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-<title>SIFTS Mapping</title>
+<title>SIFTS Mapping from UniProt for PDB Structures</title>
</head>
<body>
-
- <p><strong>SIFTS Mapping</strong></p>
-
+
<p>
- SIFTS (Structure Integration with Function, Taxonomy
- and Sequences) provides an up-to-date resource for residue-level
- mapping between Uniprot and PDB entries. The information is updated and
- released weekly simultaneously with the release of new PDB entries.
- SIFTS Entries are published as XML files and made publicly available via an FTP
- site hosted at the European Bioinformatics Institute.
+ <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>
- 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.
+ <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>Configuration</strong><br/>
- The default mapping method can be configured via <strong>Tools → Preferences →
- Structure tab</strong> Then scroll to the 'Sequence ↔ Structure method' section of
- the dialog box and change the default method. When 'SIFTS' is enabled as the default, all
- mappings between 'Sequence ↔ Structure' is performed via SIFTS provided that there
- is a valid SIFTS resource for the PDB entry. If no valid SIFTS resource is available, then
- the 'Sequence ↔ Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.
- </p>
-
- <p><strong>Multi-Chain Mappings</strong>
- <br/>One of the main merits of SIFTS is the ability to accurately achieve multi-chain mapping
- (one-to-many) between a single Uniprot sequence and its corresponding multiple chains in
- PDB. Consequently, mousing over the uniprot sequence in the alignment window results
- to highlighting multiple corresponding positions in the structure viewer for the mapped chains.
+ <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>
- To see this in action, load uniprot sequence for FER1_MAIZE then veiw PDB structure for 3B2F, you
- will notice that mousing over the sequence results to two positions being highlighted in the
- structure, also colouring the sequence transfers the color to all the mapped chains in the structure.
- </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>
- <Strong>Viewing Mapping Output</Strong> <br/>
- The mapping output is accessible via <strong>File → View mapping</strong> menu of the structure
- viewers. The screenshot below is the mapping output for the <Strong>{FER1_MAIZE ↔ 3B2F}</Strong>
- example described above. Observe that all the two chains were mapped. The mapping method used can be
- seen within the area highlighted with red boarder. This is useful for visually ascertaining the
- mapping method when in doubt.
+
+  <img src="sifts_mapping_output.png" align="left"
+ alt="SIFTS mapping output" /> <br />
<p>
-
-  <img src="sifts_mapping_output.png" align="left" alt="SIFTS mapping output" />
-
-
- <p><em>SIFTS Mapping integration was added in Jalview 2.9.1</em></p>
-
+ <em>SIFTS Mapping integration was added in Jalview 2.10</em>
+ </p>
+
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