X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=8c75586e6e9caab5b3173b400585458fca6db141;hb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f;hp=9cf53587bffe76b81ee79c7468345b43d9197d68;hpb=fd6fc6bbcf3cf91b6f218729cc014997782053b1;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9cf5358..8c75586 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,4 +1,21 @@
+
Popup Menu
@@ -11,6 +28,10 @@ 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.
- Edit
- Copy
@@ -66,15 +87,32 @@ 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.
- - Edit Name/Description
+ - Sequence Details ...
+ (Since Jalview 2.8)
Open an HTML report containing the annotation
+ and database cross references normally shown in the sequence's
+ tooltip.
+ - 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,
@@ -89,7 +127,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).
Connections tab.
Since Jalview 2.4, links will also be made for database cross
references (where the database name exactly matches the link name set up in Preferences).
-
Since Jalview 2.4.1, links are also shown for non-positional sequence features attached to
+
Since Jalview 2.5, links are also shown for non-positional sequence features attached to
the sequence, and any regular-expression based URL links that
matched the description line.
@@ -120,10 +158,11 @@ 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.