X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FpopupMenu.html;h=79e7ada6fbdf5a1c2592de70fc73f4d841369a44;hb=f9e3f75dec30e85fa177f0a5f952616fc677a1fc;hp=511b85f2e2b163e6687ad9c3ee46a850dbece35c;hpb=87fa9a883d14416ba0e7f778bad69de813048b9c;p=jalview.git
diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 511b85f..79e7ada 100755
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -1,7 +1,7 @@
-
-
Sequence Id
- This menu is only visible if you right-click on a sequence name.
-
-
+ Output to Textbox
+ The selection area will be output to a a text window in
+ the selected alignment format.
+ Create Sequence Feature...
Opens the
+ dialog box for creating sequence features over the currently
+ selected region on each selected sequence.
+ Create Group
+ This will define a new group from the current
+ selection.
+ Remove Group
+ This will undefine the selected group.
-
-
- Structure
- This menu is only visible if you right-click on a sequence name.
-
-
- - Associate Structure with Sequence
-
- - 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 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 its "View Structure"
- menu item.
- - Discover PDB ids
- This will use the service WSDBFetch, provided by the
- EBI, to retrieve all PDB ids associated with the sequences in the
- alignment if the sequences have valid Uniprot names or accession ids.
-
-
-
- - View Structure
- If the sequence has an associated PDB file added by one
- 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.
- 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
- Hides the currently selected sequences in this alignment view.
-
+ 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.
+
+ - 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.
+ - 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.
+
+ 3D Structure Data... This menu is
+ visible when you right-click on a sequence name. When this
+ option is clicked, Jalview will open the 'Structure
+ Chooser' , which allows you to discover and view 3D structures
+ for the current selection. For more info, see viewing 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.
-
+