fix up ‘enabling group consensus’ in column-based subgroup conservation analysis...

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 685fd1e..c8111d1 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -1610,8 +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}.}
 }
@@ -2295,8 +2299,8 @@ press {\sl OK}. The features will then appear on the sequences. }
  \exstep{Roll
 the mouse cursor over the new features.
 Note that the position given in the tool tip is the residue number, not the column number. 
-To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC]. Select the [SHIFT] key,
- then insert a gap in sequence 3 at column 95 by moving the mouse.
+To demonstrate that there is one feature per sequence, clear all selections by pressing [ESC]. Hold down the [SHIFT] key,
+ then insert a gap in sequence 3 at column 95 by moving the mouse to that position, then clicking and dragging to the right.
 Roll the mouse cursor over the features and you will see that the feature has moved
 with the sequence. Delete the gap you created using {\sl Edit
 $\Rightarrow$ Undo}.
@@ -2983,9 +2987,8 @@ the pattern of unlinked nodes in the tree display.}
 tree based conservation analysis exercise (exercise \ref{consanalyexerc}).} 
 \exstep{In the {\sl View} menu in the alignment window, select {\sl New View} to
 create a new view. Ensure the annotation panel is displayed ({\sl Annotations $\Rightarrow$ Show Annotations} is toggled on). Enable the
-display of {\sl Group Consensus} option by checking {\sl Group Consensus} in the {\sl Annotation $\Rightarrow$
-Autocalculated Annotation $\Rightarrow$
-Group Consensus} submenu.}
+display of consensus annotation rows for each group by selecting the {\sl Group Consensus} option in the {\sl Annotation $\Rightarrow$
+Autocalculated Annotation } submenu.}
 
 \exstep{Displaying the sequence 
 logos will make it easier to see the different residue populations within each
@@ -2995,7 +2998,8 @@ mouse and dragging it up. Alter its position, by right clicking the name of the
 and dragging it up to the top of the annotations.} 
 \exstep{In the column alignment ruler, select a column exhibiting with about 50\%
   of its residues conserved ({\em ie. about 50\% in the consensus histogram})
-  that lies within the central conserved region of the alignment.} 
+  that lies within the central conserved region of the alignment.
+  (Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).} 
 \exstep{Subdivide the alignment
 according to this selection using {\sl Select $\Rightarrow$ Make Groups for Selection}.}
 \exstep{Re-order the alignment according to the new groups that have been