From 54ab4116f1206b1864a1dce5300425f84bb3b02d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 2 Oct 2020 17:54:03 +0100 Subject: [PATCH] todo for reinstating exercise on editing alignment parameters --- TheJalviewTutorial.tex | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) 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.} -- 1.7.10.2