From: Jim Procter Date: Wed, 12 Oct 2016 15:35:28 +0000 (+0000) Subject: dropped out some sections for Glasgow 2016, and quick rework of View 3D Structure... X-Git-Tag: Version_1.9.2~19 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=4ea0ff1819678930e3fdaeef87e06f57096e0063 dropped out some sections for Glasgow 2016, and quick rework of View 3D Structure instructions. --- diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 89ca0fe..cba41ca 100644 --- a/TheJalviewTutorial.tex +++ b/TheJalviewTutorial.tex @@ -1721,37 +1721,38 @@ Preview (Mac OS X). Zoom in and note that the image has near-infinite resolution.} } -\newpage - -\section{Summary - the rest of the manual} - -The first few chapters have covered the basics of Jalview operation: from -starting the program, importing, exporting, selecting, editing and colouring -aligments, to the generation of figures for publication, presentation and web -pages. - -The remaining chapters in the manual cover: - -\begin{list}{$\circ$}{} -\item{Chapter \ref{featannot} covers the creation, manipulation and visualisation -of sequence and alignment annotation, and retrieval of sequence and feature data -from databases.} -\item {Chapter \ref{msaservices} explores the range of multiple alignment -programs offered via Jalview's web services, and introduces the use of -AACon for protein multiple alignment conservation analysis.} -\item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for -multiple sequence alignment analysis, including trees, PCA, and alignment -conservation analysis. } -\item {Chapter \ref{3Dstructure} demonstrates the structure visualization -capabilities of Jalview.} -\item {Chapter \ref{proteinprediction} introduces protein sequence based -secondary structure and disorder prediction tools, including JPred.} -\item {Chapter \ref{dnarna} covers the special functions and -visualization techniques for working with RNA alignments and protein coding -sequences.} -\item {Chapter \ref{jvwebservices} provides instructions on the -installation of your own Jalview web services.} -\end{list} +% left out for Glasgow 2016 +% \newpage +% +% \section{Summary - the rest of the manual} +% +% The first few chapters have covered the basics of Jalview operation: from +% starting the program, importing, exporting, selecting, editing and colouring +% aligments, to the generation of figures for publication, presentation and web +% pages. +% +% The remaining chapters in the manual cover: +% +% \begin{list}{$\circ$}{} +% \item{Chapter \ref{featannot} covers the creation, manipulation and visualisation +% of sequence and alignment annotation, and retrieval of sequence and feature data +% from databases.} +% \item {Chapter \ref{msaservices} explores the range of multiple alignment +% programs offered via Jalview's web services, and introduces the use of +% AACon for protein multiple alignment conservation analysis.} +% \item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for +% multiple sequence alignment analysis, including trees, PCA, and alignment +% conservation analysis. } +% \item {Chapter \ref{3Dstructure} demonstrates the structure visualization +% capabilities of Jalview.} +% \item {Chapter \ref{proteinprediction} introduces protein sequence based +% secondary structure and disorder prediction tools, including JPred.} +% \item {Chapter \ref{dnarna} covers the special functions and +% visualization techniques for working with RNA alignments and protein coding +% sequences.} +% \item {Chapter \ref{jvwebservices} provides instructions on the +% installation of your own Jalview web services.} +% \end{list} \chapter{Annotation and Features} \label{featannot} @@ -2933,48 +2934,31 @@ Chimera download page. \section{Automatic Association of PDB Structures with Sequences} Jalview can automatically determine which structures are associated with a -sequence in a number of ways. -\subsection{Discovery of PDB IDs from Sequence Database Cross-references} -If a sequence has an ID from a public database that contains cross-references to -the PDB, such as Uniprot. Right-click on any sequence ID and select {\sl Structure $\Rightarrow$ -Associate Structure with Sequence $\Rightarrow$ Discover PDB IDs } from the context menu (Figure \ref{auto}). Jalview will attempt to associate the -sequence with a Uniprot sequence and from there discover any associated PDB -structures. This takes a few seconds and applies to all sequences in the -alignment which have valid Uniprot IDs. On moving the cursor over the sequence -ID the tool tip\footnote{Tip: The sequence ID tooltip can often become large for -heavily cross referenced sequence IDs. Use the {\sl View $\Rightarrow$ Sequence -ID Tooltip $\Rightarrow$ } submenu to disable the display of database cross -references or non-positional features. } now shows the Uniprot ID and any -associated PDB structures. - -\begin{figure}[htbp] -\begin{center} -%TODO fix formatting -\parbox{1.5in}{ -{\centering -\begin{center} -\includegraphics[width=1.5in]{images/auto1.pdf} -\end{center}} -} \parbox{3.25in}{ -{\centering -\begin{center} -\includegraphics[scale=0.5]{images/auto2.pdf} -\end{center} -} -} \parbox{1.5in}{ -{\centering -\begin{center} -\includegraphics[width=1.5in]{images/auto3.pdf} -\end{center} -} -} - -\caption{{\bf Automatic PDB ID discovery.} The tooltip (left) indicates that no PDB structure has been associated with the sequence. -After PDB ID discovery (center) the tool tip now indicates the Uniprot ID and -any associated PDB structures (right).} -\label{auto} -\end{center} -\end{figure} +sequence via its ID, and any associated database references. To do this, open +the Sequence ID popup menu and select {\sl View 3D Structure}, to open the 3D +Structure Chooser. +%(Figure\ref{auto}). + +When the structure chooser is first opened, if no database identifiers are +available, Jalview will attempt to discover identifiers for the sequence and from there discover any +associated PDB structures. This can take a few seconds for each sequence and +while be performed for all selected sequences. After this is done, you can see +added database references in a tool tip by mousing over the sequence ID. +\footnote{Tip: +The sequence ID tooltip can often become large for heavily cross referenced sequence IDs. Use the {\sl View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ } submenu to disable the display of database cross references or non-positional features. } now shows the Uniprot ID and any associated PDB structures. +% +% \begin{figure}[htbp] +% \begin{center} +% %TODO fix formatting +% \begin{center} +% \includegraphics[width=3.5in]{images/pdbstructurechooser.pdf} +% \end{center} +% +% +% \caption{{\bf The PDB Structure Chooser dialog.} } +% \label{auto} +% \end{center} +% \end{figure} \subsection{Drag-and-Drop Association of PDB Files with Sequences by Filename Match}