Popup Menu
This menu is visible when right clicking either within a selected region on the alignment or on a selected sequence name. It may not be accessible when in 'Cursor Mode' (toggled with the F2 key).

• Define
  • Group
    This will display a window asking for the name of the currently selected group. Click OK to set the name, cancel to use the default group name.
    
  • Remove Group
    This will undefine the selected group.
    
  • Group Colour
    Sets the colour of the group.
    
  • Boxes
    If selected the background of a residue within the selected group will be coloured according to the assigned colour scheme.
    
  • Text
    If selected the selected group will display text.
    
  • Colour Text
    If selected the selected group will display text in a colour slightly darker than the background colour of that residue.
    
  • Border Colour
    Selecting this will display a "Colour Chooser" window. Select a colour than press OK to set the border colour of a group.
    
• Sequence
  This menu is only visible if you right-click on a sequence name.
  • Edit Name/Description
    You may edit the name and description of each sequence. A window will be displayed asking for a new sequence name and sequence description to be entered. Press OK to accept your edit. To save sequence descriptions, you must save in Fasta, PIR or Jalview File format.
    
  • View PDB Structure
    If the sequence has a PDB file associated with it Jalview will display a 3D interactive viewer of the file.
    This entry is only present if the sequence has an associated PDB structure. If you can't see this entry for your sequence, and the sequence name is a uniprot identifier, then try enabling the "View -> Sequence Features" and opening the popup menu again.
• Link
  This menu item lists all links which have been set up in the Preferences Connections tab. It is only displayed when you right click (Apple click) on a sequence id.