X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=511b85f2e2b163e6687ad9c3ee46a850dbece35c;hb=bb49a7496f16118471764acae958b416e08c152c;hp=a836c9fc15e7bde3043ab1019a8fa5ac6ee05aef;hpb=244a1460b0d7ae9a7a8c57d3a767b327788e8bd3;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index a836c9f..511b85f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,4 +1,24 @@
+
Popup Menu
@@ -11,10 +31,24 @@ 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
- 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
@@ -38,18 +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.
@@ -66,15 +104,32 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
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.
@@ -102,11 +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
@@ -117,11 +175,28 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
- View 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.
+ 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.
+ 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