explaining in more detail about disabling feature colours if they are shown in the...

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index f491be6..4f3cd2d 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -1226,8 +1226,10 @@ together). Note that the deletion will only occur if the gaps are in the same
 columns in all sequences in the selected group, and those columns are to the
 right of the selected residue.
 
+{\bf That's it for this chapter. Don't forget the exercises on the next page!}
+\newpage
 
-\exercise{Editing Alignments Homework Exercise}
+\exercise{Editing Alignments}
   %\label{mousealedit}
 % TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
 {
@@ -1236,6 +1238,8 @@ You are going to manually reconstruct part of the example Jalview
 alignment available at
  \href{http://www.jalview.org/examples/exampleFile.jvp}
  {http://www.jalview.org/examples/exampleFile.jvp}.
+ 
+ {\sl {\bf Note: this is a homework exercise for jalview course participants!}}
 
 {\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
 for key combinations such as [CTRL]-A. }
@@ -1307,12 +1311,14 @@ backwards and replay the edits you have made.}
 }
 
 
-\exercise{Keyboard Edits Homework Exercise}
+\exercise{Keyboard Edits}
 {
 \label{keyboardsex}
 This continues on from the previous exercise, and recreates the final part of the example ferredoxin
 alignment from the unaligned sequences using Jalview's keyboard editing mode.
 
+{\bf Note: This is a homework exercise for jalview course participants}
+
 {\bf Window users:} Please {\em only use} [SHIFT]-[SPACE] in this
 exercise.
 
@@ -1362,7 +1368,7 @@ appears to happen, it may be that you have sequence feature annotation
 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}.
@@ -1583,7 +1589,7 @@ assigned colours (left). The profile is saved (center) and can then be accessed
 \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.
 
@@ -1592,7 +1598,7 @@ seed database. Select the alignment menu option {\sl Colour $\Rightarrow$
 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
@@ -1604,8 +1610,12 @@ the group using {\sl Colour  $\Rightarrow$ Taylor}.
 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}.}
 }