From 5ed5a6446da385d2b317231bae73bf4f925f2280 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 2 Oct 2020 17:14:17 +0100 Subject: [PATCH] minor rewording/style fixing --- TheJalviewTutorial.tex | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index bdc77e7..685fd1e 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -1368,7 +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}. @@ -1589,7 +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. @@ -1598,7 +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 -- 1.7.10.2