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).

- Selection
  - Edit
    - Copy
      Copys the selected region. In the applet version, the copied sequences are not available to the system clipboard.
    - Cut
      Cuts the selected region from the alignment. In the applet version, the copied sequences are not available to the system clipboard.
    - Edit Sequence
      Edit the selected sequence(s) directly. Spaces will be converted to the current gap character.
    - To Upper Case
      Changes the case of selected region to lower case.
    - To Lower Case
      Changes the case of selected region to upper case.
    - Toggle Case
      Switches the case of all residues within the selected region.
  - Output to Textbox
    The selection area will be output to a a text window in the selected alignment format.
  - Create Sequence Feature...
    Opens the dialog box for creating sequence features over the currently selected region on each selected sequence.
  - Group
    Group Operations
    - Group This is the first entry in the menu, and will display the currently selected group's name. Selecting it displays a window allowing the name and description for this group to be edited. Click OK to set the new name and decription, and cancel to leave the existing name and description unchanged.
    - 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.
    - Show Unconserved
      When this is selected, all symbols in the group matching the consensus sequence at that column will be rendered as a '.', highlighting mutations in the group area.
- Sequence Id
  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.
  - Represent Group With (Sequence Id)
    All sequences in the current selection group will be hidden, apart from (Sequence Id). Any edits performed on the visible representative sequence will be propagated to the hidden sequences.
  - Link
    This menu item lists all links which have been set up in the Preferences Connections tab.
    Since Jalview 2.4, links will also be made for database cross references (where the database name exactly matches the link name set up in Preferences).
    Since Jalview 2.5, links are also shown for non-positional sequence features attached to the sequence, and any regular-expression based URL links that matched the description line.
- Structure This menu is only visible if you right-click on a sequence name.
  - Associate Structure with Sequence
    - From File
      Load a PDB file from local disk which will be associated with this sequence. This file will be used if the user subsequently clicks on "View PDB Structure" menu item.
    - Enter PDB id
      Enter the PDB id from an input window. This PDB id will be used by the service WSDBFetch, provided by the EBI, to fetch the PDB file if the user subsequently clicks on "View PDB Structure" menu item.
    - Discover PDB ids
      This will use the service WSDBFetch, provided by the EBI, to retrieve all PDB ids associated with the sequences in the alignment if the sequences have valid Uniprot names or accession ids.
  - View Structure
    If the sequence has an associated PDB file added by one of the methods described above, Jalview will open a 3D interactive view of the file.
    These entries will only be present if the sequence has associated PDB structures.
- Hide Sequences
  Hides the currently selected sequences in this alignment view.