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.
- 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
- GroupThis 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 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.
- 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 PDB Structure
If the sequence has an associated PDB file added by one of
the methods described above, Jalview will display a 3D interactive
viewer of the file.
This entry is only present if the sequence has an associated PDB structure.
- 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.
- Hide Sequences
Hides the currently selected seuqences in this alignment view.