X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=63bb815520d0cef043b2b33c22315755c1411292;hb=81edd609f9841a84d5799d221277d45413a177cf;hp=6ceccee2b945469e6c4a6db9639c6862a78dfdf3;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 6ceccee..63bb815 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,22 +1,24 @@
+ -->
Popup Menu
@@ -29,14 +31,24 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- Selection
- - Sequence Details ...
+ - Sequence Details...
(Since Jalview 2.8)
Open an HTML report containing the annotation
- and database cross references normally shown in the sequence's
+ 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
- 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
@@ -122,7 +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
@@ -148,11 +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
@@ -169,6 +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)
+
+
- Hide Sequences