From b69aba263c1ee8e6a952029ebd94a65d643c9a44 Mon Sep 17 00:00:00 2001 From: Suzanne Duce Date: Wed, 15 Feb 2017 17:41:55 +0000 Subject: [PATCH] Made changes to improve layout of manual --- TheJalviewTutorial.tex | 137 ++++++++++++++++++++++-------------------------- 1 file changed, 62 insertions(+), 75 deletions(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index f969bee..3afdd2f 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -1178,31 +1178,6 @@ any residue in the selection or group to the immediate right of the position in Gaps can be removed by dragging the residue to the immediate right of the gap leftwards whilst holding down [SHIFT] (for single sequences) or [CTRL] (for a group of sequences). -\subsection{Sliding Sequences} -Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more -sequences are selected will ``slide'' the entire selected sequences to the left -or right (respectively). Slides occur regardless of the region selection - -which, for example, allows you to easily reposition misaligned subfamilies -within a larger alignment. -% % better idea to introduce hiding sequences, and use the invert selection, hide -% others, to simplify manual alignment construction - -\subsection{Editing in Cursor mode} -Gaps can be easily inserted when in cursor mode (toggled with [F2]) by -pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue -under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then -press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE] -or [SHIFT]-[SPACE] (both keys held down together). - -Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you -have everything unselected by pressing ESC. The gap under the cursor will be -removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps -will be deleted up to the number specified. To delete gaps from all sequences of -a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down -together). Note that the deletion will only occur if the gaps are in the same -columns in all sequences in the selected group, and those columns are to the -right of the selected residue. - \newpage \exercise{Editing Alignments} @@ -1282,6 +1257,31 @@ option, or their keyboard shortcuts ([CTRL]-Z and [CTRL]-Y) to step backwards and replay the edits you have made.} } +\subsection{Sliding Sequences} +Pressing the [$\leftarrow$] or [$\rightarrow$] arrow keys when one or more +sequences are selected will ``slide'' the entire selected sequences to the left +or right (respectively). Slides occur regardless of the region selection - +which, for example, allows you to easily reposition misaligned subfamilies +within a larger alignment. +% % better idea to introduce hiding sequences, and use the invert selection, hide +% others, to simplify manual alignment construction + +\subsection{Editing in Cursor mode} +Gaps can be easily inserted when in cursor mode (toggled with [F2]) by +pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue +under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then +press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE] +or [SHIFT]-[SPACE] (both keys held down together). + +Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you +have everything unselected by pressing ESC. The gap under the cursor will be +removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps +will be deleted up to the number specified. To delete gaps from all sequences of +a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down +together). Note that the deletion will only occur if the gaps are in the same +columns in all sequences in the selected group, and those columns are to the +right of the selected residue. + \exercise{Keyboard Edits} {This continues on from the previous exercise, and recreates the final part of the example ferredoxin @@ -1533,6 +1533,23 @@ secondary structure row is present on the alignment. } \parbox[c]{3in}{ \includegraphics[width=2.75in]{images/col_rnahelix.pdf} } +\subsubsection{User Defined} +This dialog allows the user to create any number of named colour schemes at +will. Any residue may be assigned any colour. The colour scheme can then be +named. If you save the colour scheme, this name will appear on the Colour menu +(Figure \ref{usercol}). + + +\begin{figure}[htbp] +\begin{center} +\includegraphics[width=2.5in]{images/col_user1.pdf} +\includegraphics[width=2in]{images/col_user2.pdf} +\includegraphics[width=1.75in]{images/col_user3.pdf} +\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).} +\label{usercol} +\end{center} +\end{figure} + \exercise{Colouring Alignments}{ \label{color} Note: Before you begin this exercise, ensure that the {\sl Apply Colour @@ -1563,23 +1580,6 @@ toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}. {\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.} } -\subsubsection{User Defined} -This dialog allows the user to create any number of named colour schemes at -will. Any residue may be assigned any colour. The colour scheme can then be -named. If you save the colour scheme, this name will appear on the Colour menu -(Figure \ref{usercol}). - - -\begin{figure}[htbp] -\begin{center} -\includegraphics[width=2.5in]{images/col_user1.pdf} -\includegraphics[width=2in]{images/col_user2.pdf} -\includegraphics[width=1.75in]{images/col_user3.pdf} -\caption{{\bf Creation of a user defined colour scheme.} Residue types are assigned colours (left). The profile is saved (center) and can then be accessed {\sl via} the {\sl Colour} menu (right).} -\label{usercol} -\end{center} -\end{figure} - \exercise{User Defined Colour Schemes}{ \exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialog window will open.