X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=fd47dc0e4dec1abe1860b911f835ebec7c7e443f;hb=d5888333a51923fe86a35262e11be07c22e2798b;hp=756e6e961f374626917ae50b9141bcc6d2bb1663;hpb=df5ad5c09e166650d21510105f9efc3d25055b08;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index 756e6e9..fd47dc0 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -29,33 +29,35 @@
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 + 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.
- -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.
+
Mousing over the column gives the fraction of pairs classified + as Watson-Crick, Canonical or Invalid.
+- 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. -
+ 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.