todo for reinstating exercise on editing alignment parameters

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index d70a61f..fe1d102 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -2430,7 +2430,7 @@ A window will open giving the job status. After a short time, a second window wi
 \exstep{Select the last three sequences in the MAFFT alignment (you may need the scroll down the alignment), and de-align them 
 with {\sl Edit $\Rightarrow$ Remove All Gaps}. Press [ESC] to deselect these
 sequences. Then submit this view for re-alignment with {\sl ClustalO}.}
-\exstep{Return to the MAFFT alignment window in section (c), use [CTRL]-Z (undo) to
+\exstep{Return to the MAFFT alignment window in step (c), use [CTRL]-Z (undo) to
 recover the alignment of the last three sequences in this MAFFT alignment.
 Once the ClustalO re-alignment has completed, compare the results of
 re-alignment of the three sequences with their alignment in the original MAFFT result.}
@@ -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.}