-
- <p>
- At the point of viewing a PDB structure, if the default mapping method is set as 'SIFTS',
- Jalview will download a SIFTS file
- for the target entry and uses it to accurately map the sequence residues with the
- structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch
- Alignment algorithm to map sequence residues to structure residues, and that may not
- always result to a correct mapping since it is computational determined.
+ <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.