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+<html>
+<head>
+<meta charset="UTF-8">
+<title>SIFTS Mapping from UniProt for PDB Structures</title>
+</head>
+<body>
+
+ <p>
+ <strong>SIFTS Mapping for UniProt sequences and PDB
+ Structures</strong><br /> SIFTS (Structure Integration with Function,
+ Taxonomy and Sequences) is a database of residue-level mappings
+ between UniProt protein sequences, and protein structures found in
+ the PDB. The database is updated for each PDB release, and is
+ provided by the <a href="https://www.ebi.ac.uk/pdbe/docs/sifts/">PDBe
+ at EMBL-EBI</a>.
+ </p>
+ <p>When Jalview imports PDB data for a protein sequence found in
+ UniProt, either via the 'View 3D Structure...' option, or the 'Fetch
+ DB Refs' web services menu, Jalview will also download its SIFTS
+ record and use that information to construct a mapping between the
+ sequence and downloaded structure.</p>
+ <p>If, for some reason, no SIFTS mapping data exists, then Jalview
+ will generate a mapping using the built-in Needleman and Wunsch
+ global alignment algorithm. This is how sequence-structure mappings
+ were created before version 2.10.</p>
+ <p>
+ <strong>Controlling and troubleshooting SIFTS mappings</strong> <br />
+ Configuration options controlling whether SIFTS mappings are used
+ can be found in the <strong>Tools → Preferences →
+ Structure tab</strong>, under 'Sequence ↔ Structure method'.<br /> <em>Note:</em>
+ Changing the configuration will only affect how new mappings are
+ created. In order to recompute mappings for structures already
+ loaded, please reload the sequence & structural data.
+ </p>
+
+ <p>
+ <strong>Multi-Chain Mappings</strong> <br />SIFTS gives Jalview the
+ ability to display multi-chain mappings between UniProt sequences
+ and PDB structure data. This is important when working with
+ multimeric proteins, when the biological assembly can contain
+ several structures for the same protein sequence. Multi-chain
+ mapping allows all residues in a structure to be located in the
+ alignment, and also, when shading the structure by sequence colours,
+ enables conservation patterns between oligomer interfaces to be
+ explored.
+ </p>
+ <p>To see this in action, Retrieve the UniProt sequence
+ FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over
+ the sequence results to two positions being highlighted in the
+ structure, and colouring the alignment transfers the color to all
+ the mapped chains in the structure.</p>
+
+ <p>
+ <Strong>Viewing Mapping Output</Strong> <br /> The mapping provided
+ by the SIFTS record is accessible via <strong>File →
+ View mapping</strong> menu of the structure viewers. The screenshot below
+ shows the mapping created between UniProt sequence FER1_MAIZE and
+ proteins in PDB 3B2F, which reports mappings for two chains. The
+ mapping method is also reported (highlighted with red border).
+ <p>
+
+  <img src="sifts_mapping_output.png" align="left"
+ alt="SIFTS mapping output" /> <br />
+ <p>
+ <em>SIFTS Mapping integration was added in Jalview 2.10</em>
+ </p>
+
+</body>
+</html>
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