From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 2 Oct 2020 16:15:14 +0000 (+0100)
Subject: explaining in more detail about disabling feature colours if they are shown in the... 
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=c808392c66bd71045577125a4632b2f81cfe6912;hp=5ed5a6446da385d2b317231bae73bf4f925f2280

explaining in more detail about disabling feature colours if they are shown in the colouring alignments exercise
---

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 685fd1e..4f3cd2d 100644
--- 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}.}
 }