Save image: captures the viewport (the settings can be changed in the Preferences).
  • Save OBJ: saves the nodes that possible (meshes, etc) in an OBJ file.
  • Orbit: make the active camera orbit around its center.

Group Visualize:

  • A list of default visual models: select and add one of the default visual models: Ball and stick, Licorice, Lines, Van der Waals, Ribbons, Cartoon, Gaussian surface, Solvent Accessible Surface, Solvent Excluded Surface, etc.
  • Visual model: adds a visual model for the selection.
  • Visual preset: choose and apply a visual preset (Visual model, color scheme).
  • Illustrate: applies to the selection an illustrative visual preset (van der Waals visual models colorized per chain ID (illustrative)) and changes the rendering preferences to the Illustrative rendering preset. It helps to depict molecules in a style similar to David Goodsell’s artwork.

Group Colorize: A quick access to some colors and to color selection for colorization.

Group Visualize:

  • Background: changes the background.
  • Anti-aliasing: changes the anti-aliasing rendering.
  • Lighting: switch between lighting preferences.
  • Shadows: switches on/off the shadows rendering.
  • Bloom: switches on/off the bloom rendering.
  • 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.
  • Pinhole: switches on/off the pinhole rendering.
  • Silhouettes: switches on/off the silhouettes rendering.
  • Rendering preset: switches between rendering presets (Default, High quality, Illustrative).

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.

MenuVisualization.gif
The Visualization menu: a usage example

Animation

The Animation menu is used to access presentation actions and main animation effects:

MenuAnimation.png
The Animation menu
Group Add:

  • Presentation: adds a new presentation to the document.

Group Present:

  • Save movie: saves the current presentation as a movie.
  • Save frames: saves the frames of the current presentation.

Group Motion: A quick access to the main motion animations.

Group Camera: A quick access to the main camera and view animations.

Group Entrance: A quick access to the main entrance animations.

Group Exit: A quick access to the main exit animations.

Group Other: A quick access to some other standard animations.

MenuAnimation.gif
Animations: a usage example

Biology

A menu with the quick access to the commonly used commands associated to biology.

MenuBiology.png
The Biology menu

MenuBiology.gif
The Biology menu: a usage example

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.

MenuApps.png
The Apps menu

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.

MenuEditors.png
The Editors menu

Interface

The Interface menu is used to manage SAMSON interface, update SAMSON, Preferences, and access logs:

MenuInterface.png
The Interface menu

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.
  • Job manager: shows/hides the job manager.
  • Python Scripting: shows/hides the Python scripting console.
  • Animator: shows/hides the Animator.

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:

Group Update:

  • Update SAMSON: checks for SAMSON updates.

Help

The Help menu allows you to access various documentation, tutorials, and the forum.

MenuHelp.png
The Help menu

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.

ViewportMenu.png
The viewport menu

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.

FindCommands.gif
Find commands

Viewport

The viewport is dedicated to showing the visual representation of molecules.

Viewport-3J27.png
The Viewport with a visual representation of a molecule

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:

DataGraph.png
The document view shows SAMSON's document structure

DocumentView-Selecting.gif
The document view

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.

HistoryView.png
The history view

HistoryView.gif
The history view

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.

InspectorAtom.png
The Inspector

Inspector-Path.gif
The Inspector: viewing trajectories

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.

InspectorControls.png
The Inspector controls

Animator

The Animator can be opened by clicking on Animation in the Interface menu.

The Animator provides a possibility to view and edit a presentation, add and modify animation effects.

To open the Animator, go to Interface menu > Animator or press Ctrl/ Cmd⌘+ 8, or if you already have a presentation in the document simply double-click on the presentation.

Animator-empty.png
The empty Animator

Animator-example.png
The Animator with a presentation opened in it

Status bar

The status bar is dedicated to showing status messages from SAMSON and SAMSON Extensions.