X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=756e6e961f374626917ae50b9141bcc6d2bb1663;hb=df5ad5c09e166650d21510105f9efc3d25055b08;hp=033f0c0bfca877044ffe6467fbe15fd4b81ef82c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 033f0c0..756e6e9 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -19,29 +19,43 @@
* along with Jalview. If not, see
Alignment RNA Structure Consensus Annotation
+ ++ Alignment RNA Structure Consensus Annotation +
-The RNA structure consensus displayed below the alignment is the
-percentage of valid base pairs per column. It is calculated in
-relation to a secondary structure and just paired columns are
-calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and
-the wobble base pair (G-T/U) are regarded as valid pairings.
-The amount of valid base pairs is indicated by the profile in the
-Alignment Annotation row.
-By default this calculation includes gaps in columns. You can choose
-to ignore gaps in the calculation by right clicking on the label
-"StrConsensus" to the left of the structure consensus bar
-chart.
-
-
Structure logo
-By clicking on the label you can also activate the structure logo. It is very -similar to a sequence logo but counts the numbers of base pairs. There -are two residues per column, the actual column and the interacting -base. The opening bracket is always the one on the left side.The RNA structure consensus displayed below the alignment gives + the percentage of valid base pairs per column for the first + secondary structure annotation shown on the annotation panel. The + symbol below each histogram indicates whether the majority of base + pairs are: +
Mousing over the column gives the fraction of pairs classified as Watson-Crick, Canonical or Invalid.
+ +By default
+ this calculation includes gaps in columns. You can choose to ignore
+ gaps in the calculation by right clicking on the label
+ "StrConsensus" to the left of the structure consensus bar
+ chart.
+
+ Structure logo +
+ Right-clicking on the label allows you to enable the structure logo. + It is very similar to a sequence logo but instead shows the + distribution of base pairs. There are two residues per column, the + actual column and the interacting base. The opening bracket is always + the one on the left side. +