X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FcolourSchemes%2FrnahelicesColouring.html;h=9b9d41ab338e444cdd6d2ac121103fb7a7917923;hb=d30a1e3993c5538efdecd3149dc8e5a1e4e42936;hp=daca474737ca6387e579d09dfc7361a0122e406f;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/help/html/colourSchemes/rnahelicesColouring.html b/help/html/colourSchemes/rnahelicesColouring.html
index daca474..9b9d41a 100644
--- a/help/html/colourSchemes/rnahelicesColouring.html
+++ b/help/html/colourSchemes/rnahelicesColouring.html
@@ -1,51 +1,68 @@
-RNA Helices Colouring
+ -->
+
+RNA Helices Colouring
+
- RNA Helices Colouring
-An RNA alignment loaded from a Stockholm file can be coloured
- based on its helices. The helices are determined from the
- secondary structure line in the Stockholm file (#GC SS_cons)
- written in WUSS notation
- that specifies base pairing. See
- Wikipedia or
- Jalview RNA Support Blog for more information about Stockholm files and WUSS notation.
-Select "Colour" → "
- By RNA Helices" to colour the alignment by RNA helices.
+
+ RNA Helices Colouring
+
+
+ An RNA alignment loaded from a Stockholm file can be coloured based
+ on its helices. The helices are determined from the secondary
+ structure line in the Stockholm file (#GC SS_cons) written in WUSS
+ notation that specifies base pairing. See
+ Wikipedia or
+ Jalview RNA Support Blog for more information about Stockholm
+ files and WUSS notation.
+
+ Select "Colour"
+ → " By RNA Helices" to colour the
+ alignment by RNA helices.
-Features
-
-- Colours are generated randomly for the number of helices present.
-Reselect the "By RNA Helices" option to generate another set of random colors.
-- Sequence logo is in
-Purine/Pyrimidine colour scheme.
-- Line above the "Secondary Structure" line in annotation panel is WUSS notation present
-in the input file.
-
-
-
-
+
+
+ Features
+
+
+ - Colours are generated randomly for the number of helices
+ present. Reselect the "By RNA Helices" option to generate another
+ set of random colors.
+ - Sequence logo is in
+ Purine/Pyrimidine colour scheme.
+
+ - Line above the "Secondary Structure" line in annotation
+ panel is WUSS notation present in the input file.
+
+
+
+
-
