VARNA: Visualization Applet for RNA

Using the mouse, various editing/annotation tasks can be performed. Here are some of these tasks, along with the mouse button that trigger them:

• Move helix/base/base-pair: Clicking the left mouse button and then dragging it to another position (while keeping the button pressed) will modify the structure in a contextual way. Namely, in radiate mode the selected helix (Containing the closest base to where the mouse click occurred) will be rotated around its axis, along with all subsequent helices. In circular and NAView modes, a single base will be displaced. In linear mode, both bases of the selected base-pair will be moved.
• Open popup menu: On a right mouse button click, a menu (Further described in this section) pops-up. For the buttonly impaired Mac users with mono-button mouses, the combination Ctrl+left button will also popup the contextual menu.
• Drag and drop files: Upon drag and drop in VARNA GUI or applet, an RNA file (Encoded using a supported formats) is automatically loaded within the interface.
• Zoom in/out: Rolling the mouse wheel upward or downward will zoom in and out. Alternatively, the + and - keyboard keys can be used.
• Shift RNA left/right/up/down: Clicking the third button (Usually the mouse wheel) and dragging it around will scroll the RNA model. Such an action can also be obtained using the arrow keys.
• Helix flipping: In radiate mode, dragging an exterior helix past its supporting base-pair will flip it around its baseline. This, combined with the flat mode, allow for an alternation of upward and downward helices, a classic representation for RNA biologists.
• Annotation: The Edit>Selection submenu features many options to customize the appearance and properties of each individual bases/base-pairs/structures. Upon opening the menu, the closest structural elements are added to the menu, and contextual features are proposed. Among other things, one can:
  • Set base content
  • Customize base inner and outer colors
  • Set individual numbering color
  • Edit base-pair types (Including non-canonical properties)
  • Customize base-pairs appearance (Thickness, color)
  • Add annotations anchored on a base, an helix or a loop
  for each of the following groups of bases containing the selected base (i.e. the closest to where the mouse was when the popup menu was opened): Individual base, Base-pair, Loop (Forward or backward if base-paired), Bulge, Helix, Stem or All.