} @@ -3266,16 +3266,6 @@ Note that the {\sl Select many views} option is useful if you have different views that colour different areas or domains of the alignment. This option is further explored in Section \ref{complexstructurecolours}. -\begin{figure}[htbp] -\begin{center} -\includegraphics[width=5.5in]{images/mviewstructurecol.pdf} -\caption{{\bf Choosing a different view for colouring a structure display} -Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control -of which alignment view is used to colour structures when the {\sl Colours -$\Rightarrow$ By Sequence} option is selected.} -\label{mviewstructurecol} -\end{center} -\end{figure} \exercise{Aligning Structures using the Ferredoxin Sequence Alignment}{\label{superpositionex} @@ -3317,6 +3307,17 @@ displaying the console). Which view do you think give the best 3D superposition, and why ?} } +\begin{figure}[htbp] +\begin{center} +\includegraphics[width=5.5in]{images/mviewstructurecol.pdf} +\caption{{\bf Choosing a different view for colouring a structure display} +Browsing the {\sl View $\Rightarrow$ Colour by ..} menu provides full control +of which alignment view is used to colour structures when the {\sl Colours +$\Rightarrow$ By Sequence} option is selected.} +\label{mviewstructurecol} +\end{center} +\end{figure} + \subsubsection{Colouring Complexes} \label{complexstructurecolours} The ability to control which multiple alignment view is used to colour @@ -3475,7 +3476,7 @@ A status window opens to inform you of the progress of the job. Upon completion, predictions are included as annotations. Consult the Jpred documentation for information on interpreting these results. -\subsection{Hidden Columns and JNet Predictions} +\subsection{Hidden Columns and JPred Predictions} \label{hcoljnet} Hidden columns can be used to exclude parts of a sequence or profile from the input sent to the JNet service. For instance, if a sequence is known to include @@ -3538,10 +3539,7 @@ original alignment window.} {\bf Homework:} Go back to the last step of exercise \ref{annotatingalignex} and follow the instructions to view the Jalview annotations file created from the annotations -generated by the JPred server for your sequence. - -} - +generated by the JPred server for your sequence.} \section{Protein Disorder Prediction} \label{protdisorderpred} @@ -3552,7 +3550,6 @@ function. The {\sl Web Service $\Rightarrow$ Disorder} menu in the alignment win allows access to protein disorder prediction services provided by the configured JABAWS servers. - \begin{figure}[htbp] \begin{center} \includegraphics[width=5in]{images/disorderpredannot.pdf} @@ -3562,7 +3559,6 @@ zoomed out view of a prediction for a single sequence. The sequence is shaded to \end{center} \end{figure} - \subsection{Disorder Prediction Results} Each service operates on sequences in the alignment to identify regions likely to be unstructured or flexible, or alternately, fold to form globular domains. @@ -3573,7 +3569,6 @@ the manipulation and display of these data in detail, and Figure thresholding (described in Section \ref{featureschemes}) can be used to highlight differences in disorder prediction across aligned sequences. - \begin{figure}[htbp] \begin{center} \includegraphics[width=5in]{images/disorderpred.pdf} @@ -3592,7 +3587,6 @@ prediction annotation rows, clicking on the annotation row label will highlight the associated sequence in the alignment display, and double clicking will select that sequence. - \subsection{Disorder Predictors provided by JABAWS 2.0} For full details of each predictor and the results that Jalview can display, please consult @@ -3706,16 +3700,10 @@ Sequence ID $\Rightarrow$ 3D Structure Data\ldots } popup menu. Hit the available temperature factors to the alignment {\sl via} the {\sl Sequence ID Popup $\Rightarrow$ Selection $\Rightarrow$ Add reference annotation} option.} -\exstep{Apply the IUPred disorder prediction method.} -\exstep{Use the {\sl Per +\exstep{Apply the IUPred disorder prediction method. Use the {\sl Per sequence option} in the {\sl Colour $\Rightarrow$ By annotation \ldots} dialog to shade -the sequences by the long and short disorder predictors. - -{\sl Note how well the regions predicted to be disordered by the methods agree -with the structure.} -} - -} +the sequences by the long and short disorder predictors. {\sl Note how well the regions predicted to be disordered by the methods agree +with the structure.}}} \chapter{DNA and RNA Sequences} \label{dnarna} @@ -4159,8 +4147,8 @@ you should ever need to reset the JABAWS server list to its defaults, use the \subsection{Running your own JABA Server} You can download and run JABA on your own machine using the `VMWare' or -VirtualBox virtual machine environments. If you would like to learn how to do -this, there are full instructions at the +VirtualBox virtual machine environments. If you would like to do +this, There are full instructions at the \href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}. \exercise{Installing a JABA Virtual Machine on your Computer}{ @@ -4181,9 +4169,8 @@ for an email with a download link).} WARNING: This is large (about 300MB) and will take some time to download. } \exstep{Unpack the archive's contents to a place on your machine with at least -2GB of free space. - -(On Windows, right click on the archive, and use the 'Extract archive..' option). +2GB of free space. (On Windows, right click on the archive, and use the 'Extract +archive..' option). } \exstep{Open the newly extracted directory and double click the VMWare virtual machine configuration file (jabaws.vcf). This will launch the VMWare player. -- 1.7.10.2