- Copy
- Copys the selected region. In the applet version, the copied sequences
+ 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
@@ -59,18 +72,22 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- Create Sequence Feature...
Opens the dialog box for creating sequence features over the currently
selected region on each selected sequence.
- - Group
- Group Operations
-
- - GroupThis 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.
+ - 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.
@@ -117,7 +134,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
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.
- -
+ - Add Reference Annotations
When enabled, copies any available alignment annotation for this sequence to the current view.
- 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
@@ -143,11 +160,11 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- 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.
+ 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 "View PDB Structure"
+ 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
@@ -164,6 +181,22 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
href="../features/viewingpdbs.html">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)
+
+