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SAMSON Interface#

See First look: the interface for the general description of the SAMSON interface.

Workspace#

SAMSON provides a number of various workspaces that modify the menu to better suit the needs and screen sizes.

Choose a workspace

The ribbon menu, located at the top of the interface, is composed of several menus depending on the currently chosen workspace.

Note

The menu changes depending on a workspace and for the same workspace may slightly differ on Windows, Linux, and Mac.

Below is the description of the menu for the Default workspace.

Home#

The Home menu is used to manage Documents, access the default editors, manage simulators, and access favorite commands (including Apps):

The Home menu

Group Documents:

  • File

  • New: creates a new document with a user-defined name.

  • 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.
  • Fetch: fetch structures from various data banks (RCSB Protein Data Bank, AlphaFold DB, ESM Metagenomic Atlas, PubChem, Crystallography Open Database, etc.).
  • 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.
  • Save selection as...: same as Save as..., but saves only the currently selected nodes.
  • Close: closes the active document.

  • Recent: shows the list of recently opened files.

  • Documents: switch between the opened Documents, the number indicates the number of opened Documents.

Group Embed:

  • Embed files: shows a model dialog to choose one or more files that will be embedded in the active document.
  • Embed folder: shows a model dialog to choose a folder that will be embedded in the active document.

Group Share:

Group Structures:

Group Tools:

Group AI:

Edit#

The Edit menu is used to edit Documents:

The Edit menu

Group History:

Group Clipboard:

  • Copy: copy the selected part to the clipboard.
  • Paste: paste from the clipboard.
  • Cut: cut the selected part.

Group Add:

  • Folder: add a folder to the active document.
  • Note: add a note to the active document. You can put in a note any plain text or html information to store it with the document.
  • Script: add a Python script to the active document.
  • Conformation: stores a conformation of selected nodes in the active document.
  • Design: create molecules in 2D and 3D simulataneously using the Interaction Designer.

Group Adjust:

  • Add hydrogens: adjust hydrogens in the selection.
  • Remove hydrogens: remove hydrogens from the selection.

Group Organize:

Group Simulate:

  • Freeze/Unfreeze: freezes or unfreezes selected atoms or all atoms in the document if the selection is empty. See Minimizing a part of a molecule.
  • Minimize: run an interactive minimization.
  • Add simulator...: add a 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).

Select#

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

The Select menu

Group Operations:

  • find Find: opens a find window which allows you to do complex searches in the active document.
  • select parent Parent: selects parent nodes of the selected nodes.
  • select descendants Descendants: selects all descendants of the selected nodes.
  • select connected component Connected: select atoms and bonds within the same connected components as the currently selected atoms.
  • select similar nodes Similar: selects structures similar to the currently selected ones based on names and/or hierarchy.
  • Invert: inverts the selection.
  • Expand: expands the selection.

Group Structures:

Actions related to selecting based on various properties.

  • Biology: select binding sites, ligands, receptors, DNA, RNA, lipids, glycans, by chain, etc.
  • Residues: select amino and nucleic acid residues based on various properties.
  • Res. and groups: select residues and structural groups based on their IDs (sequence numbers).
  • Atoms: select atoms based on various properties.
  • Bonds: select bonds based on various properties.
  • Ions: select ions: monatomic, polyatomic, by name.
  • Water: select all water.

Group Add:

  • Group: creates a group out of selected nodes.

Visualization#

The Visualization menu is used to access visualization actions:

The Visualization menu

Group Capture:

  • Trace: runs a path-tracing for better rendering.
  • Save image: captures the viewport (the settings can be changed in the Preferences), or copy the capture in the clipboard.
  • Save OBJ/glTF: saves the nodes that possible (meshes, etc) in an OBJ or glTF file.

Group Add:

  • Label: add labels based on types of nodes or other properties.
  • Color: colorize nodes using various color schemes and color palettes.
  • Visual model: 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; adds other visual model for the selection, or apply a visual preset.
  • Visualize: apply visual presets.
  • Camera: adds a camera in the active document.
  • Light: adds a light in the active document.
  • Presentation: adds a presentation in the active document.

Group Rendering:

Group Stereo:

  • Stereo on/off: switches on/off stereo.
  • Flip eyes: flips eyes in stereo.

The Visualization menu: a usage example

Interface#

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

The Interface menu

Group Select:

  • Assistant: shows/hides the SAMSON AI assistant.
  • 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.
  • Animator: shows/hides the Animator.
  • Python Console: shows/hides the Python Scripting console.
  • Code Editor: shows/hides the code editor.

