X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=20169c45cdafe01617e088f9e862f78d8c1ebfe2;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9d6a0c6b4f3bab5b07f34c6e4e428dc158c9d520;hpb=354963d0c9d69f28fa5aa642c1f13627676ff4ae;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 9d6a0c6..20169c4 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,7 +1,7 @@
-
- Hide Sequences
Hides the
- currently selected sequences in this alignment 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 sequence will be propagated to the
+ hidden sequences.
+ Link
+ This menu item lists all links which have been set
+ up in the Preferences
+ 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 2.5, 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.
+
+
+ 3D Structure Data... This menu is
+ visible when you right-click on a sequence name. When this
+ option is clicked, Jalview will open a 'Structure Chooser' dialogue with options to select the
+ structure which will eventually be opened in a 3D interactive
+ view.
These entries will only be present if the
+ sequence has associated
+ PDB structures.
+
+ VARNA 2D Structure
+ If the sequence or alignment has RNA structure, then VARNA
+ 2D Structure entries will also be present enabling you to open
+ a linked view of the RNA structure in VARNA.
+
+ Hide Insertions
+ Hides columns containing gaps in the current sequence or
+ selected region, and reveals columns not including gaps.
+ Hide Sequences
Hides the
+ currently selected sequences in this alignment view.
+
+