From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 2 Oct 2020 16:54:03 +0000 (+0100)
Subject: todo for reinstating exercise on editing alignment parameters
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=54ab4116f1206b1864a1dce5300425f84bb3b02d;p=jalview-manual.git

todo for reinstating exercise on editing alignment parameters
---

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 682b5cd..fe1d102 100644
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -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.}