Graphical user interface (GUI)

The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects. It also allows to setup and run a number of calculations and can be used to transfer between different file formats.

• GUI basics and command line options
  • Selecting a part of a trajectory
    • Basic controls
    • Plotting data from the command line
    • Configuring the GUI
      • High contrast settings
    • Polling the GUI
      • GUI.repeat_poll()
• Edit
  • Undo / Redo
  • Select all
  • Invert selection
  • Select constrained atoms
  • Select immobile atoms
  • Cut / Copy / Paste
  • Hide / Show selected atoms
  • Modify
  • Add atoms
  • Delete selected atoms
  • Edit cell
  • Edit atoms
  • First / Previous / Next / Last image
  • Append image copy
• View
  • Show unit cell
  • Show axes
  • Show bonds
  • Show velocities
  • Show forces
  • Show magmoms
  • Show labels
  • Quick info
  • Repeat
  • Rotate
  • Colors
  • Focus
  • Zoom in / out
  • Change view
  • Settings
  • VMD / RasMol / xmakemol / avogadro
• Tools
  • Graphs
  • Movie
  • Constraints
  • Render scene
  • Move / Rotate selected atoms
  • NEB plot
  • Bulk modulus
  • Reciprocal space
  • Wrap atoms
• Setup
• Calculate
  • Set calculator
  • Energy and forces
  • Energy minimization