adjust wording in secondary structure prediction exercise recommending hiding some...

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 682b5cd..913a3f3 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -2299,7 +2299,7 @@ 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]. Hold down the [SHIFT] key,
+To demonstrate that the features are linked to positions in the 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
@@ -2522,10 +2522,14 @@ it will show your custom preset amongst the options available for running the
 JABA service.
 
 %% TODO - reinstate this exercise about reinstating presets
-% 
+% * gapdist can't be set to non-integer values. 1 seems to give a good RMS
+% * looks like the jabaws service definition for clustalw has a copy-paste error in the description of transition weighting
+% * need to fix superposition instructions
+% * not really clear which is better without seeing number of superimposed positons. can that be viewed ?
+
 % \exercise{Creating and using user defined presets}{\label{createandusepreseex}
 % \exstep{Import the file at
-% \textsf{http://www.jalview.org/tutorial/fdx\_unaligned.fa} into jalview.}
+% \textsf{https://www.jalview.org/tutorial/fdx\_unaligned.fa} into jalview.}
 % \exstep{Use the `{\slDiscover Database Ids}' function to recover the PDB cross
 % references for the sequences.}
 % \exstep{Align the sequences using the default ClustalW parameters.}
@@ -3619,10 +3623,9 @@ prediction on the first sequence in the set (that is, the one that appears first
 \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 window also provides options for
-reordering and hiding autocalculated and sequence associated annotation. 
+hiding alignment associated annotation with the options provided by the {\sl Annotations} dropdown menu. You can also hide groups of sequence associated annotation by by right clicking
+the mouse in the annotation label panel and select either the ``{\sl Hide this row}'' option or for sequence associated annotation: ``{\sl Hide all } (annotation label)'' to hide rows of sequence associated annotation with the same label.
+
 
 \exstep{ Open the alignment at \url{https://www.jalview.org/tutorial/alignment.fa}. Select the sequence {\sl FER\_MESCR} by 
 clicking on the sequence ID. Then select {\sl Web Service $\Rightarrow$