-Jalview facilitates the use of protein structures for the analysis of alignments
-by providing a linked view of structures associated with sequences in
-the alignment. The Java based molecular viewing program Jmol\footnote{See the
-Jmol homepage \url{http://www.jmol.org} for more information.} has been
-incorporated\footnote{Earlier versions of Jalview included MCView - a simple
-main chain structure viewer. Structures are visualized as an alpha carbon trace
-and can be viewed, rotated and coloured in a structure viewer and the results
-interpreted on a sequence alignment.} which enables sophisticated molecular
-visualizations to be prepared and investigated alongside an analysis of
-associated sequences.
-PDB format files can be imported directly or structures can be retrieved from
-the European Protein Databank (PDBe) using the Sequence Fetcher (see
-\ref{fetchseq}).
-
-\subsection{Automatic Association of PDB Structures with Sequences}
-Jalview can automatically determine which structures are associated with a
-sequence in a number of ways.
-\subsubsection{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.
+Jalview facilitates the use of 3D structure data for the analysis of alignments
+by providing a linked view of structures associated with the aligned sequences.
+It also allows sequence, secondary structure and B-factor data to be imported
+from structure files, and supports the use of the EMBL-EBI's SIFTS database to
+construct accurate mappings between UniProt protein sequences and structures
+retrieved from the PDB.
+
+\section{Molecular graphics systems supported by Jalview}
+Jalview can interactively view 3D structure using Jmol, a Java based molecular
+viewing program\footnote{See the Jmol homepage \url{http://www.jmol.org} for
+more information.} integrated with Jalview.\footnote{Earlier
+versions of Jalview included MCView - a simple main chain structure viewer.
+Structures are visualized as an alpha carbon trace and can be viewed, rotated
+and coloured using the sequence alignment.} It also supports the use of UCSF
+Chimera, a powerful molecular graphics system that needs separate installation.
+Jalview can also read PDB and mmCIF format files directly to extract sequences
+and secondary structure information, and retrieve records from the European
+Protein Databank (PDBe) using the Sequence Fetcher (see \ref{fetchseq}).
+
+\subsection{Configuring the default structure viewer}
+\label{configuring3dviewer}
+To configure which viewer is used when creating a new
+structure view, open the Structures preferences window {\sl via} {\sl Tools $\Rightarrow$ Preferences\ldots} and
+select either JMOL or CHIMERA as the default viewer. If you select Chimera,
+Jalview will search for the installed program, and if it cannot be found,
+you will be prompted to locate the Chimera binary, or alternately, open the UCSF
+Chimera download page to obtain the software.
+
+\section{Automatic Association of PDB Structures with Sequences}
+Jalview will attempt to automatically determine which structures are associated
+with a sequence via its ID, and any associated database references. To do this
+for a particular sequence or the current selection, 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 automatically perform a database reference
+retrieval (See \ref{fetchdbrefs}) to discover identifiers for the
+sequences to use to search the PDB. This can take a
+few seconds for each sequence and will be performed for all selected
+sequences.\footnote{After this is done, you can see the added database
+references in a tool tip by mousing over the sequence ID. You can use the {\sl
+View $\Rightarrow$ Sequence ID Tooltip $\Rightarrow$ Show Db References }
+submenu option to enable or disable these data in the tooltip.}
+
+Once the retrieval has finished, the structure chooser dialog will show any
+available PDB entries for the selected sequences.