displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Sequence Features} option before you can see your colourscheme.
-There are two main types of colouring styles: {\bf simple static residue}
+There are two main types of colouring styles: simple {\bf static residue}
colourschemes and {\bf dynamic schemes} which use conservation and consensus
analysis to control colouring. {\bf Hybrid colouring} is also possible, where
static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme}.
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
-To All Groups} flag is not selected (ie unticked) in {\sl Colour} menu in the alignment window.
+To All Groups} flag is not selected (i.e. not ticked) in {\sl Colour} menu in the alignment window.
% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
% by default.
Clustalx} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
Note that some colour schemes do not colour all residues.}
\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62 score}. Select a group
-of around 4 similar sequences. Use the context menu (right click on the residues in the group)
+of around 4 similar sequences. Use the context menu (opened by right clicking on the residues in the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
-Note: Feature colours overlay residue colouring, and this may mask residue colouring. If this is an issue, he features colours can be
-toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
+
+Note: If you don't see any changes in appearance, it might be because sequence
+features are currently displayed (these are introduced later, in Section
+\ref{featannot}). To see if features are obscuring your colour scheme settings, look to see if the {\sl View
+$\Rightarrow$ Show Sequence Features} option in the alignment window menu is
+ticked. If it is, select it to disable feature colouring.
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
git://source.jalview.org / jalview-manual.git / blobdiff