X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fannotation.html;h=8e9bcdf52021349ce994c297eabcd8273903dc1f;hb=e1cd94839128776e14e51ded3f3be2dcc7e72273;hp=01353aa478d3fe77441008b9219ccf8894ffd1fc;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 01353aa..8e9bcdf 100755
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -1,21 +1,24 @@
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
Alignment Annotation
Alignment Annotation
@@ -27,11 +30,15 @@
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 +89,16 @@ 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