JAL-3111 clarify exercise step in sub-family covariation analysis

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 46ca917..64885d6 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -2939,8 +2939,9 @@ Autocalculated Annotation } submenu in the alignment window.}
 logos will make it easier to see the different residue populations within each
 group. Activate the logo by right clicking on the Consensus annotation row to
 open the context menu and select the {\sl Show Logo} option.} 
-\exstep{In the column alignment ruler, select a column exhibiting about 50\%
-conservation that lies within the central conserved region of the alignment.
+\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.
 (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}.}
@@ -3273,11 +3274,11 @@ Verify that the Jmol display is as it was when you just saved the file.}
 \exstep{Continue with the Jalview project created in exercise
 \ref{viewingstructex}}
 
-\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL
+\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_MAIZE
 by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$
 3D Structure Data \ldots } }
 
-\exstep{Pick 1A70 from the Structure Chooser dialog, and make sure the {\sl Superimpose} option is checked before clicking the {\bf Add}
+\exstep{Pick 1gaq from the Structure Chooser dialog, and make sure the {\sl Superpose} option is checked before clicking the {\bf Add}
 button to superimpose the structure associated with
 FER1\_MAIZE with the one associated with FER1\_SPIOL.
 
@@ -3477,7 +3478,7 @@ each one, open the Structure Chooser dialog box by right clicking the mouse on
 sequence name to open the context menu and select {\sl
 $\Rightarrow$ 3D Structure Data}.
 Select `Cached Structures' from
-the drop-down menu in the Structure Chooser dialog box, select the
+the drop-down menu in the Structure Chooser dialog box and select the
 DNMT1\_MOUSE.pdb structure, and click {\bf View}.
 
 {\em Part of the newly opened structure will be coloured the same way as
@@ -3488,10 +3489,9 @@ the associated DNMT1\_MOUSE sequence is in the alignment view.}
 sequences in the alignment.}
 }
 \exstep{Repeat the previous two steps for each of the other
-alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and
-hitting the `View' button on the Structure Chooser dialog. Jalview will ask if
-you wish to create a new Jmol view, respond {\bf `Yes'} each time. This will
-ensure each sequence fragment is associated with the {\bf same} Jmol view. }
+  alignments. For those, after selecting the DNMT1\_MOUSE.pdb structure you
+  should select `Add' to ensure each domain alignment is associated
+  with the {\bf same} Jmol view. }
 
 \exstep{Pick a different
 colourscheme for each alignment, and use the {\sl Colour by ..} submenu to