git://source.jalview.org
/
jalview-manual.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
1f91ef9
)
todo for reinstating exercise on editing alignment parameters
author
Jim Procter
<jprocter@issues.jalview.org>
Fri, 2 Oct 2020 16:54:03 +0000
(17:54 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Fri, 2 Oct 2020 16:54:03 +0000
(17:54 +0100)
TheJalviewTutorial.tex
patch
|
blob
|
history
diff --git
a/TheJalviewTutorial.tex
b/TheJalviewTutorial.tex
index
682b5cd
..
fe1d102
100644
(file)
--- 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
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
% \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.}
% \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.}