-<p><strong>Structure logo</strong></p>
-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.<br>
-Like sequence logos the relative amount of a specific base pair can be
-estimated by it's size in the logo. The tool tip of a column gives the
-exact numbers for all occurring valid base pairs.
-</p>
+ <p>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.<br>
+
+ <p>
+ <strong>RNA Structure logo</strong><br /> 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. <br> Like <a href="consensus.html#logo">sequence
+ logos</a>, 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 <em>normalising</em> 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.
+ </p>