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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 its built-in Needleman and Wunsch
- global alignment algorithm. This method of mapping was used for all
- structures prior to version 2.10.
+ 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
<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, since the biological unit will 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.
+ 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, load uniprot sequence for FER1_MAIZE
- then veiw PDB structure for 3B2F, you will notice that mousing over
+ <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, also colouring the sequence transfers the color to all
+ 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
- is the mapping output for the <Strong>{FER1_MAIZE ↔
- 3B2F}</Strong> example described above, and confirms that all two chains
- were mapped. The mapping method used can be seen within the area
- highlighted with red boarder.
+ 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" />
+ alt="SIFTS mapping output" /> <br />
<p>
<em>SIFTS Mapping integration was added in Jalview 2.10</em>
</p>
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