X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=d4b8b5fa5f214a64012b4bdf4832a71e81f63538;hb=0118e3685a087b37bb9d38d606f437638c9544d9;hp=10f807273b7d364724335e49811e05bc053ec5eb;hpb=c973cc268cbba93fa4ca9620c3910d30891a5abc;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 10f8072..d4b8b5f 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -2,21 +2,70 @@
Popup Menu
-Popup Menu
-Define
+Popup Menu
+ This menu is visible when right clicking either within a selected region
+ on the alignment or on a selected sequence name.
- - Group,
- - Remove Group
- - Group Colour
- - Boxes
- - Text
- - Colour Text
- - Border Colour
-
-Sequence
-
- - Edit Name
- - View PDB Structure
+ - Define
+
+ - Group
+ This will display a window asking for the name of the currently
+ selected group. Click OK to set the name, cancel to use the default group
+ name.
+
+ - Remove Group
+ This will undefine the selected group.
+
+ - Group Colour
+ Sets the colour
+ of the group.
+
+ - Boxes
+ If selected the background of a residue within the selected
+ group will be coloured according to the assigned colour scheme.
+
+
+ - Text
+ If selected the selected group will display text.
+
+ - Colour Text
+ If selected the selected group will display text in a colour
+ slightly darker than the background colour of that residue.
+
+ - Border Colour
+ Selecting this will display a "Colour Chooser"
+ window. Select a colour than press OK to set the border colour of a group.
+
+
+
+ - Sequence
+ This menu is only visible if you right-click on a sequence name.
+
+
+ - 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,
+ you must save in Fasta, PIR or Jalview File format.
+
+ - View PDB Structure
+
+ If the sequence has a PDB file associated with it Jalview will display
+ a 3D interactive viewer of the file.
+This entry is only present if the sequence has an
+ associated PDB structure.
+ If you can't see this entry for your sequence, and the sequence name
+ is a uniprot identifier, then try enabling the "View
+ -> Sequence Features" and opening the popup menu again.
+
+
+
+ - Link
+ This menu item lists all links which have been set up in the Preferences
+ Connections tab. It is only displayed when you right click (Apple click) on
+ a sequence id.
+
+