Dundee, Scotland DD1 5EH, UK
\vspace{2in}
-Manual Version 1.9.1
+Manual Version 1.9.2
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
\label{load}
\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
close all windows.}
+%% TODO: omit or combine this exercise
+%% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
Click {\sl OK} to load the alignment.}
+%%TODO: omit or combine
\exstep{{\bf Loading sequences from a file:} Close all windows using the
{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
Note, any alignment edits that affect the sequence will also affect the whole
sequence group.
+%% TODO introduce select/hide by annotation here
+%% favor coverage of these core interactions (hide, show, select, reorder, multiple view)
\exercise{Hiding and Revealing Regions}{
\label{hidingex}
\exstep{Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
\end{center}
\end{figure}
+%%TODO: multiple views - simple edits - observe changes in other views.
+
\exercise{Alignment Layout}{
\label{exscreen}
\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jvp}.
Creation of features from a selection spanning multiple sequences results in the creation of one feature per sequence.
Each feature remains associated with its own sequence.
-
+%%TODO: change EMBL to ENA in Jalview and the Manual !
\section{Importing Features from Databases}
\label{featuresfromdb}
it will show your custom preset amongst the options available for running the
JABA service.
+%% TODO - reinstate this exercise about reinstating presets
%
% \exercise{Creating and using user defined presets}{\label{createandusepreseex}
% \exstep{Import the file at
logos will make it easier to see the different residue populations within each
group. Activate the logo by right clicking on the Consensus annotation row to
open the context menu and select the {\sl Show Logo} option.}
-\exstep{In the column alignment ruler, select a column exhibiting about 50\%
-conservation that lies within the central conserved region of the alignment.
+\exstep{In the column alignment ruler, select a column exhibiting with about 50\%
+ of its residues conserved ({\em ie. about 50\% in the consensus histogram})
+ that lies within the central conserved region of the alignment.
(Column 74 is used in \href{https://youtu.be/m-PjynicXRg}{the Tree video}).}
\exstep{Subdivide the alignment
according to this selection using {\sl Select $\Rightarrow$ Make groups for selection}.}
\exstep{Continue with the Jalview project created in exercise
\ref{viewingstructex}}
-\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_SPIOL
+\exstep{Open the 3D Structure chooser dialog from the popup menu for FER1\_MAIZE
by right-clicking its ID (CMD-click on Macs), and selecting {\sl $\Rightarrow$
3D Structure Data \ldots } }
-\exstep{Pick 1A70 from the Structure Chooser dialog, and make sure the {\sl Superimpose} option is checked before clicking the {\bf Add}
+\exstep{Pick 1gaq from the Structure Chooser dialog, and make sure the {\sl Superpose} option is checked before clicking the {\bf Add}
button to superimpose the structure associated with
FER1\_MAIZE with the one associated with FER1\_SPIOL.
sequence name to open the context menu and select {\sl
$\Rightarrow$ 3D Structure Data}.
Select `Cached Structures' from
-the drop-down menu in the Structure Chooser dialog box, select the
+the drop-down menu in the Structure Chooser dialog box and select the
DNMT1\_MOUSE.pdb structure, and click {\bf View}.
{\em Part of the newly opened structure will be coloured the same way as
sequences in the alignment.}
}
\exstep{Repeat the previous two steps for each of the other
-alignments. In each case, after selecting the DNMT1\_MOUSE.pdb structure and
-hitting the `View' button on the Structure Chooser dialog. Jalview will ask if
-you wish to create a new Jmol view, respond {\bf `Yes'} each time. This will
-ensure each sequence fragment is associated with the {\bf same} Jmol view. }
+ alignments. For those, after selecting the DNMT1\_MOUSE.pdb structure you
+ should select `Add' to ensure each domain alignment is associated
+ with the {\bf same} Jmol view. }
\exstep{Pick a different
colourscheme for each alignment, and use the {\sl Colour by ..} submenu to
git://source.jalview.org / jalview-manual.git / blobdiff