Group Control:

Group Extend:

Group Update:

  • Update SAMSON: checks for SAMSON updates.

Help#

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

The Help menu

Viewport menus#

The menu in the viewport provides a quick access to the viewport associated commands, selection associated commands, favorite apps, all the editors with quick actions associated to the active editor.

The viewport menu

The menu at the bottom of the viewport has commands associated to the view, rendering, and the viewport.

The menu in the top-right 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 Select all: selects all selectable nodes in the active document based on the current selection filter.
  • deselect all Deselect all: deselects all selected nodes in the active document.

The menu on the right side of the viewport provides a quick access to the favorite apps.

The menu on the left side of the viewport provides an access to all the editors and above it, in the top-left corner of the viewport, a quick access commands for the active editor.

The editor menu

The editor menu contains:

Editors: a usage example

Viewport#

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

The Viewport with a visual representation of a molecule

Find everything#

The Find everything 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.

Find commands

Document view#

The Document view shows the hierarchical data graph of the active document. You can open the document view by clicking on Interface > Document view or via shortcut Ctrl+1 on Windows and Linux or Cmd+1 on Mac.

The document view shows a structure of a SAMSON document

In the document view you can, among other things:

  • view the document's structure
  • show/hide nodes
  • select nodes in the document
  • filter the nodes using Node Specification Language and names of the nodes via Filter nodes...
  • change the documents structure, e.g. by drag-and-dropping nodes
  • apply specialized actions on nodes via their context menu and context toolbar

Selecting nodes in the document view

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, or use Ctrl/Cmd + Tab or Ctrl/Cmd + Shift+Tab shortcuts. You can also see there the number of opened documents.

Switching between documents

See also

Documents, node types.

History#

The History shows a history of undoable operations, by clicking on any of them you may return to the associated state in the history.

To open the History click on Interface > History or via shortcut Ctrl+3 on Windows and Linux orCmd+3 on Mac.

Note

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.

The history view

The history view

See also

History: undo and redo

Inspector#

The Inspector provides a possibility to view and edit the properties of the selected nodes.

To open the Inspector, click on Interface > Inspector or press Ctrl+2 on Windows and Linux or Cmd+2 on Mac.

Note

The Inspector inspects all the selected nodes and edits all the selected nodes.

The Inspector

You can use the filter to see matching attributes only.

Filter attributes in the Inspector

The Inspector: viewing trajectories

See also

Inspecting

Asset Browser#

The Asset Browser gathers the assets included by default in SAMSON together with the assets you can obtain from SAMSON Connect.

To open the Asset Browser, click on Interface > Assets or press Ctrl+4 on Windows and Linux or Cmd+4 on Mac.

Asset browser

See also

Building molecules

Periodic Table#

The Periodic table shows the periodic table and can be used to build and modify molecules - simply click on an atom and you will be switched to the Add editor mode.

To open the Periodic table, click on Interface > Periodic table or press Ctrl+5 on Windows and Linux or Cmd+5 on Mac.

Periodic Table

See also

Building molecules

Job Manager#

The Job manager lets you manage jobs launched in the Cloud (for e.g., protein structure prediction using AlphaFold and NVIDIA BioNeMo Services, or molecular dynamics simulations using GROMACS).

To open the Job manager, click on Interface > Job manager or press Ctrl+6 on Windows and Linux or Cmd+6 on Mac.

Job manager

See also

Cloud computations

Animator#

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

To open the Animator, click on Interface > Animator or press Ctrl/Cmd + 7, or if you already have a presentation in the document simply double-click on the presentation.

The empty Animator

The Animator with a presentation opened in it

See also

Presenting and animating, Animations

Python Console#

The Python Console provides the possibility to access SAMSON's functionality using Python and automate your workflow using scripts.

To open the Python Console, click on Interface > Python Console or press Ctrl+8 on Windows and Linux or Cmd+8 on Mac.

Python Console

See also

Python Scripting

Code editor#

The Code editor provides the possibility to open and modify text files, including Python scripts. It also provides the possibility to run Python files.

To open the Code editor, click on Interface > Code editor or press Ctrl+9 on Windows and Linux or Cmd+9 on Mac.

Code editor

See also

Python Scripting

Status bar#

The status bar is placed at the bottom of the SAMSON window and shows status messages from SAMSON and SAMSON Extensions .