reopen. Are they the same as when they were saved ? } {\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.} }
+%% Suzanne: Jim's comment: this now appears at the end of the section, over the page from the exercise. I doubt anyone will read it there.
\subsection{Jalview Projects}
\parbox[c]{4in}{If you wish to save a complete Jalview session rather than
just a single alignment (e.g. because you have calculated trees or multiple
different alignments) then save your work as a Jalview Project
-file (.jvp).\footnote{Tip: Ensure that you have allocated plenty of memory to
+file (.jvp).\footnote{Tip: Ensure that that plenty of memory is available to
Jalview when working with large alignments in Jalview projects. See Section
-\ref{memorylimits} for how to do this.}
+\ref{memorylimits} for how to check this.}
From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save
dialog box will appear. Loading a project will restore Jalview to exactly the
view at which the file was saved, complete with all alignments, trees,
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] ([CMD] on Mac) or [SHIFT] and use the mouse to select and deselect sequences in
+\exstep{Hold down [CTRL] ([CMD] on Mac) and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
to include newly selected sequences, and the Percentage Identity colouring changes. }
-\exstep{ Another way to resize the group is by using the mouse to click and drag
+\exstep{ Another way to resize the group is simply to use the mouse to click and drag
the right-hand edge of the selected group.}
\exstep{The current selection can be exported and saved, place mouse on the text
git://source.jalview.org / jalview-manual.git / blobdiff