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
- Sequence Details...
(Since Jalview 2.8)
Open an HTML report containing the annotation
and database cross references normally shown in the sequence's
tooltip.
- Show Annotations...
Choose to show (unhide) either All or
a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)
- Hide Annotations...
Choose to hide either All or
a selected type of annotation for the selected sequences. (Since Jalview 2.8.2)
- Add Reference Annotations...
Add to the alignment window any annotations on the selected sequences
which have been read from reference sources or calculated (for example,
secondary structure derived from 3D structure). (Since Jalview 2.8.2)
- Edit
- Copy
Copies 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.
- Create Group
This will define a new group from the current selection.
- Remove Group
This will undefine the selected group.
- Edit (New) Group
Group Editing Menu
Options in this menu modify
the name and display properties of the currently selected group, or
a new group defined using the current selection.
- Name: <Group> or Edit name and description
The first entry in the
menu displays the name for the currently selected group, if it has one. Selecting this option opens 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.
- 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.
- 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 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 its "View 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.
If the sequence or alignment has RNA structure, then 2D RNA entries will also be present enabling you to open a linked view of the RNA structure in VARNA.
Other menu entries may also be shown if the current selection includes sequences with associated structure data:
- "Structure→View all N
structures
Opens a new window containing all structures associated
with the current selection, superposed according to the currently selected region of the alignment.
(This
capability was added in Jalview 2.7)
- "Structure→View all N
representative structures
Open a new window containing exactly one structure per
currently selected sequence.
(The View representative structures option was introduced in
Jalview 2.8.1)
- Hide Sequences
Hides the currently selected sequences in this alignment view.