hints should always be placed on a new line in the exercise.

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index a51cab1..e677945 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -1186,6 +1186,8 @@ 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.
 
+\newpage
+
 \exercise{Editing Alignments}
   %\label{mousealedit}
 % TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
@@ -1215,9 +1217,10 @@ key.}
 
 \exstep{ Select FER1\_SPIOL, FER1\_ARATH, FER2\_ARATH, Q93Z60\_ARATH and
 O80429\_MAIZE
-(Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
+
+{\sl Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then
 deselect FER1\_MAIZE), and use the $\Rightarrow$ key to slide them to so they
-begin at column 5 of the alignment view.} 
+begin at column 5 of the alignment view.}} 
 
 \exstep{ Select all the visible
 sequences (those not hidden) in the block by pressing [CTRL]-A.
@@ -1865,6 +1868,7 @@ calculations can be found in the on-line documentation.
 
 
 \exercise{Annotating Alignments}{
+  \label{annotatingalignex}
 \exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. 
 Right-click on the {\sl Conservation} annotation row to
 bring up the context menu and select {\sl Add New Row}. A dialog box will
@@ -1879,6 +1883,12 @@ Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again
 and select {\sl Colour}.
 Choose a colour from the colour chooser dialog 
 and click {\sl OK}. Press [ESC] to remove the selection.
+
+{\sl Note: depending on your Annotation sort settings, your newly
+created annotation row might 'jump' to the top or bottom of the annotation
+panel. Just scroll up or down to find it again - the column you marked will
+still be selected. }
+
 }
 \exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
  context menu. You will be prompted for a label. Enter ``B" and press {\sl OK}. A new line showing the 
@@ -1897,6 +1907,7 @@ pane. }
 row. Save the file and drag it onto the alignment view.}
 \exstep{Add an additional helix somewhere along the row by editing the file and 
 re-importing it.
+
 {\sl Hint: Use the Export Annotation function to view what helix annotation looks like in 
 a Jalview annotation file.}}
 \exstep{Use the {\sl Alignment Window $\Rightarrow$ File $\Rightarrow$ Export Annotations...} 
@@ -1904,14 +1915,18 @@ function to export all the alignment's annotation to a file.}
 \exstep{Open the exported annotation in a text editor, and use the Annotation File Format 
 documentation to modify the style of the Conservation, Consensus and Quality annotation rows so 
 they appear as several lines on a single line graph.
+
 {\sl Hint: You need to change the style of annotation row in the first field of the annotation 
 row entry in the file, and create an annotation row grouping to overlay the three quantitative 
 annotation rows.}
 }
 \label{viewannotfileex}
-{\sl Homework  for after you have completed exercise \ref{secstrpredex}:}
+      {\sl Homework for after you have completed exercise \ref{secstrpredex}:}
+      
 Recover or recreate the secondary structure prediction that you made in exercise \ref{secstrpredex}. Use the {\sl File $\Rightarrow$ Export 
-Annotation} function to view the Jnet secondary structure prediction annotation row. Note the 
+  Annotation} function to view the Jnet secondary structure prediction annotation row.
+
+Note the 
 SEQUENCE\_REF statements surrounding the row specifying the sequence association for the 
 annotation. }
 
@@ -3423,6 +3438,13 @@ highlight differences in disorder prediction across aligned sequences.
 
 \exercise{Secondary Structure Prediction}{
 \label{secstrpredex}
+
+{\sl Note: The annotation panel can get quite busy during this exercise. Try
+hiding some annotations rows by right clicking
+the mouse in the annotation label panel and select the ``Hide this row'' option.
+The Annotations dropdown menu on the alignment wndow also provides options for
+reording and hiding autocalculated and sequence associated annotation. }
+
 \exstep{ Open the alignment at \url{http://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by 
 clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$ Secondary Structure Prediction $\Rightarrow$ JNet Secondary Structure Prediction} 
 from the alignment window menu. A status window will appear and after some time (about 2-4 min) a new window with the JPred prediction will appear. 
@@ -3461,10 +3483,12 @@ Reference Annotation} option.
 {\bf All} the JNet predictions for the sequences will now be visible in the
 original alignment window.}
 
-{\sl Note: The annotation panel can get quite busy and it may be
-helpful to hide some of the annotations rows, by right clicking the mouse in
-the annotation label panel and select ``Hide this row'' option in the context
-menu}. }
+{\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and
+follow the instructions to view the Jalview annotations file created from the annotations
+generated by the JPred server for your sequence.
+
+}
+
 
 \begin{figure}[htbp]
 \begin{center}
@@ -3604,7 +3628,9 @@ $\Rightarrow$ Disorder Prediction } submenu.}
 IDs} to retrieve all the PDB structures for the sequences.}
 
 \exstep{Open and align
-the structures for all sequences. ({\sl Hint: see \ref{viewAllStructures} to see
+the structures for all sequences. (
+
+{\sl Hint: see \ref{viewAllStructures} to see
 how to do this.})}
 
 \exstep{Compare the disorder predictions to the structure data by mapping any