X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=fd47dc0e4dec1abe1860b911f835ebec7c7e443f;hb=480d7b96f089281a3caf77d2a4e5adec09dc5bfa;hp=033f0c0bfca877044ffe6467fbe15fd4b81ef82c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git
diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 033f0c0..fd47dc0 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -19,29 +19,45 @@
* 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.
+
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. These + values are shown as a histogram labeled "StrucConsensus", + where a symbol below each bar indicates whether the majority of base + pairs are: +
Mousing over the column gives the fraction of pairs classified + as Watson-Crick, Canonical or Invalid.
-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.
+ By default this calculation includes gaps in columns. You can choose
+ to ignore gaps in the calculation by right clicking on the label
+ "StrucConsensus" to the left of the structure consensus
+ bar chart.
+
+ RNA 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.
Like sequence
+ logos, the relative amount of a specific base pair can be
+ estimated by its size in the logo, and this can be made more obvious
+ by normalising the logo (enabled via the popup menu). When
+ the logo is displayed, the tool tip for a column gives the exact
+ percentages for all base pairs at that position.
+