X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=8d78c59996c8f97e6877ea06f2626629addfe202;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=4e4ea734ca2cef3ea13c3e5941e8034026b82461;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 4e4ea73..8d78c59 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -1,20 +1,21 @@
Alignment Annotation
@@ -27,11 +28,15 @@
Annotation is not ticked). Any displayed annotation row can be hidden (using the pop-up
menu obtained by right-clicking the label), or re-ordered by dragging the label to a new
position with the left mouse button.
-Web services can also add annotation to an alignment (see the
- JNet web service), and as of Jalview 2.08 quantitative and symbolic
- annotations can be added to an alignment via an Annotations
- File dragged into the alignment window or loaded from the
- alignment's file menu.
+
+Web services can also add annotation to an alignment (see the JNet and Disorder protein
+structure prediction services), and as of Jalview 2.08 quantitative
+and symbolic annotations can be added to an alignment via an Annotations File dragged into the
+alignment window or loaded from the alignment's file menu.
+
Interactive Alignment Annotation
Annotation rows are added using the Annotation Label
@@ -82,6 +87,16 @@ arrow oriented from left to right), and optional text label (see
below). A dialog box will open for you to enter the text. Consecutive
arrows will be joined together to form a single green arrow.
+
RNA Helix (only shown when working with nucleotide sequences)
+Mark selected positions as participating in a base pair
+either upstream or downstream. When the dialog box opens, enter a
+'(' to indicate these bases pair with columns upstream (to right),
+and ')' to indicate this region pairs with bases to the left of the
+highlighted columns.
If any brackets do not match up, then an
+orange square will highlight the first position where a bracket was
+found not to match.
+
+
Label
Set the text label at the selected positions. A
dialog box will open for you to enter the text. If
more that one consecutive position is marked with the same label, only