dropped out some sections for Glasgow 2016, and quick rework of View 3D Structure...

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 89ca0fe..cba41ca 100644 (file)
--- 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}